# Patent

## Title
Protein expression enhancing polypeptides

## Abstract

Fusion proteins comprising a protein expression enhancing polypeptide linked to a target protein binding domain and nucleic acid molecules encoding such fusion proteins are described for use in enhancing expression and/or location of a targeted protein of interest, for restoring lost functions in cells, and for treating disease. Additional fusion proteins comprising a target protein of interest modified with a fusion partner comprising a protein expression enhancing polypeptide are also disclosed.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a United States national stage filing under 35 U.S.C. §371 of international application No. PCT/US2013/073442, filed Dec. 5, 2013, designating the U.S., which claims priority to U.S. Provisional Application No. 61/733,743, filed Dec. 5, 2012, and U.S. Provisional Application No. 61/733,884, filed Dec. 5, 2012.


FIELD OF THE INVENTION
This invention is in the field of engineered proteins. In particular, the invention is directed to polypeptides for enhancing expression of proteins and nucleic acid molecules encoding such protein expression enhancing polypeptides. Methods of increasing production levels of a protein of interest are also provided.
BACKGROUND OF THE INVENTION
Expressing a protein of interest in a culture of genetically engineered cells at levels that permit easy isolation in quantities sufficient for research, development, or commercial use requires the optimization of a variety of recombinant techniques and cell culture methodologies. Such techniques include in vitro methods of isolating and recombining nucleic acid molecules to encode a desired protein molecule, operably linking the desired coding sequences with appropriate transcriptional and translational elements, inserting the engineered genetic material into an appropriate expression vector, introducing the resulting recombinant expression vector into compatible host cells, and culturing the host cells containing the recombinant expression vector under conditions that permit expression of the desired recombinant protein. Proper selection and optimization of such methods has permitted expression and use of a variety of recombinant proteins from a wide variety of host cells, including bacterial, fungal, insect, plant, and mammalian host cells.
Despite many advances in recombinant and cell culture methodologies, the problem of ensuring proper protein folding can still thwart the most extensive efforts to produce useful amounts of a desired recombinant protein. All proteins must achieve a proper two- and three-dimensional conformation in order to function properly at their intended location. Proper conformation ensures that a protein will provide a cell or multi-cell organism with its intended function (for example, enzymatic activity, signal transduction, or structural feature) at its intended location (for example, cytoplasm, nucleus, intracellular structure, organelle, cell membrane, or extracellular (secreted) location). Although the information for the proper structure and conformation resides in a protein's amino acid sequence, the general intracellular environment and a variety of stimuli and environmental stresses, including oxidative stress, nutrient deprivation, and high temperature, can make proper folding of even endogenously produced proteins more difficult to the point that many protein molecules take on an undesired structure and thus fail to provide a cell with their intended function. To deal with the continual risk of not attaining or maintaining proper functional conformations, cells possess a system of proteins that serve as molecular chaperones to assist in the folding and refolding of nascent and mature proteins into their proper conformations. The heat shock 70 kDa proteins (referred herein as “Hsp70s”) constitute one of the most ubiquitous classes of chaperone proteins in the cells of a wide variety of species. The Hsp70 machinery includes the participation of co-factor (or co-chaperone) proteins, such as J proteins, and nucleotide exchange factors (NEFs).
In a current model of the Hsp70 chaperone machinery for folding proteins, Hsp70 cycles between ATP- and ADP-bound states. In this model, a J protein binds to a protein in need of folding or refolding (referred to as a “client protein”) and interacts with an ATP-bound state of Hsp70 (Hsp70-ATP). Binding by the J protein-client complex to Hsp70-ATP stimulates ATP hydrolysis, which causes a conformational change in the Hsp70 protein that closes a helical lid, thereby stabilizing the interaction between the client protein with the Hsp70-ADP, and release of the J protein, which is then free to bind another client protein. While bound to the Hsp70-ADP, the client protein is provided with an environment that permits folding or refolding into a proper conformation. Next, a nucleotide exchange factor (NEF) binds to Hsp70-ADP resulting in release of ADP and binding of ATP. The client protein is then released because of its low affinity (in the absence of J protein) for Hsp70-ATP. If the client protein has not achieved a proper conformation, it may be rebound by a J protein and enter the cycle again. See, Kampinga et al., Nat. Rev., 11: 579-592 (2010). Thus, according to this model, J proteins play a critical role in the Hsp70 machinery by associating with individual client proteins and also with the Hsp70 chaperone protein to provide a bridging function that facilitates the capture and submission of a wide variety of client proteins into the Hsp70 machinery to promote folding or refolding into proper conformations. When attempts by the Hsp70 chaperone machinery fail to fold or refold a protein into proper functional conformations, the Hsp70 chaperone machinery also can facilitate the transfer of the improperly folded protein to the cell's proteolytic system (e.g., the proteasome) for degradation and recycling of amino acids. For a review of the Hsp70 chaperone machinery, including the critical role of J proteins, see, Kampinga et al, Nature Rev., 11: 579-592 (2010) and Voisine et al., Neurobiol. Dis., 40: 12-20 (2010).
Expressed proteins are thus subjected to a strict quality control system of the Hsp70 machinery for maintaining proper conformations. The problem of proper protein folding is of particular concern in the case of producing useful quantities of functional exogenous (recombinant) proteins expressed in various recombinant host cells. The problem can arise in both eukaryotic and prokaryotic host cells. The failure to properly fold exogenous proteins expressed in bacterial host cells frequently can result in the formation within the cells of large, potentially toxic, aggregates of inactive molecules of the exogenous protein. Such aggregates are referred to as “inclusion bodies” and are considered to be the result of ineffective protein folding that leads to non-functional conformations with exposed hydrophobic domains that in turn promote association and aggregation with other improperly folded protein molecules.
When a wild-type gene encoding a protein undergoes a mutation, the encoded mutant form of the protein may still be expressed in the cell. Such expressed mutant proteins usually fail to achieve a proper functional conformation of the wild-type protein and may form inactive aggregates. Such improperly folded mutant protein species are typically ushered by the Hsp70 machinery into the cells proteolytic system for degradation and recycling of amino acids Elimination of the improperly folded mutant protein still, of course, leaves the cell with a loss of functional protein and the consequence of such loss of function can be debilitating or even fatal to the cell. In fact, loss of properly folded functional protein species has been demonstrated or is implicated in a number of diseases, including prion-associated diseases (transmissible spongiform encephalopathies), Alzheimer's disease, Parkinson's disease, Huntington's disease, and cystic fibrosis.
Members of the BAG family of proteins found in eukaryotes are nucleotide exchange factors (NEFs) that possess diverse N-terminal domains and a conserved C-terminal Hsp70-binding domain (the BAG domain) that can interact with the ATPase domain of Hsp70. See, for example, Kampinga et al., Nat. Rev. Biol., 11:579-592 (2010). Thus, BAG proteins have a topology, binding domains, and binding specificities that are consistent with a protein designed to participate in recruiting the Hsp70 chaperone machinery. Although a BAG protein might participate as a NEF in the Hsp70 machinery, many studies suggest that BAG proteins may predominantly be involved in regulatory mechanisms to control a variety of activities, including promoting cell growth, quiescence, or apoptosis; regulating transcription complex formation; and modulating signal transduction. See, for example, the review by Takayama et al., Nat. Cell Biol., 3: E237-E241 (2001). Recently, it has been reported that when desired recombinant proteins are linked to a BAG domain, the resulting fusion proteins are expressed at levels that are greater than those of the protein alone. See, International Publication No. WO 2012/087835 A2.
In general, with an increasing level of expression of a protein in a cell (as can easily occur in recombinant gene expression systems), there is an increasing risk that such proteins may fail to fold or refold into proper functional conformations. Accordingly, along with a constant desire for increasing expression of desired exogenous or endogenous proteins, needs remain for means for enhancing the proper folding of exogenous and endogenous proteins expressed in cells, i.e., to increase the yield of properly conformed, functional proteins.
SUMMARY OF THE INVENTION
The present invention provides compositions and methods for enhancing the level of expression of a target protein of interest produced by a cell. In particular, the invention provides protein expression enhancing polypeptides that can be incorporated into genetically engineered fusion proteins, which when expressed by a host cell are able to enhance the level of expression of a specific target protein of interest at its intended location.
In one embodiment, a protein expression enhancing polypeptide of the invention is selected from the group consisting of:

    
    
        (a) an isolated J domain of a J protein;
        (b) an isolated protein expression enhancing polypeptide fragment of a J domain;
        (c) an isolated protein expression enhancing polypeptide analog of a J domain, said J domain analog polypeptide comprises the amino acid sequence of formula I:
    
    









(SEQ ID NO: 47)









(I) X1-X2-X3-X4-X5-X6-X7-X8-X9,






    
    
        
        
            X1 is isoleucine (I), leucine (L), valine (V), alanine (A), or methionine (M);
            X2 and X3 are each independently any amino acid with the proviso that one or both are K or R;
            X4 is any amino acid or X4 may be absent when X1 through X3 are present and X5 through X9 are present;
            X5 is tyrosine (Y), tryptophan (W), or phenylalanine (F);
            X6 and X7 are each independently any amino acid with the proviso that one or both are lysine (K) or arginine (R); or either one of X6 and X7 may be absent when the other is K or R and when X1 through X5 are present and X8 and X9 are present; and
            X8 and X9 are any amino acid with the proviso that one or both are leucine (L) or alanine (A); or one of X8 and X9 may be absent when the other is L or A and when X1 through X7 are present; and
        
        
        (d) an isolated protein expression enhancing polypeptide selected from the group of decapeptides consisting of:
    
    









(SEQ ID NO: 49)









IKKAYKLALQ,


 







(SEQ ID NO: 50)









IKKAYRLALQ,


 







(SEQ ID NO: 51)









IKKAYRKALQ,



or


 







(SEQ ID NO: 52)









IKKAYRKLLQ.






In accordance with the invention, a protein expression enhancing polypeptide enhances the level of expression of a target protein of interest expressed in a host cell as compared to the level of expression of the target protein of interest in the absence of the protein expression enhancing polypeptide. Use of the polypeptides of the present invention provides a means for increasing the amount of a desired recombinant protein in the desired location (compartment) with respect to the producing cell.
In a particular embodiment, a protein expression enhancing polypeptide of the invention is an isolated J domain that has an amino acid sequence selected from any of the J domain sequences set forth in Table 1, infra.
Preferably, a protein expressing enhancing polypeptide of the invention is an isolated J domain of an Erdj protein, a large T antigen of SV40, or a mammalian cysteine string protein alpha (CSP-α). A preferred isolated J domain of an Erdj protein of the invention is an isolated J domain of Erdj1, Erdj2, Erdj3, Erdj4, Erdj5, Erdj6 or Erdj7. Particularly preferred is an isolated J domain of Erdj3.
In another embodiment, a protein expression enhancing polypeptide of the invention is a polypeptide fragment of a J domain that has an amino acid sequence that is selected from any of the following:







(SEQ ID NO: 48)









I-K-K-A-Y-R-K-L-A,


 







(SEQ ID NO: 83)









I-R-K-A-Y-R-K-L-S-L-T-L,


 







(SEQ ID NO: 84)









I-K-K-Q-Y-R-L-L-S-L-K-Y,


 







(SEQ ID NO: 85)









I-K-K-A-F-H-K-L-A-M-K-Y,


 







(SEQ ID NO: 86)









I-R-Q-A-F-K-K-L-A-L-K-L,


 







(SEQ ID NO: 87)









I-I-K-A-Y-R-K-L-A-L-Q-W,


 







(SEQ ID NO: 88)









I-A-R-A-Y-R-Q-L-A-R-R-Y,


 







(SEQ ID NO: 89)









I-K-R-A-Y-R-R-Q-A-L-R-Y,


 







(SEQ ID NO: 90)









I-K-K-S-Y-R-K-L-A-L-K-Y,



and


 







(SEQ ID NO: 91)









I-K-K-A-Y-K-R-L-A-M-K-Y.






In another embodiment, a protein expression enhancing polypeptide is a J domain analog polypeptide having the amino acid sequence of formula I, supra. In particular embodiments, a protein enhancing polypeptide of the invention comprises a polypeptide having the sequence: X1-X2-X3-X4-X5-X6-X7-X8-X9 (SEQ ID NO:326), wherein:
X1 is I, L, V, A, or M;
the dipeptide X2-X3 is selected from the group consisting of: KR, KK, RK, RR, AK, AR, KA, IK, NK, KQ, RQ, and RD;
X4 is A, S, T, R, S, Q, E, F, C, or I;
X5 is Y or F;
the dipeptide X6-X7 is selected from the group consisting of: KR, KK, RK, RR, RQ, FR, RL, KL, HK, LK, QK, and KV; and
the dipeptide X8-X9 is selected from the group consisting of: LA, LL, AL, AA, LC, LV, QA, KA, LS, LI, LY, and RA.
In particular embodiments, a J domain analog polypeptide of the invention comprises one of the following amino acid sequences:















Amino Acid Sequence



Sequence Identifier
123456789012345









SEQ ID NO: 48
IKKAYRKLA



 



SEQ ID NO: 49
IKKAYKLALQ



 



SEQ ID NO: 50
IKKAYRLALQ



 



SEQ ID NO: 51
IKKAYRKALQ



 



SEQ ID NO: 52
IKKAYRKLLQ



 



SEQ ID NO: 53
IKKYRKLA



 



SEQ ID NO: 54
IKKAYKLA



 



SEQ ID NO: 55
IKKAYRLA



 



SEQ ID NO: 56
IKKAYRKA



 



SEQ ID NO: 57
LKKAYRKLA



 



SEQ ID NO: 58
VKKAYRKLA



 



SEQ ID NO: 59
MKKAYRKLA



 



SEQ ID NO: 60
AKKAYRKLA



 



SEQ ID NO: 61
IAKAYRKLA



 



SEQ ID NO: 62
IKAAYRKLA



 



SEQ ID NO: 63
IKKRYRKLA



 



SEQ ID NO: 64
IKKSYRKLA



 



SEQ ID NO: 65
IKKQYRKLA



 



SEQ ID NO: 66
IKKEYRKLA



 



SEQ ID NO: 67
IKKFYRKLA



 



SEQ ID NO: 68
IKKCYRKLA



 



SEQ ID NO: 69
IKKAFRKLA



 



SEQ ID NO: 70
IKKAWRKLA



 



SEQ ID NO: 71
IKKAYRKQA



 



SEQ ID NO: 72
IKKAYRKMA



 



SEQ ID NO: 73
IKKAYRKIA



 



SEQ ID NO: 74
IKKAYRKAA



 



SEQ ID NO: 75
IKKAYRKVA



 



SEQ ID NO: 76
IKKAYRKRA



 



SEQ ID NO: 77
IKKAYRKLM



 



SEQ ID NO: 78
IKKAYRKLI



 



SEQ ID NO: 79
IKKAYRKLV



 



SEQ ID NO: 80
IKKAYRKLC



 



SEQ ID NO: 81
IKKAYRKLS



 



SEQ ID NO: 82
IKKAYRKLY



 



SEQ ID NO: 83
IRKAYRKLSLTL



 



SEQ ID NO: 84
IKKQYRLLSLKY



 



SEQ ID NO: 85
IKKAFHKLAMKY



 



SEQ ID NO: 86
IRQAFKKLALKL



 



SEQ ID NO: 87
IIKAYRKLALQW



 



SEQ ID NO: 88
IARAYRQLARRY



 



SEQ ID NO: 89
IKRAYRRQALRY



 



SEQ ID NO: 90
IKKSYRKLALKY



 



SEQ ID NO: 91
IKKAYKRLAMKY










In a further embodiment, the invention provides a fusion protein comprising a protein expression enhancing polypeptide fused to a target protein of interest, wherein the protein expression enhancing polypeptide fusion partner is a J domain of a J protein, a J domain fragment having the ability to enhance expression of the protein of interest fusion partner, or a J domain analog polypeptide having the amino acid sequence of formula I (SEQ ID NO:47) as described above. Expression of this fusion protein leads to increased expression of the fused target protein of interest, as compared with expression of the target protein of interest without the use of the protein expression enhancing polypeptide fusion partner. Removal of the protein expression enhancing polypeptide portion of the fusion protein by standard methods results in increased recovery of the target protein of interest.
A fusion protein of the invention comprising a protein expression enhancing polypeptide described herein linked to a target protein of interest may be used in a method to restore a protein function in cells of a mammalian subject that are deficient in the secretion of a native secreted protein that provides the protein function comprising the steps of inserting into cells of the mammalian subject (such as a human, non-human primate, rodent, or livestock) an exogenous nucleic acid molecule encoding a fusion protein comprising a protein expression enhancing polypeptide as described above linked to the secreted protein, wherein expression of the fusion protein provides the function of the native secreted protein whose secretion is deficient in cells of the subject in the absence of the exogenous nucleic acid.
In a preferred embodiment, the above method for restoring a protein function in cells of a mammalian subject is used to treat a subject that has a disease associated with the deficient secretion of a native secreted protein in the subject. Such diseases include, but are not limited to, prion-associated disease, Alzheimer's disease, Parkinson's disease, Huntington's disease, cystic fibrosis (CF), and α1-antitrypsin deficiency. In a particularly preferred embodiment, a method for restoring a protein function is used to treat a human subject deficient in the secretion of cystic fibrosis transmembrane conductance regulator protein (CFTR) and the disease is cystic fibrosis. In this embodiment, an exogenous nucleic acid molecule that is inserted into cells of the human subject encodes a fusion protein comprising a protein expression enhancing polypeptide described above linked to CFTR. Expression of the fusion protein in the cells of the human subject restores the deficiency of CFTR function.
In a further embodiment, the invention provides a fusion protein comprising a protein expression enhancing polypeptide linked to a target protein binding domain, wherein the protein expression enhancing polypeptide element is a J domain of a J protein, a J domain fragment having the ability to enhance expression of the protein of interest fusion partner, or a J domain analog polypeptide having the amino acid sequence of formula I (SEQ ID NO:47) as described above, and the target protein binding domain is a polypeptide capable of binding to a target protein of interest when the fusion protein and the target protein of interest are co-expressed in the same host cell. A fusion protein that binds a target protein of interest enhances the level of expression of the target protein and/or enhances the level of the target protein at its proper cellular or extracellular location. Accordingly, fusion proteins described herein may be used to enhance the level of expression of a target protein of interest that is not expressed in adequate amounts or at the proper cellular or extracellular location for a given purpose. Such situations in which a fusion protein described herein is useful include, without limitation, failure to express desired quantities of an endogenous or heterologous (recombinant) protein of interest in cell culture and failure to express sufficient levels of a protein in vivo where inadequate expression of one or more functional proteins leads to a pathological state (such as, without limitation, a prion-associated disease (a transmissible spongiform encephalopathy); Alzheimer's disease; Parkinson's disease; Huntington's disease; cystic fibrosis; α1-antitrypsin deficiency).
A protein that is targeted by a fusion protein of the invention for an enhanced level of expression and/or enhanced expression at a desired cellular or extracellular location may be a soluble protein, a membrane-associated protein, or a secreted protein.
A target protein binding domain of a fusion protein of the invention is a polypeptide that binds a target protein. Preferably, the target binding domain has a binding affinity for a target protein that is sufficiently specific as to exclude other proteins from interfering with the enhancement in the level of expression of the target protein. Examples of polypeptides that may be used as a target binding domain of the invention include, but are not limited to, an antibody or antigen binding portion thereof that binds a target protein, an immunoglobulin-specific binding protein (such as Protein A, Protein L, and Protein G) that binds a target immunoglobulin or fragment thereof, an Fc binding protein (such as Protein A and Protein G) that binds an Fc domain of a target protein, an Fc binding peptide that binds an Fc domain of a target protein, a ligand binding domain of a receptor protein that binds the target protein of interest, a protein ligand of the target protein (such as a protein ligand of a receptor), a PDZ domain of a PDZ protein that binds a PDZ binding domain of a target protein, and the like.
In an embodiment of the invention, when the target protein is a cytokine, the target binding domain of a fusion protein of the invention may comprise a ligand binding domain of a cytokine receptor protein that binds the target cytokine protein.
In another embodiment, when the target protein is a receptor protein or ligand binding portion thereof, then the target binding domain of a fusion protein of the invention may comprise a protein ligand which is bound by the receptor or the ligand binding portion thereof. In a preferred embodiment, when the target protein is a cytokine receptor protein or cytokine binding portion thereof, the target binding domain comprises the cytokine that is bound by the cytokine receptor or cytokine binding portion of such receptor.
In an embodiment wherein the target protein, such as the cystic fibrosis transmembrane conductance regulator (CFTR) protein, possesses a PDZ-binding domain, then the target binding domain of a fusion protein of the invention may comprise a PDZ domain from any of a variety of proteins that possess a PDZ domain. In a preferred embodiment, when a target protein possesses a PDZ-binding domain, a target binding domain of a fusion protein of the invention comprises a PDZ domain from any of the members of the NHERF family of PDZ adapter proteins including, but not limited to, of NHERF1 (also known as NHERF, EBP50, or SLC9A3R1), NHERF2 (also known as E3KARP or SLC9A3R2), and PDZK1 (also known as CAP70 or NHERF3).
Particular embodiments of a target protein-binding fusion protein of the invention comprise a J domain of a J protein, or an active (expression enhancing) fragment thereof, or a protein expression enhancing polypeptide of formula I, fused to a target protein binding domain with or without a linker peptide. When a linker peptide is present in a target protein-binding fusion protein of the invention, the linker may be one or more amino acids, including 1 to 10 amino acids, 1 to 20 amino acids, and even 1 to 50 amino acids. Typically, a linker will not be more than 20 amino acids and will be selected or designed so that linker does not interfere with (and hopefully enhances) the function of either the target protein binding domain or the protein expression enhancement polypeptide. The linker, if present, preferably is selected to optimize the contribution of both elements of the fusion protein and thereby increase the level of expression and/or proper location of a target protein of interest. The linker may be omitted if direct attachment of a protein expression enhancement polypeptide to a target protein binding domain does not unacceptably diminish the function of either element or does not unacceptably diminish the desired enhancement in the level of expression and/or location of the target protein.
A linker useful in a fusion protein of the invention may include an enzymatically cleavable peptide, i.e., a cleavage site for an enzyme such as an enterokinase, the light chain of enterokinase, thrombin, urokinase, tobacco etch virus protease (TEV), tissue plasminogen activator, a zinc-dependent endopeptidase, a matrix metalloproteinase (MMP), a serralysin, an astacin, an adamalysin, a disintegrin, an ADAM, a caspase, a cathespsin, a calpain, and the like. Use of a cleavable linker in a fusion protein described herein may be advantageous to halt or slow the function of the fusion protein or to eliminate its presence in a cell or presence in a population of target protein molecules. Some cells possess one or more intracellular proteases that can cleave polypeptide linker molecules that contain a corresponding proteolytic recognition site. Accordingly, a cleavable linker used in a fusion protein of the invention may be selected that permits an intracellular protease to cleave the fusion protein after expression in the cell.
A fusion protein of the invention may further comprise an epitope tag to assist in detecting or isolating the fusion protein. An epitope tag useful in the invention includes, but is not limited to; a polyhistidine tag (such as hexaHis, SEQ ID NO:112), a V5 epitope tag, a Myc epitope tag, a Flag epitope tag, and an HA (human influenza hemagglutinin) epitope tag.
Fusion proteins of the present invention are demonstrated to enhance the level of expression of target proteins compared to the level of expression of the target proteins alone, i.e., in the absence of a fusion protein. The level of expression of a target protein of interest can be increased at least about 1.5-fold and up to 2-fold, 4-fold, 6-fold, 8-fold, 10-fold, 25-fold or more by following the methods described herein. Moreover, fusion proteins of the invention also enhance the level of target proteins at their proper cellular or extracellular locations.
In another embodiment, the invention provides compositions comprising a fusion protein useful for providing the fusion protein to an individual to enhance expression of a target protein. Compositions of the invention also include pharmaceutical compositions comprising a fusion protein and a pharmaceutically acceptable carrier for use in treating a disease or disorder in an individual, including in a human individual. Pharmaceutical compositions comprising a fusion protein as described herein may further comprise one or more other therapeutically active compounds. Examples of such additional therapeutically active compounds that may be incorporated into a pharmaceutical composition of the invention include, but are not limited to, an antibiotic, an anti-viral compound, an anti-cancer compound, a sedative, a stimulant, a local anesthetic, a corticosteroid, an analgesic, an anti-histamine, a non-steroid anti-inflammatory drug (NSAID), and appropriate combinations thereof.
The invention also provides methods of treating a human or animal subject for a disease state characterized by a loss or diminution of a function or property that can be provided by a target protein of interest whose expression is enhanced by one of the types of fusion proteins described herein. Such methods may include administering a fusion protein as described herein to a patient in need of treatment.
The invention also provides isolated nucleic acids encoding a protein expression enhancing polypeptide selected from the group consisting of an isolated J domain of a J protein, an isolated J domain fragment having the ability to enhance expression of a target protein of interest, or an isolated J domain analog polypeptide having the amino acid sequence of formula I (SEQ ID NO:47) as described above.
The invention also provides nucleic acid vectors comprising an isolated nucleic acid described above.
In another embodiment, the invention comprises a host cell comprising an isolated nucleic acid or a nucleic acid vector described above.
The invention provides isolated nucleic acid molecules encoding a fusion protein described herein. Also provided are recombinant vector molecules into which has been inserted an isolated nucleic acid molecule encoding a fusion protein of the invention. Such recombinant vector molecules include cloning vectors to replicate the inserted nucleic acid in a transfected host cell and also expression vectors for expressing the encoded fusion protein in a compatible transfected host cell. Any of a variety of expression vectors available in the art may be used to produce a fusion protein of the invention. Examples of expression vectors useful for expressing a fusion of the invention include, but are not limited to, plasmid pcDNA, pcDNA3.3 TOPO (Life Technologies, New York), plasmid pTT3, plasmid pEF-BOS, and the like.
The invention also provides expression vector molecules into which has been inserted an isolated nucleic acid encoding an isolated J domain, an active J domain fragment, or a J domain analog of formula I, for use in expressing a fusion protein of the invention in vitro in a compatible host cell.
Expression vectors of the invention also include gene therapy vectors for expressing a fusion protein of the invention in vivo in a gene therapy to restore a lost or deficient target protein function in a plant or animal (including mammals, such as humans, non-human primates, rodents, and livestock).
In another aspect, the invention provides a host cell comprising an expression vector for expressing a protein expression enhancing polypeptide described here or a fusion protein described herein. Host cells useful in the invention include, without limitation, eukaryotic host cells. Preferred eukaryotic host cells include, without limitation, a mammalian host cell, an insect host cell, a plant host cell, a fungal host cell, a eukaryotic algal host cell, a nematode host cell, a protozoan host cell, and a fish host cell. Preferably, a mammalian host cell is a Chinese Hamster Ovary (CHO) cell, a COS cell, a Vero cell, an SP2/0 cell, an NS/0 myeloma cell, a human embryonic kidney (HEK293) cell, a baby hamster kidney (BHK) cell, a HeLa cell, a human B cell, a CV-1/EBNA cell, an L cell, a 3T3 cell, an HEPG2 cell, a PerC6 cell, or an MDCK cell. Preferred fungal host cells include Aspergillus, Neurospora, Saccharomyces, Pichia, Hansenula, Schizosaccharomyces, Kluyveromyces, Yarrowia, and Candida. More preferably, a Saccharomyces host cell is a Saccharomyces cerevisiae cell.
The invention provides a method of expressing a fusion protein comprising a J domain of a J protein, a protein expression enhancing fragment thereof, or a J domain analog of formula I linked to a target protein of interest comprising culturing a host cell comprising a vector molecule comprising an isolated nucleic acid molecule encoding the fusion protein under conditions sufficient to produce the fusion protein.
In another embodiment, the invention provides a method of expressing a fusion protein comprising a J domain of a J protein, a protein expression enhancing fragment thereof, or a J domain analog of formula I as described above linked to a target protein of interest comprising transfecting a host cell with an expression vector comprising a structural gene encoding the fusion protein and culturing the transfected host cell under conditions causing the expression of the fusion protein.
The invention also provides a method of expressing a fusion protein comprising a protein expression enhancing polypeptide described herein linked to a target protein of interest comprising the steps of:

    
    
        1) constructing a recombinant gene sequence encoding the fusion protein;
        2) inserting the recombinant gene sequence into an expression vector to form a recombinant expression vector wherein said recombinant gene sequence is operably linked to a transcriptional promoter sequence;
        3) transfecting said recombinant expression vector into host cells that are compatible with said promoter sequence; and
        4) culturing said transfected host cells under conditions that permit expression said fusion protein.
    
    


The invention also provides a method of expressing a fusion protein comprising an isolated expression enhancing polypeptide described herein linked to a target protein binding domain comprising culturing a host cell comprising a vector comprising an isolated nucleic acid encoding the fusion protein under conditions sufficient to produce the fusion protein.
In another embodiment, the invention provides a method of enhancing the expression of a target protein of interest expressed by a host cell comprising transfecting the host cell with an expression vector comprising a structural gene encoding a fusion protein comprising an isolated J domain of a J protein, an isolated J domain fragment having the ability to enhance expression of a target protein of interest, or an isolated J domain analog polypeptide having the amino acid sequence of formula I (SEQ ID NO:47) as described above linked to the target protein binding domain, and culturing said transfected host cell under conditions causing the co-expression of said fusion protein encoded by said structural gene and of said target protein of interest.
The invention provides a method of enhancing the expression of a target protein of interest comprising (a) transfecting a host cell with an expression vector comprising a structural gene encoding a fusion protein, wherein the fusion protein comprises a J domain of a J protein, an active fragment thereof, or a J domain analog of formula I linked to a target protein binding domain and wherein the fusion protein binds the target protein of interest, and (b) culturing said transfected host cell under conditions causing the expression of the fusion protein encoded on the structural gene. Said structural gene may also include optional segments encoding a linker peptide connecting the J domain/J domain fragment/J domain analog element and the target protein binding domain element, and may also include segments encoding epitope tags, enzyme cleavage sites, and the like. The method may advantageously be carried out by following the steps:

    
    
        1) constructing a recombinant gene sequence encoding a fusion protein comprising a protein expression enhancing polypeptide linked to a target binding domain;
        2) inserting the recombinant gene sequence into an expression vector to form a recombinant expression vector wherein said recombinant gene sequence is operably linked to a transcriptional promoter sequence;
        3) transfecting suitable host cells that are compatible with said promoter sequence with said recombinant expression vector; and
        4) culturing said transfected host cells under conditions that lead to expression of said fusion protein.
    
    


In an embodiment of the invention, a nucleic acid encoding a fusion protein of the invention is inserted into the cells of a plant or non-human animal to express the fusion protein and enhance the level of expression of a target protein to provide a missing or desired function to the plant or non-human animal. Such methods include producing transgenic plants and transgenic non-human animals in which a nucleic acid encoding a fusion protein is permanently incorporated into the genome as a functional gene (transgene) such that the plant or non-human animal not only expresses the fusion protein, but also passes a copy of the expressible transgene on to progeny.
In another embodiment, the invention provides a method of restoring a function provided by a target protein in cells of a subject that are deficient in the expression of the target protein comprising inserting into cells of the subject an exogenous nucleic acid molecule encoding a fusion protein according to the invention, wherein after inserting the exogenous nucleic acid molecule into the cells, the fusion protein is expressed and enhances the level expression of the target protein (which enhancement may be the result of stabilizing the endogenous target protein, increasing the amount of properly folded target protein, improving the localization of the target protein to the desired cellular or extracellular compartment (e.g., improving secretion of a secreted protein), etc.), to provide the function of the target protein whose expression is deficient in the cells of the subject in the absence of the exogenous nucleic acid. Such a method is particularly useful in treating a subject that has a disease associated with the deficient expression of a protein in the subject. Such diseases include, but are not limited to, a prion-associated disease (a transmissible spongiform encephalopathy), Alzheimer's disease, Parkinson's disease, Huntington's disease, cystic fibrosis, and α1-antitrypsin (AAT) deficiency. Particularly preferred, are embodiments of the method wherein the subject is a human subject that is deficient in the expression of cystic fibrosis transmembrane conductance regulator (CFTR) protein and the disease is cystic fibrosis or wherein the subject is a human subject that is deficient in α1-antitrypsin and the disease is α1-antitrypsin (AAT) deficiency.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A-1C illustrate a series of experiments described in Example 2 that demonstrate improvement in the level of expression of a target protein of interest (the IL13Rα2 receptor protein) in a modified arrangement in which the target protein is linked to a J domain (from Hsp40, SV40, or CSP J proteins) in comparison to the protein alone (IL13Rα2WT) or expressed as a fusion protein with a BAG domain (from BAG3, BAG4, BAG5, or BAG6 proteins). FIG. 1A depicts diagrams of the structural genes for insertion into an expression vector plasmid used to transfect host cells. A cDNA encoding an IL13Rα2 protein (wild-type protein, “WT”) was augmented with a segment encoding a V5 epitope tag at the 3′ end for the “IL13Rα2WT” expression product. For BAG domain fusion proteins, a cDNA encoding IL13Rα2 was linked in frame to a segment encoding a BAG domain, which was linked in turn to a segment encoding a V5 epitope tag to provide BAG domain fusion protein expression products. For J domain fusion proteins of the invention, a cDNA encoding IL13Rα2 was linked in frame to a segment encoding a J domain, which was linked in turn to a segment encoding a V5 epitope tag to provide J domain fusion protein expression products. FIG. 1B shows x-ray film images of chemiluminescent signals of a Western blot (immunoblot) analysis of cell lysates indicating relative levels of expression of the tagged IL13Rα2 wild-type (WT) protein or fusion protein counterparts in transfected cells. It can be seen that employing a J domain of J proteins Hsp40, SV40, or CSP as a fusion partner for the IL13Rα2 protein of interest resulted in significantly greater protein expression compared to the wild-type IL13Rα2 protein (WT) or any of the BAG domain fusion counterparts comprising a BAG domain of BAG proteins BAG3, BAG4, BAG5, or BAG6. All transfectants were co-transfected with a reporter plasmid expressing green fluorescent protein (GFP) to show successful transfection and operability of the transfectants. See, lower panel of FIG. 1B. FIG. 1C provides the results of a densitometry analysis of the chemiluminescent signals in the immunoblot of FIG. 1B using the ImageJ image processing program. The bar graphs in FIG. 1C clearly show a significantly higher level of expression of all three secreted IL13Rα2-J domain fusion proteins compared to that for any of the four IL13Rα2-BAG domain fusion proteins or the wild-type IL13Rα2 protein (IL13α2WT expression=100%).
FIGS. 2A and 2B show the results of an experiment described in Example 2 that examined improvement in the level of expression of a secreted target protein of interest in a modified arrangement in which a truncated form (“TF”) of the IL13Rα2 receptor protein (which is the extracellular portion of the IL13Rα2 receptor protein containing the ligand binding domain) is linked to a J domain (J-IL13Rα2TF) in comparison to the truncated receptor protein alone (IL13Rα2TF). FIG. 2A depicts diagrams of the structural gene constructs for insertion into an expression vector plasmid used to transfect host cells. A cDNA encoding IL13Rα2TF was augmented with a segment encoding a V5 epitope tag at the 3′ end for the IL13Rα2TF expression product. A cDNA encoding IL13Rα2TF was augmented at the 3′ end with a segment encoding a V5 epitope tag and linked at the 5′ end with a segment encoding a J domain (from J protein Erdj3) for a J domain fusion protein expression product of the invention (J-IL13Rα2TF). FIG. 2B shows x-ray film images of chemiluminescent signals in a Western blot indicating relative levels of expression in cells (cell lysates) and secreted into culture medium (medium) of the V5-tagged IL13Rα2TF protein and J domain fusion protein counterpart. It can be seen that employing a J domain as a fusion partner for the IL13Rα2TF protein of interest resulted in significantly greater level of protein expression compared to IL13Rα2TF protein without a J domain. All transfectants were co-transfected with a reporter plasmid expressing green fluorescent protein (GFP) to show successful transfection and operability of the transfectants. See, lower panel of FIG. 2B. Mock cultures contained cells transfected with an “empty” vector, i.e., an expression vector lacking a structural gene for expressing any protein.
FIGS. 3A and 3B show results of an experiment an experiment described in Example 2 comparing relative levels of expression of protein secreted into the culture medium of host cells transfected with an expression vector for expressing a truncated receptor protein (IL13Rα2TF), a BAG domain-IL13Rα2TF fusion protein (BAG-IL13Rα2TF), and a J domain-IL13Rα2TF fusion protein (J-IL13Rα2TF). FIG. 3A shows x-ray film images of chemiluminescent signals of a dot blot analysis of IL13Rα2TF, BAG domain-IL13Rα2TF fusion protein, and J domain-IL13Rα2TF fusion protein secreted into culture medium of transfected cells. All proteins carried a V5 epitope tag for innnunodetection with anti-V5 antibody. FIG. 3B provides the results of a densitometry analysis of the chemiluminescent signals in FIG. 3A using the NIH ImageJ image processing program. The bar graphs in FIG. 3B clearly show the significantly higher level of expression of secreted J domain-IL13Rα2TF fusion protein (bar graph 4) compared to either the IL13Rα2TF (bar graph 2) or the BAG domain-IL13Rα2TF fusion protein (bar graph 3). Mock cultures (bar graph 1) contained cells transfected with expression vector lacking a structural gene for expressing any protein.
FIGS. 4A-4C show results of an experiment described in Example 2 to examine improvement in the level of expression of a secreted α1 anti-trypsin (α1AT) in a modified arrangement in which α1AT is linked to (fused with) a J domain fusion partner in comparison to the protein alone or expressed as a fusion with a BAG domain. FIG. 4A depicts diagrams of the structural gene constructs for insertion into an expression vector plasmid used to transfect host cells. A cDNA encoding α1AT was augmented with a segment encoding a V5 epitope tag at the 3′ end for the α1AT expression product. A cDNA encoding α1AT was linked in frame to a segment encoding a BAG domain, which was linked in turn to a segment encoding a V5 epitope tag for a BAG domain fusion protein (α1AT-BAG) expression product. A cDNA encoding α1AT was linked in frame to a segment encoding a J domain, which was linked in turn to a segment encoding a V5 epitope tag for a J domain fusion protein (α1AT-J) expression product of the invention. FIG. 4B shows x-ray film images of chemiluminescent signals of a dot blot analysis indicating relative levels of expression of secreted α1AT protein or secreted fusion protein counterparts secreted into culture media. It can be seen that employing a J domain as a fusion partner for the α1AT protein of interest (α1AT-J) resulted in significantly greater expression of the secreted protein (α1AT-J) compared to the α1AT protein alone or BAG domain fusion counterpart (α1AT-BAG). Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein. FIG. 4C provides the results of a densitometry analysis of the chemiluminescent signals in FIG. 4B using the NIH ImageJ image processing program. The bar graphs in FIG. 4C clearly show the significantly higher level of expression of secreted α1AT-J fusion protein (bar graph 4) compared to either the (unfused) α1AT (bar graph 2) or the BAG domain-α1AT fusion protein (bar graph 3).
FIGS. 5A-5C show results of an experiment described in Example 2 that demonstrate improvement in the level of expression of a secreted truncated form of a TNF-α receptor1 protein (TNFR1TF) in a modified arrangement in which TNFR1TF is linked to a J domain fusion partner in comparison to the protein alone (TNFR1TF). FIG. 5A depicts diagrams of the structural gene constructs for insertion into an expression vector plasmid used to transfect host cells. A cDNA encoding TNFR1TF was augmented with a segment encoding a V5 epitope tag at the 3′ end for the TNFR1TF expression product. A cDNA encoding TNFR1TF was linked in frame to a segment encoding a J domain, which was linked in turn to a segment encoding a V5 epitope tag to provide a J domain fusion protein expression product of the invention. FIG. 5B shows x-ray film images of chemiluminescent signals of dot blots indicating relative levels of TNFR1TF and TNFR1TF-J domain fusion protein secreted into culture media. It can be seen that employing a J domain as a fusion partner for the TNFR1TF protein of interest (TNFR1TF-J) resulted in significantly greater expression of the secreted protein than for the (unfused) TNFR1TF protein. FIG. 5C provides the results of a densitometry analysis of the chemiluminescent signals in the dot blots of FIG. 5B using the NIH ImageJ image processing program. The bar graphs in FIG. 5C clearly show the significantly higher level of expression of secreted TNFR1TF-J domain fusion protein (bar graph 3) compared to TNFR1TF (bar graph 2). Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein.
FIGS. 6A-6C-3 show results of a series of experiments described in Example 2 that demonstrate improvement in the level of expression of target Fc fusion proteins of interest in a modified arrangement in which each of three target proteins of interest is linked to a J domain fusion partner. FIG. 6A depicts diagrams of structural gene constructs used in this example. For the Fc fusion proteins, a cDNA encoding each protein of interest (TNFR1TF, IL13Rα2TF, or α1AT) was augmented with a segment encoding a V5 epitope tag at the 3′ end, which was linked in turn to a segment (“Fc”) encoding constant domains of an immunoglobulin Fc region. For J domain fusions, a cDNA encoding a J domain was linked in frame between the cDNA encoding each protein of interest and the segment encoding a V5 epitope tag. See, FIG. 6A. FIGS. 6B-1-6B-3 show dot blot analysis for secreted proteins in media from cultures of transfected cells. Each of the Fc fusion proteins (TNFR1-V5-Fc, IL13Rα2TF-Fc, and α1AT-Fc) were expressed in culture media as shown in the dot blots in the middle lane of each panel in FIGS. 6B-1-6B-3. This level of expression of the Fc fusion proteins was greater than that for each of the proteins of interest alone (i.e., without fusion to an Fc domain; data not shown). Significantly higher levels of expression were obtained in each case when a J domain was linked to the protein of interest segment within the Fc fusion proteins as shown in the dot blots in the right lane of each panel in FIGS. 6B-1-6B-3. The results of a densitometry analysis of the chemiluminescent signals of the dot blots in FIGS. 6B-1-6B-3 are shown in the corresponding panels of FIGS. 6C-1-6C-3, where the significantly higher level of expression of the J domain fusion proteins is clearly evident by comparing bar graph 2 (protein of interest-Fc fusion proteins) with bar graph 3 (protein of interest-J domain-Fc fusion proteins) in each of the panels of FIGS. 6C-1-6C-3. Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein.
FIGS. 7A and 7B show results of an experiment described in Example 2 that demonstrates improvement in the level of expression of the cytoplasmic p53 protein in a modified arrangement in which p53 is linked to (fused with) a J domain fusion partner in comparison to the p53 protein alone. FIG. 7A depicts diagrams of the constructs used in this experiment. A cDNA encoding p53 was augmented at its 5′ end with a segment encoding a V5 epitope tag for the p53 expression product. A cDNA encoding p53 was linked in frame at its 5′ end to a segment encoding a J domain of an SV40 J protein, which was in turn linked at its 5′ end to a segment encoding a V5 epitope tag for a J domain fusion protein (J-p53) expression product of the invention. FIG. 7B shows x-ray film images of chemiluminescent signals of a Western blot of cell lysates indicating relative levels of expression in cells of the tagged p53 protein and the J domain fusion protein counterpart (J-p53). It can be seen that employing a J domain as a fusion partner for the p53 protein of interest (J-p53) resulted in a significantly greater level of expression in transfected cells compared to the level of expression in transfected cells of the p53 protein without a J domain (p53). Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein.
FIGS. 8A and 8B show results of a series of experiments described in Example 2 that demonstrate improvement in the levels of expression of two target proteins of interest, i.e., a wild-type CFTR protein and the corresponding CFTR Δ508F mutant protein (deletion at position 508 of a phenylalanine residue results in defective folding and rapid degradation of the CFTR Δ508F mutant protein), in a modified arrangement in which each of the proteins is linked to (fused with) a J domain fusion partner in comparison to each of the proteins alone or each of the proteins expressed as a fusion with a BAG domain. FIG. 8A depicts diagrams of constructs for insertion into an expression vector plasmid used to transfect host cells. A cDNA encoding each protein of interest, i.e., the wild-type CFTR protein (CFTR WT) or the CFTR Δ508F mutant protein (Δ508F), was augmented at the 5′ end with a segment encoding a V5 epitope tag. For BAG domain fusions, a cDNA encoding a BAG domain was linked in frame between the cDNA encoding each protein of interest and the 5′ segment encoding a V5 epitope tag. For J domain fusion protein expression products of the invention, a cDNA encoding an SV40 J domain was linked in frame between the cDNA encoding each protein of interest and a 5′ segment encoding a V5 epitope tag for the J domain. See, FIG. 8A. FIG. 8B shows x-ray film images of chemiluminescent signals of a Western blot analysis of cell lysates indicating relative levels of expression in cells of the tagged proteins of interest (CFTR WT and CFTR Δ508F), BAG domain fusion proteins (BAG-CFTR WT and BAG-CFTR Δ508F), and J domain fusion proteins (J-CFTR WT and J-CFTR Δ508F). It can be seen that employing a J domain as a fusion partner for both CFTR WT and CFTR Δ508F proteins resulted in a significantly greater level of expression in transfected cells as compared to the levels of expression of (unfused) CFTR WT and mutant CFTR Δ508F proteins or of the BAG domain fusion counterparts. All transfectants were co-transfected with a reporter plasmid expressing green fluorescent protein (GFP) to show successful transfection and operability of the transfectants (lower panel of FIG. 8B).
FIG. 9A depicts a diagram of a general scheme of an unmodified arrangement for enhancing expression of a target protein on interest in which co-expression of a fusion protein of the invention enhances expression of a target protein of interest as described in Example 4. In the scheme, a fusion protein of the invention comprises a protein expression enhancing polypeptide (PEEP) domain linked to a target protein binding domain, wherein the target protein binding domain binds a target protein of interest thereby bringing the target protein into close proximity with the PEEP domain, which in turn results in an elevation of the level of expression of the target protein in its proper cellular or extracellular location.
FIG. 9B is a diagram of a structural gene encoding an IL13Rα2TF fusion protein (target protein) for insertion into an expression vector plasmid, which was used to transfect host cells as described in Example 4, below. A cDNA encoding a truncated form of the IL13Rα2 receptor protein (IL13Rα2TF), which comprises the extracellular IL13 ligand binding domain of IL13Rα2, was augmented with a segment encoding a V5 epitope tag at the 3′ end.
FIG. 9C depicts a construct for expressing a fusion protein of the invention to enhance expression of the V5-tagged IL13Rα2TF target protein depicted in FIG. 9B and as described in Example 4. A cDNA encoding a J domain of an Erdj3 J protein (protein expression enhancing polypeptide domain) was linked to a segment encoding the IL13 protein (target protein binding domain). A segment encoding a Flag epitope tag was linked to the 3′ end of the segment encoding the IL13 target protein binding domain.
FIG. 10 shows x-ray film images of chemiluminescent signals of a Western blot analysis of culture medium (upper panel) and cell lysates (middle panel) of transfected cells expressing a truncated form of the IL13Rα2 receptor protein (IL13Rα2TF) when expressed alone (lane 2 from the left), when co-expressed with its IL13 ligand (IL13 Only, lane 3 from the left), and when co-expressed in an unmodified arrangement with a J domain-IL13 fusion protein of the invention (J-IL13, lane 4 from the left), as described in Example 4. A properly folded IL13Rα2TF protein (target protein) is expected to be secreted from the transfected host cells. It can be seen that co-expression of the IL13Rα2TF protein with the J domain-IL13 fusion protein significantly enhanced the level of expression of secreted IL13Rα2TF protein (top panel, lane 4 from the left) as compared to expression of IL13Rα2TF protein alone (top panel, lane 2 from the left) or co-expression of IL13Rα2TF protein with its IL13 ligand (top panel, lane 3 from the left). Moreover, co-expression of the IL13Rα2TF protein with the J domain-IL13 fusion protein significantly enhanced the level of expression of intracellular IL13Rα2TF protein (middle panel, lane 4 from the left) as compared to the level expression of IL13Rα2TF protein alone (middle panel, lane 2 from the left) or co-expression of IL13Rα2TF protein with its IL13 ligand (middle panel, lane 3 from the left). All transfectants were co-transfected with a reporter plasmid expressing green fluorescent protein (GFP) to show successful transfection and operability of the transfectants. See, lower panel of FIG. 10. Mock cultures contained cells transfected with “empty vector”, i.e., an expression vector lacking a structural gene for expressing any protein (no IL13Rα2TF protein, no co-expression; “none” in lane 1 from the left of the blot). The empty vector transfectants were, however, co-transfected with the GFP vector, and successful co-transfection is shown by GPF expression detected in the lower panel of FIG. 10.
FIGS. 11A and 11B show schematic diagrams of nucleic acid constructs encoding proteins for insertion into expression vector plasmids used to transfect host cells for the experiments described in Example 5 below. FIG. 11A depicts a DNA construct encoding an Fc fusion protein (target protein) comprising a cDNA encoding a protein of interest augmented at its 3′ end with a segment encoding a V5 epitope tag, which in turn was linked to a segment encoding the constant domains of an immunoglobulin Fc domain. For Example 5 below, the Fc fusion protein target comprised a truncated form of the IL13Rα2 receptor protein (IL13Rα2TF), which was linked to a V5 epitope tag, which in turn was linked to an Fc domain to yield the desired IL13Rα2TF-Fc fusion protein. FIG. 11B depicts a DNA construct encoding a fusion protein of the invention in which a protein expression enhancing polypeptide (PEEP) domain (such as a J domain of a J protein) is linked to a target protein binding domain (such as Protein A, which is known to bind Fc domains). The construct was further augmented at the 3′ end with a coding segment for a Flag epitope tag for easy identification and isolation with a standard anti-Flag antibody.
FIGS. 12A-12D show results of an experiment described in Example 5 that demonstrate significant enhancement in the expression of an IL13Rα2TF-Fc fusion protein (target protein) in an unmodified arrangement in which the target protein is co-expressed with a J domain-Protein A fusion protein but not when the target protein is co-expressed with Protein A alone.
FIG. 12A shows x-ray film images of chemiluminescent signals of a Western blot analysis of media from cultures of transfected cells expressing the IL13Rα2TF-Fc fusion protein (target protein) when expressed alone (lane 2, none), when co-expressed with Protein A alone (lane 3, Protein A Only), when co-expressed with an Erdj3 J domain-Protein A fusion protein (lane 4, J-Protein A), and when co-expressed with an Erdj5 J domain-Protein A fusion protein (lane 5, J2-Protein A), as described in Example 5. Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein (lane 1 from the left). It can be seen that co-expression of the IL13Rα2TF-Fc fusion target protein and either J domain-Protein A fusion protein (lanes 4 and 5 from the left) resulted in a significantly greater level of expression of the IL13Rα2TF-Fc fusion target protein secreted into culture medium as compared to the level of expression in transfectant cells expressing the IL13Rα2TF-Fc fusion target protein alone (lane 2 from the left) or co-expressing the IL13Rα2TF-Fc fusion target protein with unfused Protein A (lane 3 from the left).
FIG. 12B shows results of a densitometry analysis of the chemiluminescent signals in FIG. 12A using the NIH ImageJ image processing program. Bar graphs 1-5 of FIG. 12B correspond to signals in lanes 1-5 in FIG. 12A. The bar graphs in FIG. 12B clearly show that co-expression of the IL13Rα2TF-Fc target protein with either J domain-Protein A fusion protein (bar graphs 4 and 5) significantly enhanced the level of expression of secreted IL13Rα2TF-Fc as compared to expression of IL13Rα2TF-Fc alone (bar graph 2) or co-expression of IL13Rα2TF-Fc with (unfused) Protein A alone (bar graph 3).
FIG. 12C shows x-ray film images of chemiluminescent signals of a Western blot analysis of media from cultures of transfected cells expressing the IL13Rα2TF (no Fc domain) protein alone (lane 1, none), when co-expressed with an Erdj3 J domain-Protein A fusion protein (lane 2, J-Protein A), and when co-expressed with Protein A alone (lane 3, Protein A Only), as described in Example 5. The results show that little if any expression of secreted IL13Rα2TF protein was observed, as expected if the enhanced level of the secreted IL13Rα2TF-Fc fusion target protein in FIGS. 12A and 12B was dependent on the specificity of the target protein binding domain of the J domain-Protein A fusion protein for the Fc domain of IL13Rα2TF-Fc target protein. FIG. 12D provides the results of a densitometry analysis of the chemiluminescent signals in FIG. 12C using the NIH ImageJ image processing program: FIGS. 12C and 12D thus show a control experimental result in that the IL13Rα2TF protein was not recognized by the J domain-Protein A fusion (the Fc ligand for the target binding domain (Protein A) being absent), and thus the enhancement in the level of expression that could be provided by the J domain (a protein expression enhancing polypeptide domain) was not targeted to the IL13Rα2TF, as the results indicate.
FIGS. 13A-1-13C-2 provide results of a series of experiments that demonstrate significant enhancement of the level of expression of three different Fc fusion target proteins when co-expressed with a corresponding fusion protein of the invention as described in Example 6 below. FIG. 13A-1 shows x-ray film images of chemiluminescent signals of a Western blot assay for expression of an IL13Rα2TF-Fc fusion protein (target protein) secreted into the media of cultures of transfected cells expressing the IL13Rα2TF-Fc fusion protein alone (lane 1 from the left) and of transfected cells co-expressing the IL13Rα2TF-Fc fusion protein and the J domain-Protein A fusion protein (lane 2 from the left) as described in Example 6.1 below and similar to the experiment described in Example 5. FIG. 13A-2 provides the results of a densitometry analysis of the chemiluminescent signals in FIG. 13A-1 using the NIH ImageJ image processing program. Bar graphs 1 and 2 (from left to right) in FIG. 13A-2 correspond to the signals in lanes 1 and 2 (from left to right) in FIG. 13A-1. The results show that co-expression of the J domain-Protein A fusion protein of the invention significantly elevated (8-fold) the level of expression of the IL13Rα2TF-Fc target protein secreted into the culture medium as compared to the level of expression of the target protein in the absence of the J domain-Protein A fusion protein. Results are consistent with those described in Example 5 and FIG. 12.
FIG. 13B-1 shows x-ray film images of chemiluminescent signals of a Western blot assay for expression of a TNFR1TF-Fc fusion protein (target protein) secreted into the media of cultures of transfected cells expressing the TNFR1TF-Fc fusion target protein alone (lane 1 from the left) and of transfected cells co-expressing the TNFR1TF-Fc fusion protein and the J domain-Protein A fusion (lane 2 from the left) as described in Example 6.2 below. FIG. 13B-2 provides the results of a densitometry analysis of the chemiluminescent signals in FIG. 13B-1 using the NIH ImageJ image processing program. Bar graphs 1 and 2 (from left to right) in FIG. 13B-2 correspond to the signals in lanes 1 and 2 (from left to right) in FIG. 13B-1. The results show that co-expression of J domain-Protein A fusion protein significantly elevated (6-fold) the level of expression of the TNFR1TF-Fc target protein secreted into the culture medium as compared to the level of expression of the target protein in the absence of the J domain-Protein A fusion protein.
FIG. 13C-1 shows x-ray film images of chemiluminescent signals of a Western blot assay for expression of an α1 anti-trypsin (α1AT)-Fc fusion protein (target protein) secreted into the media of cultures of transfected cells expressing the α1AT-Fc fusion target protein alone (lane 1 from the left) and of transfected cells co-expressing the α1AT-Fc fusion target protein and the J domain-Protein A fusion protein (lane 2 from the left) as described in Example 6.3. FIG. 13C-2 provides the results of a densitometry analysis of the chemiluminescent signals in FIG. 13C-1 using the NIH ImageJ image processing program. Bar graphs 1 and 2 (from left to right) in FIG. 13C-2 correspond to the signals in lanes 1 and 2 (from left to right) in FIG. 13C-1. The results show that co-expression of J domain-Protein A fusion protein significantly elevated (3-fold) the level of expression of the OAT-Fc fusion target protein secreted into the culture medium as compared to the level of expression of the target protein in the absence of the J domain-Protein A fusion protein.
FIGS. 14A and 14B provide results from a series of experiments that test the enhancement in the level of expression of a secreted humanized anti-IL8 IgG1 antibody in an unmodified arrangement described in Example 7 below. FIG. 14A shows x-ray film images of chemiluminescent signals of a dot blot assay for expression of the anti-IL8 antibody (target protein) secreted into the media of cultures of transfected cells expressing the anti-IL8 antibody alone (lane 2), co-expressing anti-IL8 antibody and Protein A (lane 3, Protein A Only), co-expressing anti-IL8 antibody and an Erdj3 J domain-Protein A fusion protein of the invention (lane 4, J-Protein A), co-expressing anti-IL8 antibody and Protein L (lane 5, Protein L Only), co-expressing anti-IL8 antibody and an Erdj3 J domain-Protein L fusion protein of the invention (lane 6, J-Protein L), co-expressing anti-IL8 antibody and its IL8 ligand (lane 7, IL8), co-expressing an Erdj3 J domain-IL8 ligand fusion protein of the invention (lane 8, J-IL8), expressing the Erdj3 J-Protein A fusion protein alone (lane 9, J-Protein A), expressing the Erdj3 J domain-Protein L fusion protein alone (lane 10, J-Protein L), and expressing the Erdj3 J domain-IL8 ligand fusion protein (lane 11, J-IL8). Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein (no anti-IL8 antibody, lane 1). Expression of the anti-IL8 antibody in culture media was analyzed in the dot blot assay using an anti-human IgG antibody (“anti-huIgG Ab”) (catalog no. AP112P, Millipore). It can be seen that co-expression in transfected cells of the anti-IL8 antibody with a J domain-Protein A fusion protein (lane 4), with a J domain-Protein L fusion protein (lane 6), or with a J domain-IL8 fusion protein (lane 8) significantly enhanced the level of expression of anti-IL8 antibody secreted into the culture medium as compared to the level of the antibody expressed in transfected cells expressing the anti-IL8 antibody alone (lane 2), co-expressing with Protein A alone (lane 3, Protein A Only), co-expressing Protein L alone (lane 5, Protein L Only), or co-expressing IL8 ligand protein alone (lane 7). No signal was detected in culture media of transfected cells expressing the J domain-Protein A fusion protein alone (lane 9, J-Protein A), of transfected cells expressing the J domain-Protein L fusion protein alone (lane 10, J-Protein L), or of transfected cells expressing the J domain-IL8 fusion protein alone (lane 10, J-IL8), indicating that all three fusion proteins specifically targeted and enhanced expression of the co-expressed anti-IL8 antibody target protein.
FIG. 14B shows the results of a densitometry analysis of the chemiluminescent signals in each of the lanes in FIG. 14A using the NIH ImageJ image processing program. The bar graphs of FIG. 14B are numbered to correspond to the lane numbers of FIG. 14A. The results of this series of experiments clearly show that co-expression of the targeted anti-IL8 antibody with a fusion protein of the invention comprising a protein expression enhancing polypeptide (here, an Erdj3 J domain) linked to a target protein binding domain (here, Protein A, Protein L, or IL8) significantly enhanced the expression of secreted anti-IL8 antibody as compared to co-expression of the antibody with the unfused target protein binding domain protein alone (Protein G only, Protein L only, or IL8 only).
FIGS. 15A and 15B provide results that demonstrate that a fusion protein according to the invention can be used to enhance the level of expression of a target protein that is already stably produced in an established commercially relevant cell line as described in Example 8 below. FIG. 15A shows x-ray film images of chemiluminescent signals of a dot blot assay for expression of the anti-IL8 antibody (target protein) secreted into the media of cultures of cells of a CHO-DP12 cell line (accession no. CRL-124444, American Type Culture Collection, Manassas, Va.) expressing the anti-IL8 antibody alone (lane 2) and in transfected cells co-expressing anti-IL8 antibody and an Erdj3 J domain-Protein A fusion protein (lane 3, J-Protein A). Expression of the anti-IL8 antibody in culture media was analyzed in the dot blot assay using an anti-human IgG antibody (“anti-huIgG Ab”). It can be seen that co-expression of the antibody with the J domain-Protein A fusion protein significantly enhanced the level of expression of the antibody secreted into the culture medium (lane 3) as compared to the level of the antibody expressed in the absence of the J domain-Protein A fusion protein (lane 2, none). Lane 1 is control (Medium Only). FIG. 15B shows the results of a densitometry analysis of the chemiluminescent signals in the dot blots in the lanes in FIG. 15A using the ImageJ image processing program is shown in the respective bar graphs in FIG. 15B. The results indicate that co-expression of the antibody with the J domain-Protein A fusion protein (bar graph 3) significantly enhanced expression of the secreted antibody, providing an approximately four- to five-fold greater enhancement in the level of expression, as compared to that obtained when the antibody was expressed in the absence of the J domain-Protein A fusion protein (bar graph 2). The results indicate that a fusion protein of the invention can be employed to significantly enhance the level of production of a target protein that is already stably expressed in an established production cell line.
FIGS. 16A and 16B provide results from a series of experiments that tested various fusion proteins comprising a J domain (as a protein expression enhancing polypeptide domain) of a J protein linked to any of a variety of proteins, as described in Example 9.1 below. The various J domain fusion proteins and other proteins were then tested and compared for their ability to enhance levels of expression of the IL13Rα2TF-Fc fusion protein (target protein) secreted into media of cultures of transfected HEK293 cells. FIG. 16A shows x-ray film images of chemiluminescent signals of a Western blot analysis of samples of media from cultures of transfected cells expressing the IL13Rα2TF-Fc fusion protein (target protein) alone (lane 1), co-expressing IL13Rα2TF-Fc with a J domain-Protein A fusion protein (lane 2), co-expressing IL13Rα2TF-Fc with Protein A alone (lane 3, Protein A Only), co-expressing IL13Rα2TF-Fc with a J domain-Protein G fusion protein (lane 4), co-expressing IL13Rα2TF-Fc with a J domain-hFcR fusion protein (lane 5, J-hFcR), co-expressing IL13Rα2TF-Fc with a J domain-vFcR fusion protein (lane 6, J-vFcR), co-expressing IL13Rα2TF-Fc with a J domain-gI fusion protein (lane 7, J-gI), co-expressing IL13Rα2TF-Fc with a J domain-gE fusion protein (lane 8, J-gE), and co-expressing IL13Rα2TF-Fc with both J domain-gI fusion protein and J domain-gE fusion protein (lane 9, J-gI+J-gE). The results of a densitometry analysis of the chemiluminescent signals in the Western blot in FIG. 16A using the NIH ImageJ image processing program are shown in the respective bar graphs in FIG. 16B. See, Example 9.1 for details.
FIGS. 17A-1 and 17B provide results from a series of experiments that tested various fusion proteins comprising a J domain (as a protein expression enhancing polypeptide domain) of a J protein linked to each of six Fc-binding peptides (FcBP1 through FcBP6) for use in enhancing the level of expression of proteins that possess an Fc domain as described in Example 9.2 below. The amino acid sequences of the Fc binding peptides are given in FIG. 17A-2 (SEQ ID NOS:240-245, respectively). FIG. 17A-1 shows x-ray film images of chemiluminescent signals of a Western blot assay of samples of media of cultures of transfected cells expressing the IL13Rα2TF-Fc fusion protein (target protein) alone (lanes 1 and 3), co-expressing IL13Rα2TF-Fc with a J domain-Protein A fusion protein (lane 2, J-Protein A), co-expressing IL13Rα2TF-Fc with a J domain-FcBP1 fusion protein (lane 4, J-FcBP1), co-expressing IL13Rα2TF-Fc with a J domain-FcBP2 fusion protein (lane 5, J-FcBP2), co-expressing IL13Rα2TF-Fc with a J domain-FcBP3 fusion protein (lane 6, J-FcBP3), co-expressing IL13Rα2TF-Fc with a J domain-FcBP4 fusion protein (lane 7, J-FcBP4), co-expressing IL13Rα2TF-Fc with a J domain-FcBP5 fusion protein (lane 8, J-FcBP5), co-expressing IL13Rα2TF-Fc with a J domain-FcBP6 fusion protein (lane 9, J-FcBP6), and co-expressing IL13Rα2TF-Fc with a J domain-Protein G fusion protein (lane 10, J-Protein G). As shown in FIG. 17A-1, co-expression of the IL13Rα2TF-Fc fusion protein with each of the six J domain-peptide fusion proteins in HEK293 transfectants significantly enhanced the level of expression of secreted IL13Rα2TF-Fc fusion protein (lanes 4-9) as compared to the level of expression of IL13Rα2TF-Fc fusion protein alone (lanes 1 and 3). The experiment also included for comparison the effect of co-expression of IL13Rα2TF-Fc fusion protein with a J domain-Protein A fusion protein (lane 2) or with a J domain-Protein G fusion protein (lane 10) on the expression of secreted IL13Rα2TF-Fc fusion protein. As shown in FIG. 17A-1, co-expression of IL13Rα2TF-Fc fusion protein with either J domain-Protein A fusion protein (lane 2) or the J domain-Protein G fusion protein (lane 10) significantly enhanced the level of expression of secreted the IL13Rα2TF-Fc fusion protein as also observed in Examples 5 (FIGS. 12A and 12B), 6.1 (FIGS. 13A-1 and 13A-2), and 9.1 (FIGS. 16A and 16B). The results of a densitometry analysis of the chemiluminescent signals in the Western blot in FIG. 17A-1 using the NIH ImageJ image processing program are shown in the respective bar graphs in FIG. 17B.
FIG. 18 shows x-ray film images of chemiluminescent signals of a dot blot assay showing examples of relative levels of target protein expression enhancing activity of three polypeptides used in an unmodified arrangement described in Example 10. The levels of expression indicated in the dot blot, i.e., High Activity (HA), Activity (A), and No Activity (NA), were determined for polypeptides designated “3 (J domain)”, “3-45”, and “3-72” (see Table 58, infra.). Each polypeptide was linked to Protein A to form a fusion protein that was co-expressed with a V5-tagged IL13Rα2-Fc target protein in transfected cells. The level of expression of the V5-tagged IL13Rα2-Fc target protein in culture media was determined in the dot blot using an anti-V5 antibody. The dot blot shows expression of the V5-tagged IL13Rα2-Fc target protein in the media of cultures of transfected cells expressing the target protein alone (lane 2 from left), of transfected cells co-expressing the target protein and the polypeptide 3-Protein A fusion protein (lane 3 from left), of transfected cells co-expressing the target protein and the polypeptide 3-45-Protein A fusion protein (lane 4 from left), and of transfected cells co-expressing the target protein and the polypeptide 3-72-Protein A fusion protein (lane 5 from left). The high activity (HA) of a polypeptide for enhancing expression of a target protein in an unmodified arrangement is represented by the level of expression shown in lane 3 (from the left) of the dot blot. Improved activity compared to negative control (A) of a polypeptide for enhancing expression of a target protein is represented by the level of expression shown in lane 4 (from the left) of the dot blot. No activity (NA) of a polypeptide for enhancing expression of a target protein is shown in lane 5 (from the left) of the dot blot. Lane 1 (from the left) of the dot blot shows no target protein was expressed in the medium of a mock culture of cells that did not express the target protein or any polypeptide-Fc fusion protein.
FIG. 19 shows an alignment of the amino acid sequence of the J domain of Erdj3 with the amino acid sequences of a series of polypeptides that were generated as N- and C-terminal deletion mutations of the full-length J domain as described in Example 11. The alpha helices and loop domains of the J domain are indicated by brackets. Also shown are a designation number, length (amino acid residues), protein expression enhancing activity (HA, NA), and sequence identification number for each of the polypeptides. (See, FIG. 18 and Example 10 for a description of high activity (HA), improved activity (A), and no activity (NA) for enhancing target protein expression.) As shown in the alignment, the J domain is designated polypeptide 3, is 61 amino acids in length, and has high activity (HA) for enhancing expression of a target protein in an unmodified arrangement.
FIGS. 20A and 20B show results of a series of experiments described in Example 12 that compares the target protein expression enhancing activity of two polypeptides used in a modified arrangement. FIG. 20A shows diagrams of nucleic acid constructs for insertion into an expression vector used to transfect cells. The IL13Rα2TF construct encodes a fusion polypeptide comprising a truncated form of IL13Rα2 that contains the extracellular IL13 binding domain fused to a C-terminal V5 epitope tag. The IL13Rα2TF-BSC1 construct encodes a fusion polypeptide comprising the truncated form of IL13Rα2 fused to the BSC1 sequence (polypeptide 3-29, IKKAYRKLA, SEQ ID NO:48), which is fused to a C-terminal V5 epitope tag. The IL13Rα2TF-BSC1MT construct encodes the truncated from of IL13Rα2 fused to the BSC1MT sequence (polypeptide 3-55, IAQAYRKLA, SEQ ID NO:298), which is fused to a C-terminal V5 epitope tag. The amino acid sequence of polypeptide 3-55 differs from that of polypeptide 3-29 at two positions as shown at the bottom of FIG. 20A. Cells transfected with a vector containing the IL13Rα2TF construct were taken as the control (no fusion with a BSC1 or BSC1MT polypeptide).
FIG. 20B shows X-ray film images of chemiluminescent signals of a dot blot analysis of the media of cultures of transfected cells expressing the IL13Rα2TF, IL13Rα2TF-BSC1, and IL13Rα2TF-BSC1MT proteins using an anti-V5 antibody. Lane 2 (from the left) of FIG. 20B shows that only a very low level of IL13Rα2TF fusion protein was detected in medium of a culture of control cells. Lane 3 (from the left) in FIG. 20B shows that a significant level of the IL13Rα2TF-BSC1 fusion protein was expressed in the medium of a culture of cells transfected with a vector containing the IL13Rα2TF-BSC1 construct. Lane 4 (from the left) in FIG. 20B shows that only a very low level of the IL13Rα2TF-BSC1MT fusion protein was expressed in the medium of culture of cells transfected with a vector containing the IL13Rα2TF-BSC1MT construct. The results indicate that polypeptide 3-29 has “high activity” for enhancing expression of a target protein in a modified arrangement, whereas polypeptide 3-55 is considered to have “no activity” for enhancing expression of a target protein in a modified arrangement.
FIG. 21 is a bar graph showing IL13 binding activity of IL13Rα2TF-Fc target protein co-expressed in an unmodified arrangement with a BSC1-Protein A in HEK293 cells as described in Example 13. The BSC1-Protein A protein if a fusion protein comprising the polypeptide 3-29 (IKKAYRKLA, SEQ ID NO:48) linked to Protein A as shown in Example 13. The assay used for determining IL13 binding activity is a sandwich ELISA in which detection of human IL13 decreases when the IL13 is trapped by the IL13Rα2TF-Fc protein. The first bar graph (from the left) in FIG. 21 shows no IL13 binding activity was present in medium from a culture of control cells that did not express either IL13Rα2TF-Fc or the BSC1-Protein A fusion protein. Bar 2 (middle) in FIG. 21 shows that some low level of IL13 binding activity was detected in medium from a culture of cells expressing only the IL13Rα2TF-Fc protein. In contrast, as shown in Bar 3 (far right) in FIG. 21, a significant level of human IL13 binding activity was present in the medium of a culture of cells co-expressing IL13Rα2TF-Fc and the BSC1-Protein A fusion protein. The results shown that the IL13Rα2TF-Fc target protein expressed at enhanced levels in culture medium in an unmodified arrangement retains its IL13 binding activity.
FIGS. 22A and 22B show results of an experiment that demonstrates significant enhancement in the level of expression of a Factor VII (FVII)-Fc fusion protein (target protein) secreted into culture medium when co-expressed in an unmodified arrangement with a BSC1-Protein G fusion protein comprising polypeptide 3-29 (IKKAYRKLA, SEQ ID NO:48) linked to Protein G as described in Example 14. FIG. 22A shows X-ray film images of chemiluminescent signals of a Western blot assay for expression of an FVII-Fc fusion protein (top panel) secreted into the media of cultures of transfected cells expressing the FVII-Fc fusion protein alone (lane 2) and of transfected cells co-expressing the FVII-Fc fusion protein and the BSC1-Protein G fusion protein (lane 3). Lane 1 shows non-expressing cell culture medium as a control. Anti-Flag antibody was used to detect BSC1-Protein G in cell lysate (middle panel) and secreted BSC1-Protein G (bottom panel), respectively. FIG. 22B provides the results of a densitometry analysis of the chemiluminescent signals in the top panel of FIG. 22A using the NIH ImageJ image processing program. Bar graphs 1, 2, and 3 in FIG. 22B correspond to the signals in lanes 1, 2, and 3 in the top panel of FIG. 22A. The results show that co-expression of the FVII-Fc target protein and the BSC1-Protein G fusion protein significantly elevated the level of expression of the FVII-Fc target protein secreted into the culture medium as compared to the level of expression of the target protein expressed in the absence of the BSC1-Protein G fusion protein. In addition, the BSC1-Protein G fusion protein was not secreted but remained in the cells. Compare expression of BSC1-Protein G fusion protein cell lysates (middle panel of FIG. 22A) with that in medium (bottom panel of FIG. 22A).
FIGS. 23A and 23B show results of an experiment to demonstrate improvement in the level of expression of a Factor IX (FIX)-Fc fusion protein (FIX-Fc) target protein in the presence of a BSC1-Protein A fusion protein comprising polypeptide 3-29 (IKKAYRKLA, SEQ ID NO:48) linked to Protein A as described in Example 15. FIG. 23A shows X-ray film images of chemiluminescent signals of a Western blot assay for expression of an FIX-Fc fusion protein secreted into the media of cultures of transfected cells expressing the FIX-Fc fusion protein alone (row 2) and of transfected cells co-expressing the FIX-Fc fusion protein and the BSC1-Protein A fusion protein (row 3). Row 1 shows non-expressing cell culture medium as a control. FIG. 23B provides the results of a densitometry analysis of the chemiluminescent signals in the top panel of FIG. 23A using the NIH ImageJ image processing program. Bar graphs 1, 2, and 3 in FIG. 23B correspond to the signals in rows 1, 2, and 3 in FIG. 23A. The results show that co-expression of the FIX-Fc target protein and the BSC1-Protein A fusion protein significantly elevated the level of expression of the FIX-Fc target protein secreted into the culture medium as compared to the level of expression of the target protein in the absence of the BSC1-Protein A fusion protein.
FIG. 24 provides results of a series of experiments that demonstrate significant enhancement of the level of expression of a Factor VIII (FVIII)-Fc fusion protein (FVIII-Fc) when co-expressed in an unmodified arrangement with a BSC1-Protein G fusion protein comprising polypeptide 3-29 (IKKAYRKLA, SEQ ID NO:48) linked to Protein G as described in Example 16. Media was harvested from cultures of transfected HEK293 cells co-expressing the FVIII-Fc fusion protein (target protein) with BSC1-Protein G fusion protein or cells expressing the FVIII-Fc fusion protein alone. The media was assayed for FVIII activity by ELISA (VisuLizeTM FVIII Antigen Kit, Affinity Biologicals Inc.). Cell culture medium in which empty vector was transfected was used for a negative control (first bar from the left). Second bar from the left shows no FVIII was detected in medium from cells expressing the FVIII-Fc target protein alone. Third bar from the left shows that significant level of FVIII-Fc target protein was secreted into the medium of cells co-expressing the FVIII-Fc target protein and the BSC1-Protein G fusion protein. Human serum was used as a positive control (last bar from left). The results show that co-expression of the FVIII-Fc target protein and the BSC1-Protein G fusion protein significantly elevated the level of expression of the FVIII-Fc target protein secreted into the culture medium as compared to the level of expression of the target protein in the absence of the BSC1-Protein G fusion protein.
FIGS. 25A-25C show results of an experiment demonstrating improved levels of expression of an anti-IL8 antibody (target protein) secreted into the culture medium when co-expressed in an unmodified arrangement with a BSC1-Protein A comprising the 3-29 polypeptide (IKKAYRKLA, SEQ ID NO:48) linked to Protein A as described in Example 17. FIG. 25A shows X-ray film images of chemiluminescent signals of a dot blot assay for expression of the anti-IL8 antibody (target protein) secreted into the media of cultures of transfected cells expressing the anti-IL8 antibody alone (row 2) and of cells co-expressing the anti-IL8 antibody and a BSC1-Protein A fusion protein (row 3, BSC1-Protein A). Expression of the anti-IL8 antibody in culture media was analyzed in the dot blot assay using an anti-human IgG antibody. Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein (no anti-IL8 antibody, row 1). It can be seen that co-expression in transfected cells of the anti-IL8 antibody with a BSC1-Protein A fusion protein (row 3) significantly enhanced the level of expression of anti-IL8 antibody secreted into the culture medium as compared to the level of the antibody expressed in transfected cells expressing the anti-IL8 antibody alone (row 2).
FIG. 25B shows the results of a densitometry analysis of the chemiluminescent signals in each of the rows in FIG. 25A using the NIH ImageJ image processing program. The bars of FIG. 25B are numbered to correspond to the row numbers of FIG. 25A. The results of this series of experiments clearly show that co-expression of the targeted anti-IL8 antibody with a BSC1-Protein A fusion protein significantly enhanced the expression of secreted anti-IL8 antibody compared to the level of expression of the antibody in the absence of the BSC1-Protein A fusion protein.
FIG. 25C shows a bar graph of the results of an ELISA to detect IL8 binding activity by the expressed anti-IL8 antibody (target protein). A 96-well plate was coated with recombinant purified human IL8, and incubated with the anti-IL8 antibody (target protein) secreted into the media of cultures of transfected cells expressing the anti-IL8 antibody alone (bar graph 2) or co-expressing the anti-IL8 antibody with the BSC1-Protein A fusion protein (bar graph 3, BSC1-Protein A). Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein (no anti-IL8 antibody, bar graph 1). The results of this series of experiments clearly show that the anti-IL8 antibody expressed at enhanced levels and secreted into the culture medium retains its binding activity for human IL8, indicating proper conformation of the antibody.
FIGS. 26A-26C show results of a series of experiments demonstrating significant enhancement in the level of expression of the anti-VEGF antibody, bevacizumab, when co-expressed with a BSC1-Protein A fusion comprising the 3-29 polypeptide (IKKAYRKLA, SEQ ID NO:48) linked to Protein A as described in Example 18. FIG. 26A shows X-ray film images of chemiluminescent signals of a dot blot assay for expression of the anti-VEGF antibody secreted into the media of cultures of transfected cells expressing the anti-VEGF antibody alone (row 2) or co-expressing the anti-VEGF antibody and a BSC1-Protein A fusion protein (row 3). Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein (no anti-VEGF antibody, row 1). Expression of the anti-VEGF antibody in culture media was analyzed in the dot blot assay using an anti-human IgG antibody. It can be seen that co-expression in transfected cells of the anti-VEGF antibody with the BSC1-Protein A fusion protein (row 3) significantly enhanced the level of expression of anti-VEGF antibody secreted into the culture medium as compared to the level of the antibody expressed in transfected cells expressing the anti-VEGF antibody alone (row 2).
FIG. 26B shows the results of a densitometry analysis of the chemiluminescent signals in each of the rows in FIG. 26A using the NIH ImageJ image processing program. The bar graphs in FIG. 26B are numbered to correspond to the row numbers in FIG. 26A. The results clearly show that co-expression of the anti-VEGF antibody with a BSC1-Protein A fusion protein significantly enhanced the expression of secreted anti-VEGF antibody compared to the level of the antibody expressed alone.
FIG. 26C shows the results of an ELISA to detect VEGF binding by the anti-VEGF antibody expressed in the media of cultures of transfected cells. A 96-well plate was coated with recombinant purified human VEGF-A, and incubated with the anti-VEGF antibody (target protein) secreted into the media of cultures of transfected cells expressing the anti-VEGF antibody alone (bar graph 2) or co-expressing anti-VEGF antibody and the BSC1-Protein A fusion protein of the invention (bar graph 3). Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein (no anti-VEGF antibody, bar graph 1). The results of this series of experiments clearly show that the anti-VEGF antibody expressed at enhanced levels and secreted into the culture medium retains its binding activity for human VEGF-A, indicating proper conformation of the secreted antibody.
FIGS. 27A-27C show results from a series of experiments demonstrating significant enhancement in the level of expression the therapeutic anti-TNFα antibody, adalimumab (Humira®, AbbVie), when co-expressed with a BSC1-Protein A fusion comprising the 3-29 polypeptide (IKKAYRKLA, SEQ ID NO:48) linked to Protein A as described in Example 19. FIG. 27A shows X-ray film images of chemiluminescent signals of a dot blot assay for expression of the anti-TNFα antibody secreted into the media of cultures of transfected cells expressing the anti-TNFα antibody alone (row 2) or co-expressing the anti-TNFα antibody and the BSC1-Protein A fusion (row 3). Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein (row 1, no anti-TNFα antibody). Expression of the anti-TNFα antibody in culture media was analyzed in the dot blot assay using an anti-human IgG antibody. It can be seen that co-expression in transfected cells of the anti-TNFα antibody with a BSC1-Protein A fusion protein (bottom row) significantly enhanced the level of expression of anti-TNFα antibody secreted into the culture medium as compared to the level of the antibody expressed in transfected cells expressing the anti-TNFα antibody alone (middle).
FIG. 27B shows the results of a densitometry analysis of the chemiluminescent signals in each of the rows in FIG. 27A using the NIH ImageJ image processing program. The bar graphs of FIG. 27B are numbered to correspond to the row numbers of FIG. 27A. The results of this series of experiments clearly show that co-expression of the anti-TNFα antibody (target protein) with the BSC1-Protein A fusion protein significantly enhanced the expression of secreted anti-TNFα antibody.
FIG. 27C shows the results of an ELBA to detect TNFα binding activity by the anti-TNFα antibody expressed in the media of cultures of transfected cells. A 96-well plate was coated with recombinant purified human TNFα and incubated with the anti-TNFα antibody (target protein) secreted into the media of cultures of transfected cells expressing the anti-TNFα antibody alone (bar graph 2) or cells co-expressing the anti-TNFα antibody and the BSC1-Protein A fusion protein (bar graph 3). Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein (bar graph 1). The results of this series of experiments clearly show that the anti-TNFα antibody expressed at enhanced levels and secreted into the culture medium retains its binding activity for human TNFα, indicating proper conformation of the secreted antibody.
FIGS. 28A-28C provide results that demonstrate that the level of expression of a protein that is already stably produced in an established commercially relevant cell line can be enhanced when co-expressed with as BSC1-Protein A fusion comprising the 3-29 polypeptide (IKKAYRKLA, SEQ ID NO:48) linked to Protein A as described in Example 20. FIG. 28A shows X-ray film images of chemiluminescent signals of a dot blot assay for expression of the anti-IL8 antibody (target protein) secreted into the media of cultures of cells of a CHO-DP12 cell line (accession no. CRL-124444, American Type Culture Collection, Manassas, Va.) expressing the anti-IL8 antibody alone (row 2) and of transfected cells co-expressing the anti-IL8 antibody and the BSC1-Protein A fusion protein (row 3). It can be seen that co-expression of the antibody with the BSC1-Protein A fusion protein significantly enhanced the level of expression of the antibody secreted into the culture medium (row 3) as compared to the level of the antibody expressed in the absence of the BSC1-Protein A fusion protein (row 2). Row 1 is control (Medium Only). FIG. 28B shows the results of a densitometry analysis of the chemiluminescent signals in the dot blots in the rows in FIG. 28A using the NIH ImageJ image processing program are shown in the respective bar graphs in FIG. 28B. The results indicate that co-expression of the antibody with the BSC1-Protein A fusion molecule (bar graph 3) significantly enhanced expression of the secreted antibody, providing an approximately four to five-fold greater enhancement in the level of expression, as compared to that obtained when the antibody was expressed in the absence of the BSC1-Protein A fusion molecule (bar graph 2).
FIG. 28C shows the results of an ELISA to detect IL8 binding activity by the anti-IL8 antibody expressed in the media of cultures of transfected cells. A 96-well plate was coated with recombinant purified human IL8 and incubated with the anti-IL8 antibody (target protein) secreted into the media of cultures stably expressing the anti-IL8 antibody (bar graph 2) or co-expressing the antibody and the BSC1-Protein A fusion protein (bar graph 3). Culture medium was used as a negative control (bar graph 1, no IL8 binding activity). The results of this series of experiments clearly show that the anti-IL8 antibody secreted at enhanced levels into the culture medium retains its binding activity for human IL8, indicating proper conformation of the secreted antibody.
FIG. 29 provides results of an experiment described in Example 21 that indicate that protein expression enhancing polypeptides of the invention may be used to treat a disease caused by a mutant protein that does not fold into its proper conformation. FIG. 29 shows X-ray film images of chemiluminescent signals of a Western blot assay for expression of fusion proteins comprising wild type alpha1-antitrypsin (AAT) or the mutant alpha1-antitrypsin containing the Z mutation (AATZ, wherein Glu is replaced by Lys at codon 342) linked to the Fc domain from human IgG with or without co-expression of a BSC1-Protein A comprising the 3-29 polypeptide (IKKAYRKLA, SEQ ID NO:48) linked to Protein A. The top panel of FIG. 29 shows expression of Fc fusion proteins in the media of cultures of transfected cells expressing the AAT-Fc fusion protein alone (lane 2, from the left), of transfected cells expressing the AATZ-Fc fusion protein alone (lane 3, from the left), and of transfected cells co-expressing the AATZ-Fc fusion protein and the BSC1-Protein A fusion protein (lane 4, from the left). Lane 1 shows non-expressing cell culture medium as a control. Clearly, no AATZ-Fc fusion protein was secreted into media of cultures of cells expressing AATZ-Fc fusion protein alone (lane 3, from the left). As shown in the middle panel (Cell Lysate) of FIG. 29, for cells expressing the AATZ-Fc fusion protein alone, the AATZ-Fc fusion protein remained in the cells (lane 3, from the left), presumably lodged in the endoplasmic reticulum as is known for the unfused AATZ protein. In contrast, co-expression of the AATZ-Fc fusion protein and the BSC1-Protein A fusion protein significantly enhanced the level of AATZ-Fc fusion protein secreted into the culture medium as shown in lane 4 (from the left) in the top panel (medium) of FIG. 29. Moreover, as shown in lane 4 (from the left) in the middle panel (Cell Lysate) of FIG. 29, virtually no AATZ-Fc fusion protein was retained in the cells. The same membrane was blotted with anti-Tubulin antibody for a loading control (lower panel) in FIG. 29. The results show that co-expression of the BSC1-Protein A fusion protein significantly elevated the level the AATZ-Fc target protein secreted into the culture medium as compared to the level of expression of the target protein in the absence of the BSC1-Protein A fusion protein with virtually no AATZ-Fc retained in the cells.



DETAILED DESCRIPTION OF THE INVENTION
The invention provides a new family of polypeptides for enhancing the level of expression of a target protein of interest. The invention is based on the discovery that a target protein of interest can be expressed at a significantly higher level and in the proper cellular or extracellular location when co-expressed in either of two arrangements in a host cell with a protein expression enhancing polypeptide comprising:
an isolated J domain of a J protein,
a protein expression enhancing polypeptide fragment of a J domain, or
a protein expression enhancing J domain analog polypeptide comprising the formula:
X1-X2-X3-X4-X5-X6-X7-X8-X9 (SEQ ID NO:47), wherein:

    
    
        X1 is isoleucine (I), leucine (L), valine (V), alanine (A), or methionine (M);
        X2 and X3 are each independently any amino acid with the proviso that at least one is lysine (K) or arginine (R);
        X4 is any amino acid; or X4 may be absent when X1 through X3 are present and X5 through X9 are present;
        X5 is tyrosine (Y), tryptophan (W), or phenylalanine (F);
        X6 and X7 are each independently any amino acid with the proviso at least one is lysine (K) or arginine (R); or one of X6 and X7 may be absent when the other is K or R and when X1 through X5 are present and X8 and X9 are present; and
        X8 and X9 are any amino acid with the proviso that at least one is leucine (L) or alanine (A); or one of X8 and X9 may be absent when the other is L or A and when X1 through X7 are present.
    
    


A protein expression enhancing polypeptide of the invention may be employed in either of two arrangements for enhancing expression of a target protein of interest by a host cell. In a “modified” arrangement, a fusion protein comprises a protein expression enhancing polypeptide linked (fused) to a target protein of interest. The fusion protein is thus a “modified” target protein that acts as a functional surrogate for the target protein of interest and is expressed at an enhanced level by a host cell compared to the level of expression of the unmodified target protein alone. In an “unmodified” arrangement, a fusion protein comprises a protein expression enhancing polypeptide of the invention linked to a target protein binding domain that has an affinity for and binds the regular “unmodified” target protein of interest, wherein co-expression of the fusion protein and the target protein of interest in a host cell enhances the expression of the unmodified target protein as compared to the level of expression in the absence of the target protein-binding fusion protein according to the invention. In accordance with the invention, the enhanced level of protein expression in the modified and unmodified arrangements includes expression of the respective modified or unmodified target protein of interest in the proper location (cellular or extracellular) of the target protein of interest.
Accordingly, the invention provides a technical solution when there is a failure to express desired quantities of an endogenous or heterologous (recombinant) protein of interest in cells. The present invention also provides compositions and methods for treating individuals for a disease or disorder in which there is a failure to express sufficient levels of a functional protein in vivo, where inadequate expression of the protein or a functional version thereof leads to a pathological state. Examples of diseases in which an improperly folded protein species has been demonstrated or implicated include, but are not limited to, prion-associated disease (transmissible spongiform encephalopathy), Alzheimer's disease; Parkinson's disease; Huntington's disease; and cystic fibrosis (CF).
In order to more clearly describe the invention the following comments and definitions of terms apply.
Unless otherwise defined herein, scientific and technical terms used in connection with the present invention shall have the meanings that are commonly understood by those of ordinary skill in the art. The meaning and scope of the terms should be clear; however, in the event of any latent ambiguity, definitions provided herein take precedent over any dictionary or extrinsic definition. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. In this application, the use of the term “or” means “and/or,” unless stated otherwise. Furthermore, the use of the term “including”, as well as other forms, such as “includes” and “included”, is not limiting.
Generally, nomenclatures used in connection with and techniques of protein and nucleic acid chemistry (including methods of recombinant nucleic acid and polymerase chain reaction (PCR)), cell and tissue culture, molecular biology, genetics, microbiology, biochemistry, proteomics, pharmacology, and pharmaceutical science described herein are those well-known and commonly used in the art. The methods and techniques of the present invention are generally performed according to conventional methods in the art and as described in various general and more specific references available in the art. Assays and purification techniques are performed according to protocols available in the art, including in manuals of laboratory techniques and manufacturer's specifications, as commonly accomplished in the art or as described herein.
Unless indicated otherwise, when the terms “about” and “approximately” are used in combination with an amount, number, or value, then that combination describes the recited amount, number, or value alone as well as the amount, number, or value plus or minus 10% of that amount, number, or value. By way of example, the phrases “about 40%” and “approximately 40%” disclose both “40%” and “from 36% to 44%, inclusive”.
The term “target protein of interest”, “target protein”, or “protein of interest” refers to any protein for which there is a need or desire to enhance the level of expression in its intended cellular (including intracellular and membrane-associated) or extracellular (secreted) location.
The term “isolated” as in an “isolated molecule” (e.g., “isolated protein” or “isolated nucleic acid”) is a molecule that by virtue of its origin or source of derivation: is not associated with naturally associated components that accompany it in its native state; is substantially free of other kinds of molecules from the same species; is expressed by a cell from a different species; or does not occur in nature. Thus, a protein or nucleic acid molecule that is chemically synthesized or synthesized in a cellular system different from the cell from which it naturally originates will be “isolated” from its naturally associated components. A protein or nucleic acid molecule may also be rendered substantially free of naturally associated components by isolation, using respectively protein or nucleic acid purification techniques well known in the art.
The term “vector”, as used herein, is intended to refer to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked One type of vector is a “plasmid”, which refers to a circular double stranded nucleic acid (typically, DNA) loop into which additional nucleic acid segments may be inserted. Another type of vector is a viral vector, wherein additional DNA segments may be inserted into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked Such vectors are referred to herein as “recombinant expression vectors” (or simply, “expression vectors”). In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, “plasmid” and “vector” may be used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, lentivirus-derived vectors, and adenovirus-derived viruses), which serve equivalent or comparable functions.
The term “operably linked” refers to a juxtaposition of described components wherein the components are in a relationship permitting them to function in their intended manner. A control sequence “operably linked” to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences. “Operably linked” sequences may include both expression control sequences that are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest. The term “expression control sequence” refers to polynucleotide sequences that are necessary to effect the expression and processing of coding sequences to which they are ligated. Expression control sequences include appropriate transcription initiation, termination, promoter and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (such as, a Kozak consensus sequence); sequences that enhance protein stability; and when desired, sequences that enhance protein secretion. The nature of such control sequences differs depending upon the host organism; in prokaryotes, such control sequences generally include promoter, ribosomal binding site, and transcription termination sequence; in eukaryotes, generally, such control sequences include promoters and transcription termination sequence. The term “control sequences” is intended to include components whose presence is essential for expression and processing, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences. Unless stated otherwise, a description or statement herein of inserting a nucleic acid molecule encoding a fusion protein of the invention into an expression vector means that the inserted nucleic acid has also been operably linked within the vector to a functional promoter and other transcriptional and translational control elements required for expression of the encoded fusion protein when the expression vector containing the inserted nucleic acid molecule is introduced into compatible host cells or compatible cells of an organism.
As used herein, the term “recombinant” when used as an adjective describes non-naturally altered or manipulated nucleic acids, host cells transfected with exogenous nucleic acids, or polypeptides expressed non-naturally, through manipulation of isolated nucleic acid (typically DNA) and transfection of host cells or through manipulation of endogenous nucleic acid to alternative expression by introduction of non-endogenous nucleic acid. “Recombinant” is a term that specifically encompasses DNA molecules that have been constructed in vitro using genetic engineering techniques, and use of the term “recombinant” as an adjective to describe a molecule, construct, vector, cell, protein, polypeptide, peptide, or polynucleotide specifically excludes naturally occurring (“endogenous”) such molecules, constructs, vectors, cells, proteins, polypeptides, peptides, and polynucleotides in their respective, unisolated, native locations (for example, intracellular, tissue, or organ locations).
The term “recombinant host cell” (or simply, in context, “host cell”), as used herein, is intended to refer to a cell into which exogenous nucleic acid has been introduced. It should be understood that such terms are intended to refer not only to the particular subject cell but to the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein. Host cells useful in various aspects of the invention may be prokaryotic and eukaryotic cells. Preferred prokaryotic host cells include various bacterial cells, including Escherichia coli. While some manipulations, constructions, expressions, or replications of nucleic acids or encoded polypeptides related to the invention may be conducted using prokaryotic or eukaryotic host cells, the preferred host cells for enhanced expression of a target protein of interest, whether in the modified or unmodified arrangements described herein, are eukaryotic host cells. Preferred eukaryotic host cells include, without limitation, a mammalian host cell, an insect host cell, a plant host cell, a fungal host cell, a eukaryotic algal host cell, a nematode host cell, a protozoan host cell, and a fish host cell. Preferably, a mammalian host cell is a Chinese Hamster Ovary (CHO) cell, a COS cell, a Vero cell, an SP2/0 cell, an NS/0 myeloma cell, a human embryonic kidney (HEK293) cell, a baby hamster kidney (BHK) cell, a HeLa cell, a human B cell, a CV-1/EBNA cell, an L cell, a 3T3 cell, an HEPG2 cell, a PerC6 cell, or an MDCK cell. Preferred fungal host cells include Aspergillus, Neurospora, Saccharomyces, Pichia, Hansenula, Schizosaccharomyces, Kluyveromyces, Yarrowia, and Candida. A particularly preferred Saccharomyces host cell is a Saccharomyces cerevisiae cell. A particularly preferred insect host cell is an Sf9 cell.
The terms “heterologous” and “exogenous” are synonymous and are used broadly as adjectives to describe any molecule (e.g., protein, polypeptide, nucleic acid) that is not native to a host cell containing or expressing the molecule. Accordingly, “heterologous” and “exogenous” encompass the term “recombinant” as defined above.
“Transgenic organism”, as known in the art and as used herein, refers to an organism having cells that contain a transgene, wherein the transgene introduced into the organism (or an ancestor of the organism) expresses a polypeptide not naturally expressed in the organism or not naturally expressed at the normal or proper level to provide the intended function of the polypeptide to the organism. A “transgene” is a nucleic acid construct, which is stably and operably integrated into the genome of a cell from which a transgenic organism develops, directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic organism.
The terms “disease” and “disorder” are used interchangeably to indicate a pathological state identified according to acceptable medical standards and practices in the art.
As used herein, the term “effective amount” refers to the amount of a therapy that is sufficient to reduce or ameliorate the severity and/or duration of a disease or one or more symptoms thereof; to prevent the advancement of a detrimental or pathological state; to cause regression of a pathological state; to prevent recurrence, development, onset, or progression of one or more symptoms associated with a pathological state; to detect a disorder; or to enhance or improve the prophylactic or therapeutic effect(s) of a therapy (e.g., the administration of another prophylactic or therapeutic agent).
A “biological sample,” as used herein, includes, but is not limited to, any quantity of a substance from a living organism or formerly living organism. Such organisms include, but are not limited to, humans, non-human primates, mice, rats, monkeys, dogs, rabbits, ruminants, and other animals. Such substances of a biological sample may include, but are not limited to, blood, serum, plasma, urine, saliva, sputum, mucus, synovial fluid, milk, semen, cells, organs (for example, heart, spleen, lung, kidney, breast, brain, eye, tongue, stomach, pancreas, intestines, gall bladder, reproductive organs, appendix), tissues (for example, bone, cartilage, muscle, skin), bone marrow, and lymph nodes.
A composition or method described herein as “comprising” (or which “comprises”) one or more named elements or steps is open-ended, meaning that the named elements or steps are essential, but other elements or steps may be added within the scope of the composition or method. To avoid prolixity, it is also understood that any composition or method described as “comprising” (or which “comprises”) one or more named elements or steps also describes the corresponding, more limited, composition or method “consisting essentially of” (or which “consists essentially of”) the same named elements or steps, meaning that the composition or method includes the named essential elements or steps and may also include additional elements or steps that do not materially affect the basic and novel characteristic(s) of the composition or method. It is also understood that any composition or method described herein as “comprising” or “consisting essentially of” one or more named elements or steps also describes the corresponding, more limited, and close-ended composition or method “consisting of” (or which “consists of”) the named elements or steps to the exclusion of any other unnamed element or step.
The term “J domain analog” as used herein refers to a target protein expression enhancing polypeptide (or PEEP) that comprises the sequence of amino acids of formula I (SEQ ID NO:47). Such polypeptides, where incorporated into a target protein sequence to make a modified target protein or when used to construct a protein expression enhancing polypeptide-target protein binding domain fusion protein, are useful for effecting an increase in expression of a target protein of interest.
The terms “J domain active fragment” or “active fragment of a J domain” refer to a fragment of a J domain of a J protein which retains the ability to increase the level of expression of a target protein when used in the two types of fusion proteins (PEEP/target protein fusion or PEEP/target protein binding domain fusion) described herein. The Examples below indicate that J domain active fragments will commonly retain the region of a J domain at the C-terminal extremity of a helix II. Larger portions of a J domain may be active as well, but excision of all or part of the C-terminal nine amino acids of a helix II invariably leads to loss of protein expression enhancement activity.
In any composition or method disclosed herein, known or disclosed equivalents of any named essential element or step may be substituted for that element or step.
Unless specifically indicated, a composition or method is not limited by any particular order of the listed elements or steps, unless a particular method step requires the prior performance of another step.
It is also understood that an element or step “selected from the group consisting of” or “any of” (or equivalent phrase) refers to one or more of the elements or steps in the list that follows, including combinations of any two or more of the listed elements or steps.
J Domains Useful in the Invention
The J domains of a variety of J proteins have been determined. See, for example, Kampinga et al., Nat. Rev., 11: 579-592 (2010); Hennessy et al., Protein Science, 14:1697-1709 (2005). A J domain useful in preparing a fusion protein of the invention (whether in the modified or unmodified arrangement) has the key defining features of a J domain of any member of the J protein family. Accordingly, an isolated J domain useful in the invention comprises a polypeptide domain from a J protein, which is characterized by four α-helices (I, II, III, IV) and usually having the highly conserved tripeptide sequence of histidine, proline, and aspartic acid (referred to as the “HPD motif”) between helices II and III. Typically, the J domain of a J protein is between fifty and seventy amino acids in length, and the site of interaction (binding) of a J domain with an Hsp70-ATP chaperone protein is believed to be a region extending from within helix II and including the HPD motif. Representative J domains include, but are not limited, a J domain of an ERdj protein (for example, a J domain of ERdj3 or ERdj5), a J domain of a large T antigen of SV40, and a J domain of a mammalian cysteine string protein (CSP-α). The amino acid sequences for these and other J domains that may be used in fusion proteins of the invention are provided in Table 1.







TABLE 1







Amino acid sequences of representative isolated J domains.










SEQ ID
J Domain Amino Acid Sequence


J Protein Source of J Domain
NO:
123456789012345678901234567890












human Hsp40
1
KDYYQTLGLARGASDEEIKRAYRRQALRYH


(NP_006136; Heat Shock Protein

PDKNKEPGAEEKFKEIAEAYDVLSDPRK


40)


 


human ErdJ1
2
LNFYQFLGVQQDASSADIRKAYRKLSLTLH


(NM_022365; DnaJC1, HTJ1,

PDKNKDENAETQFRQLVAIYEVLKDDER


MTJ1,


DnaJ homolog subfamily C


member 1 protein, DNAJL1)


 


human ErdJ2
3
YNPYEVLNLDPGATVAEIKKQYRLLSLKYH


(NM_001017975; HFM1,

PDKGGDEVMFMRIAKAYAALTDEES


SEC63 domain containing 1


protein, MER3, hHFM1)


 


human ErdJ3
4
RDFYKILGVPRSASIKDIKKAYRKLALQLH


(NM_016306; DNAJB11, DnaJ

PDRNPDDPQAQEKFQDLGAAYEVLSDSEK


(Hsp40) homolog, subfamily B,


member 11, ERj3p, HEDJ, ERj3,


ABBP2, ER-associated DNAJ


protein 3)


 


human ErdJ4
5
KSYYDILGVPKSASERQIKKAFHKLAMKYH


(NM_012328; DNAJB9,

PDKNKSPDAEAKFREIAEAYETLSDANR


microvascular differentiation gene


1 protein, MDG1, endothelial


Mdg1)


 


human ErdJ5
6
QDFYSLLGVSKTASSREIRQAFKKLALKLH


(NM_018981; DNAJC10, ER-

PDKNPNNPNAHGDFLKINRAYEVLKDEDL


resident protein ERdj5, JPD1, J-


domain-containing protein


disulfide isomerase-like protein,


DnaJ (Hsp40)


homolog,


subfamily C,


member 10,


hMTHr protein)


 


human ErdJ6
7
RDYYKILGVKRNAKKQEIIKAYRKLALQWH


(NM_006260; DNAJC3,

PDNFQNEEEKKKAEKKFIDIAAAKEVLSDP


DnaJ (Hsp40)

EM


homolog,


subfamily C, member 3 protein,


protein-kinase, interferon-


inducible double stranded RNA


dependent inhibitor protein,


P58IPK protein, PRKRI, 58 kDa


cellular inhibitor protein, p58


inhibitor of protein kinase)


 


human CSP
8
ESLYHVLGLDKNATSDDIKKSYRKLALKYH


(NP_079495; cysteine string

PDKNPDNPEAADKFKEINNAHAILTDATK


protein alpha, CSPalpha protein,


DNAJC5 protein, cysteine string


protein, DnaJ (Hsp40) homolog,


subfamily C, member 5 protein,


CSP protein)


 


SV40 large T antigen
9
LQLMDLLGLERSAWGNIPLMRKAYLKKCKE


(YP_003708382; large tumor

FHPDKGGDEEKMKKMNTLYKKMEDGVK


antigen T-ag [Simian virus 40])


 


DnaJ
10
QDYYEILGVSKTAEEREIKKAYKRLAMKYH




PDRNQGDKEAEAKFKEIKEAYEVLTDSQK


 


human dnaJ homolog subfamily C,
11
NPFEVLQIDPEVTDEEIKKRFRQLSILVHP


member 8

DKNQDDADRAQKAFEAVDKAYKLLLDQEQK




KRALDVIQ


 


human dnaJ homolog subfamily C,
12
EALYEILGLHKGASNEEIKKTYRKLALKHH


member 5B

PDKNPDDPAATEKFKEINNAHAILTDISK


 


human dnaJ homolog subfamily C,
13
LNPFHVLGVEATASDVELKKAYRQLAVMVH


member 14

PDKNHHPRAEEAFKVLRAAWDIVSNAEK


 


human dnaJ homolog subfamily C,
14
RDCYEVLGVSRSAGKAEIARAYRQLARRYH


member 25 precursor

PDRYRPQPGDEGPGRTPQSAEEAFLLVATA




YETLKDEET


 


human dnaJ homolog subfamily B,
15
ASYYEILDVPRSASADDIKKAYRRKALQWH


member 2, isoform a

PDKNPDNKEFAEKKFKEVAEAYEVLSDKHK


 


human dnaJ homolog subfamily B,
16
ASYYEILDVPRSASADDIKKAYRRKALQWH


member 2, isoform b

PDKNPDNKEFAEKKFKEVAEAYEVLSDKHK


 


Chain A,
17
TTYYDVLGVKPNATQEELKKAYRKLALKYH


nmr structure of Bc008182 protein,

PDKNPNEGEKFKQISQAYEVLSDAKK


a human Dnaj-like domain


 


Chain A,
18
ASYYEILDVPRSASADDIKKAYRRKALQWH


solution structure of J Domain of

PDKNPDNKEFAEKKFKEVAEAYEVLSDKHK


Hsj1a


 


Chain A,
19
KDSWDMLGVKPGASRDEVNKAYRKLAVLLH


solution structure of a Dnaj-like

PDKCVAPGSEDAFKAVVNARTALLKNIK


domain from human ras-associated


protein Rap1


 


Chain A,
20
VDYYEVLDVPRQASSEAIKKAYRKLALKWH


solution structure of Dnaj domain

PDKNPENKEEAERRFKQVAEAYEVLSDAKK


of human protein Hcg3, a


hypothetical protein


Tmp_locus_21


 


Chain A,
21
GDYYQILGVPRNASQKEIKKAYYQLAKKYH


solution structure of J domain from

PDTNKDDPKAKEKFSQLAEAYEVLSDEVK


Dnaj homolog, human Tidl protein


 


Chain A,
22
GSYYDILGVPKSASERQIKKAFHKLAMKYH


solution structure of J domain from

PDKNKSPDAEAKFREIAEAYETLSDANR


human Dnaj subfamily B, member 9


 


Chain A,
23
GDYYEILGVSRGASDEDLKKAYRRLALKFH


solution structure of J domain from

PDKNHAPGATEAFKAIGTAYAVLSNPEK


human Dnaj subfamily B, member


12


 


Chain A,
24
KDYYQTLGLARGASDEEIKRAYRRQALRYH


human Hsp40 (HDJ-1), nmr

PDKNKEPGAEEKFKEIAEAYDVLSDFRK


 


Chain A, solution structure of Dnaj
25
TALYDLLGVPSTATQAQIKAAYYRQCFLYH


domain from human Williams-

PDRNSGSAEAAERFTRISQAYVVLGSATL


Beuren syndrome chromosome


region 18 protein


 


Chain A, solution structure of J
26
ANYYEVLGVQASASPEDIKKAYRKLALRWH


domain of Dnaj homolog

PDKNPDNKEEAEKKFKLVSEAYEVLSDSKK


subfamily B,


member 8


 


Chain A, solution structure of J
27
EDYYTLLGCDELSSVEQILAEFKVRALECH


domain of Dnaj homolog

PDKHPENPKAVETFQKLQKAKEILTNEES


subfamily C,


member 12


 


Chain A, Dnaj domain of human
28
SILKEVTSVVEQAWKLPESERKKIIRRLYL


Kiaa0730 protein

KWHPDKNPENHDIANEVFKHLQNEINR


 


human DnaJ homolog, subfamily
29
VDYYEVLGVQRHASPEDIKKAYRKLALKWH


B,

PDKNPENKEEAERKFKQVAEAYEVLSDAKK


member 6, isoform a


 


human DnaJ homolog, subfamily
30
VDYYEVLGVQRHASPEDIKKAYRKLALKWH


B,

PDKNPENKEEAERKFKQVAEAYEVLSDAKK


member 6, isoform b


 


human DnaJ homolog, subfamily
31
KSYYDILGVPKSASERQIKKAFHKLAMKYH


B,

PDKNKSPDAEAKFREIAEAYETLSDANR


member 9 precursor


 


human DnaJ (Hsp40) homolog,
32
LNPFEVLQIDPEVTDEEIKKRFRQLSILVH


subfamily C,

PDKNQDDADRAQKAFEAVDKAYKLLLDQEQ


member 8,


isoform CRA_c


 


human DnaJ (Hsp40) homolog,
33
DDAYEVLNLPQGQGPHDESKIRKAYFRLAQ


subfamily C,

KYHPDKNPEGRDMFEKVNKAYEFLCTKSA


member 13,


isoform CRA_b


 


human DnaJ (Hsp40) homolog,
34
REAALILGVSPTANKGKIRDAHRRIMLLNH


subfamily C,

PDKGK


member 19,


isoform CRA_e


 


human DnaJ (Hsp40) homolog,
35
ESLYHVLGLDKNATSDDIKKSYRKLALKYH


subfamily C,

PDKNPDNPEAADKFKEINNAHAILTDATK


member 5,


isoform CRA_b


 


human DnaJ (Hsp40) homolog,
36
STYYELLGVHPGASTEEVKRAFFSKSKELH


subfamily C,

PDRDPGNPSLHSRFVELSEAYRVLSREQS


member 4,


isoform CRA_f


 


human zinc finger, CSL-type
37
KDWYSILGADPSANISDLKQKYQKLILMYH


containing 3, isoform CRA_c

PDKQSTDVPAGTVEECVQKFIEIDQAWKIL




GNEET


 


human DnaJ (Hsp40) homolog,
38
MDLYALLGIEEKAADKEVKKAYRQKALSCH


subfamily C,

PDKNPDNPRAAELFKQLSQALEVLTDAAA


member 17,


isoform CRA_a


 


human DnaJ (Hsp40) homolog,
39
KSYYDILGVPKSASERQIKKAFHKLAMKYH


subfamily B,

PDKNKSPDAEAKFREIAEGASVPAASSF


member 9,


isoformCRA_a


 


human DnaJ (Hsp40) homolog,
40
STYYELLGVHPGASTEEVKRAFFSKSKELH


subfamily C,

PDRDPGNPSLHSRFVELSEAYRVLSREQS


member 4,


isoform CRA_g


 


human DnaJ (Hsp40) homolog,
41
STYYELLGVHPGASTEEVKRAFFSKSKELH


subfamily C,

PDRDPGNPSLHSRFVELSEAYRVLSREQS


member 4,


isoform CRA_a


 


human DnaJ (Hsp40) homolog,
42
EDYYSLLNVRREASSEELKAAYRRLCMLYH


subfamily C,

PDKHRDPELKSQAERLFNLVHQAYEVLSDP


member 11,

QT


isoform CRA_c


 


human zinc finger, CSL-type
43
KDWYSILGADPSANISDLKQKYQKLILMYH


containing 3, isoform CRA_b

PDKQSTDVPAGTVEECVQKFIEIDQAWKIL




GNEET


 


human J-type co-chaperone
44
RDYFSLMDCNRSFRVDTAKLQHRYQQLQRL


HSC20, isoform CRA_c

VHPDFFSQRSQTEKDFSEKHSTLVNDAYKT




LLAPLS


 


human hCG1994888, isoform
45
RDCYEVLGVSRSAGKAEIARAYRQLARRYH


CRA_d

PDRYRPQPGDEGPGRTPQSAEEAFLLVATA




YETLKDEET


 


human DnaJ (Hsp40) homolog,
46
TTYYDVLGVKPNATQEELKKAYRKLALKYH


subfamily A,

PDKNPNEGEKVKMLY1SSQ


member 1,


isoform CRA_a









J Domain Fragments and Analogs with Protein Expression Enhancing Activity

Further study of J domains using sequence analysis, including amino and carboxy terminal deletion analysis, revealed that only a relatively small portion of a J domain is required to provide protein expression enhancement activity. Surprisingly, the analysis determined that protein expression enhancement activity according to the invention can be provided by a polypeptide fragment isolated from within a J domain and that consists of as little as 9 or 10 amino acids. See, Examples 10 and 11, infra. As with isolated J domains, such J domain polypeptide fragments may be used in the methods and compositions described herein to enhance expression of a target protein of interest in its intended cellular (intracellular, membrane-associated) or extracellular (secreted) location. The individual J domain polypeptide fragments are not all identical in amino acid sequence, but may share some sequence homology and structural features in addition to providing a protein expression enhancement activity in either a modified or an unmodified arrangement described herein.
Further deletion and substitution mutation analysis of the above-mentioned J domain polypeptide fragments provided the basis for defining a structural formula for a new family of J domain analog polypeptides that possess target protein expression enhancement activity. The members of this family of analog polypeptides comprise 8 to 9 amino acids and include some J domain polypeptide fragments as well as polypeptides that have not been previously identified in the current library of J domains. See, Example 11.
The smaller size of J domain polypeptide fragments and of J domain analog polypeptides compared to complete (full-length) J domains reduces the size of fusion proteins that can be constructed and expressed in the modified and unmodified arrangements of the invention for enhancing expression of a target protein of interest. Thus, the size of recombinant nucleic acid molecules encoding such fusion proteins can be correspondingly smaller than nucleic acid molecules that encode fusion proteins comprising a complete J domain. The relatively small size of J domain polypeptide fragments and J domain analog polypeptides of the invention may be particularly beneficial in reducing the immunogenicity of fusion proteins of the modified arrangement in which a protein expression enhancing polypeptide is linked (fused) to a target protein of interest to form a modified (fusion) target protein that is expressed in or administered to a subject in place of the (unlinked) target protein of interest. The less immunogenic the fusion protein is, the more likely the fusion protein can persist in the subject in order to provide the subject with the beneficial property or effect of the fusion protein without being rapidly eliminated or inhibited by an immune response directed to the fusion protein.
Fusion Proteins Comprising a Protein Expression Enhancing Polypeptide
According to the invention, a protein expression enhancing polypeptide described herein is used as a component of a fusion protein that enhances expression of a target protein of interest for which there is a need to improve expression in a host cell. The protein expression enhancing polypeptide is used to enhance expression of a target protein of interest in either of two arrangements that describe the primary structure (amino acid sequence) of the expressed target protein of interest.
In the “modified” arrangement for enhancing protein expression, a protein expression enhancing polypeptide is linked to a target protein of interest to form a fusion protein, i.e., a “modified” target protein of interest, which is expressed at an enhanced level compared to that of the unmodified target protein that is poorly expressed in the absence of a protein expression enhancing polypeptide. Thus, the fusion protein in the modified arrangement is a modified form of the target protein of interest that is expressed and employed as a surrogate in place of the poorly expressed, unmodified target protein.
In the “unmodified” arrangement for enhancing protein expression, the primary structure of the target protein of interest remains unaltered (“unmodified”) in that it is not fused to a protein expression enhancing polypeptide. A protein expression enhancing polypeptide of the invention is linked to a target protein binding domain that has an affinity for and binds to a target protein of interest. Co-expression of the fusion protein and the unmodified target protein of interest in a host cell results in an enhanced level of expression of the target protein of interest as compared to the level of expression in the absence of the target protein-binding fusion protein.
As the primary structure (amino acid sequence) of a target protein of interest remains unaltered (not linked in a fusion protein) in the unmodified arrangement, it is likely that for many applications, the unmodified arrangement for enhancing protein expression will be preferred over the modified arrangement. However, as explained below, it is also possible to engineer the fusion protein of a modified arrangement so that the protein expression enhancing polypeptide component of the fusion protein is easily cleaved to liberate the target protein component comprising the original amino acid sequence of the target protein with no or only a few additional remnant amino acids from the fusion protein. Such a fusion protein may be more suitable than the unmodified target protein for certain applications.
While it is possible to synthesize a fusion protein in either arrangement using direct synthesis (for example, solid-phase peptide synthesis, solution-phase synthesis, etc.), it is likely that in most cases a fusion protein described herein will be more economically produced using standard recombinant nucleic acid techniques, including polymerase chain reaction (PCR) techniques, in concert with cell culture methods or transgenic methods.
Standard techniques may be used for recombinant DNA, oligonucleotide synthesis, transfection of cells (for example, without limitation, electroporation, liposome-mediated transfection, transformation methods), and cell and tissue culture methods to express a fusion protein of the invention. Enzymatic reactions and purification techniques may be performed as commonly accomplished in the art, as described in a manufacturer's specifications, or as described herein. The foregoing techniques and procedures may be generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification. See e.g., Sambrook et al., eds., Molecular Cloning: A Laboratory Manual, Second Edition (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989) and Ausubel et al. (eds.), Current Protocols in Molecular Biology (John Wiley & Sons, New York, 2012), which are incorporated herein by reference.
As noted above, the terms “modified” and “unmodified” refer to whether or not a target protein of interest is linked to a protein expression enhancing polypeptide. It is understood that in some embodiments of both the modified and unmodified arrangements, it may be beneficial to link one or more additional domains may to a fusion protein or target protein of interest. For example, any of the well-known epitope tag peptides (epitope tags) may be incorporated into a protein to facilitate detection and/or purification of the expressed protein. Such epitope tags include, but are not limited to, a V5 epitope tag (GKPIPNPLLGLDST (SEQ ID NO:110)), a Flag epitope tag (DYKDDDDK (SEQ ID NO:111)), a hexa-histidine epitope tag (HHHHHH (SEQ ID NO:112)), a hemagglutinin epitope tag (YPYDVPDYA (SEQ ID NO:113)), a c-myc epitope tag (EQKLISEEDL (SEQ ID NO:114)), a VSV-G epitope tag (YTDIEMNRLGK (SEQ ID NO:115)), and a HSV epitope tag (QPELAPEDPED (SEQ ID NO:116)). As explained below, it is also possible to link a protein with such an epitope tag using a linker that can be cleaved by a proteolytic enzyme and thereby removed (or substantially removed) from the protein.
Linkers
Any domain may be linked to another domain within a fusion protein of the invention by methods known in the art. For example, in the modified arrangement of the invention, a fusion protein comprises a protein expression enhancing polypeptide linked to a target protein of interest. The expressed fusion protein is therefore a modified target protein that can be used as a surrogate for the unfused and poorly expressed target protein of interest. The protein expression enhancing polypeptide may be linked directly to the target protein of interest or linked indirectly via a linker molecule. In the unmodified arrangement of the invention, a fusion protein comprises a protein expression enhancing polypeptide linked to a target protein binding domain that has an affinity for and binds to a target protein of interest. Co-expression of the fusion protein with the target protein of interest enhances the level of expression of the unmodified (unfused) target protein of interest compared to the level of expression in the absence of the fusion protein. The protein expression enhancing polypeptide may be linked directly to the target protein binding domain or linked indirectly via a linker molecule. Other domains may also be linked to a fusion protein or unfused protein in either the modified and unmodified arrangements to provide one or more additional features. For example, an epitope tag may be linked to a fusion protein or unfused protein to facilitate detection or purification of the tagged protein.
At the amino acid level, a linker may be one or more amino acids, including 1 to 10 amino acids, 1 to 20 amino acids, and even 1 to 50 amino acids. Typically, with respect to linking a protein expression enhancing polypeptide to a target protein of interest (in the modified arrangement) or to a target protein binding domain (in the unmodified arrangement), it is not necessary to use a linker that is more than 20 amino acids because linking a protein expression enhancing polypeptide directly to a target protein of interest or to a target protein binding domain does not appear to significantly diminish the necessary biochemical and functional properties of the protein of interest or the target protein binding domain (data not shown).
Selecting one or more linkers to produce a fusion protein according to the invention is within the knowledge and skill of the art. See, for example, Arai et al., Protein Eng., 14(8): 529-532 (2001); Crasto et al., Protein Eng., 13(5): 309-314 (2000); George et al., Protein Eng., 15(11): 871-879 (2003); Robinson et al., Proc. Natl. Acad. Sci. USA, 95: 5929-5934 (1998). General considerations for using a particular linker to link a protein expression enhancing polypeptide to a target protein of interest or to a target protein binding domain may include those in making other fusion proteins in which one functional domain is linked to another functional domain, for example, as may be considered in linking immunoglobulin variable and/or constant domains in a wide variety of formats for producing engineered functional binding proteins. Clearly, a linker should not interfere with the folding of a target protein of interest or a target protein binding domain that is linked to a protein expression enhancing polypeptide. A linker, if present in a fusion protein, is selected to optimize the contribution of the protein expression enhancing polypeptide to increase levels of expression or yield of the fusion protein in the modified arrangement or the (unfused) target protein of interest in the in the unmodified arrangement, and it may be omitted if direct attachment of a protein expression enhancement polypeptide to the target protein of interest or target protein binding domain achieves a desired enhanced level of expression. Linker molecules present in a fusion protein of the invention may comprise one or more amino acids encoded by a nucleotide sequence present on a segment of nucleic acid in or around a cloning site of an expression vector into which is inserted in frame a nucleic acid segment encoding a protein domain (e.g., protein expression enhancing polypeptide, protein of interest, target protein binding domain) or an entire fusion protein.
Linker molecules, especially those that are four amino acids and longer, preferably possess a flexibility that permits the protein of interest to fold into its proper conformation. A variety of relatively flexible linkers are known in the field for linking functional domains. A linker may also be used to link one or more additional domains, such as an epitope tag, to the protein expression enhancing polypeptide or protein of interest of a fusion protein of the invention. Linkers that may be used in preparing a fusion protein according to the invention, include, by are not limited to, DIAAA (SEQ ID NO:117); DIAAALE (SEQ ID NO:118); GTGSEF (SEQ ID NO:119); AS; TVA; ASTK (SEQ ID NO:120); GGGSGGSGGSGG (SEQ ID NO:121); DIGGGSGGSGGSGGAAA (SEQ ID NO:122); AKTTPKLEEGEFSEAR (SEQ ID NO:123); AKTTPKLEEGEFSEARV (SEQ ID NO:124); AKTTPKLGG (SEQ ID NO:125); SAKTTPKLGG (SEQ ID NO:126); SAKTTP (SEQ ID NO:127); RADAAP (SEQ ID NO:128); RADAAPTVS (SEQ ID NO:129); RADAAAAGGPGS (SEQ ID NO:130); RADAAAA (G4S)4 (SEQ ID NO:131); SAKTTPKLEEGEFSEARV (SEQ ID NO:132); ADAAP (SEQ ID NO:133); ADAAPTVSIFPP (SEQ ID NO:134); TVAAP (SEQ ID NO:135); TVAAPSVFIFPP (SEQ ID NO:136); QPKAAP (SEQ ID NO:137); QPKAAPSVTLFPP (SEQ ID NO:138); AKTTPP (SEQ ID NO:139); AKTTPPSVTPLAP (SEQ ID NO:140); AKTTAP (SEQ ID NO:141); AKTTAPSVYPLAP (SEQ ID NO:142); ASTKGP (SEQ ID NO:143); ASTKGPSVFPLAP (SEQ ID NO:144), GGGGSGGGGSGGGGS (SEQ ID NO:145); GENKVEYAPALMALS (SEQ ID NO:146); GPAKELTPLKEAKVS (SEQ ID NO:147); GHEAAAVMQVQYPAS (SEQ ID NO:148); GGGGGGGP (SEQ ID NO:149); GGGGGGGGP (SEQ ID NO:150); PAPNLLGGP (SEQ ID NO:151); PNLLGGP (SEQ ID NO:152); GGGGGGP (SEQ ID NO:153); PAPELLGGP (SEQ ID NO:154); PTISPAPNLLGGP (SEQ ID NO:155); TVAADDDDKSVFIVPP (SEQ ID NO:156); TVDDDDKAAP (SEQ ID NO:157); LVPRGSAAP (SEQ ID NO:158); ASTKGPSV (SEQ ID NO:159); ASTKGPSVFP (SEQ ID NO:160); TVAAPSV (SEQ ID NO:161); TVAAPSVFI (SEQ ID NO:162); and the like.
In some embodiments, a fusion protein may contain one or more linkers that can be cleaved by one or more proteases. Such linkers possess an amino acid sequence that is recognized by a protease for cleavage of the protein at or near the recognition sequence. Incorporating one or more cleavable linker molecules into a fusion protein provides the option of removing one or more domains from the expressed fusion protein. By way of non-limiting examples, in some applications or preparations, it may be desirable to remove the polypeptide expression enhancing polypeptide linked to the protein of interest (for example, to reduce potential immunogenicity) and/or to remove an epitope tag that had been incorporated into a fusion protein to facilitate detection or purification of the expressed fusion protein. In another example, if the fusion protein is secreted, a polypeptide expression enhancing polypeptide (or other domain) linked by a cleavable linker to the protein of interest may be removed by adding the appropriate protease directly to the medium of cultures expressing the fusion protein. Alternatively, the protein expression enhancing polypeptide (or other domain) linked by the cleavable linker may be removed after performing one or more steps to purify the fusion protein from the culture medium.
It may be useful in some situations to remove a domain or epitope tag linked to a protein. This can be accomplished, for example, by expressing the protein comprising the additional domain or tag in cells in which the expression of a protease that can cleave a linker of the protein is regulated, such as incorporating into the cell a recombinant gene for the appropriate protease under the control of a promoter that can be regulated by a signal (e.g., temperature shift) or agent (ion change) that can be applied to a culture after the cells have expressed the fusion protein. A variety of promoters are available in the art for regulating gene expression in prokaryotic or eukaryotic cells. In addition, some cells express one or more proteases that can cleave a linker molecule containing a corresponding cleavage site. It is within the skill of a practitioner in the art to determine whether use of a protease that may be expressed by a host cell may be useful to cleave a linker in a fusion protein expressed by the same host cell. Alternatively, it is possible to add an appropriate protease to a sample, such as culture medium or cell lysate, containing a protein linked to an additional domain or tag via a protease-cleavable linker.
A variety of linker molecules containing proteolytic cleavage sites are known and available in the art for linking one protein or protein domain to another. Such linkers include, but are not limited to, one of more of the following examples, where the asterisk (*) indicates the proteolytic cleavage site: DYKDDDDK* (SEQ ID NO:163); ASDDDDK*GGP (SEQ ID NO:164); ALVPR*GSGP (SEQ ID NO:165); ASTDDDDK*SVFPLAP (SEQ ID NO:166); TVALVPR*GSVFIFPP (SEQ ID NO:167); ASTLVPR*GSVFPLAP (SEQ ID NO: 168); TVAADDDK*SVFIVPP (SEQ ID NO:169); ASTDDDK*SVFPLAP (SEQ ID NO:170); LEVLFQ*GP (SEQ ID NO:171); TVAALEVLFQ*GPAP (SEQ ID NO:172); ASTLEVLFQ*GPLAP (SEQ ID NO:173); PAPLEVLFQ*GP (SEQ ID NO:174); TAENLYFQ*GAP (SEQ ID NO:175); AENLYFQ*GA (SEQ ID NO:176); PGPFGR*SAGGP (SEQ ID NO:177); PGPFGR*SAGG (SEQ ID NO:178); PQRGR*SAG (SEQ ID NO:179); PHYGR*SGG (SEQ ID NO:180); GPFGR*SAGP (SEQ ID NO:181); GDDDDK*GGP (SEQ ID NO:182); AGDDDDK*GGP (SEQ ID NO:183); GGDDDDK*GGP (SEQ ID NO:184); ENLYFQ*G (SEQ ID NO:185); ENLYFQ*S (SEQ ID NO:186); and the like.
A variety of proteolytic enzymes are known in the art that may be used to cleave a cleavable linker employed in a protein of the invention. Clearly, a protease that is selected to cleave a cleavable linker in a fusion protein comprising a target protein of interest should not also cleave the target protein of interest or any other domain that is desired to be retained after cleavage of the linker Proteolytic enzymes that may be used to cleave a fusion protein at a site in a linker within the fusion protein include, but are not limited to, enterokinase, factor Xa, thrombin, PreScission, tobacco etch virus (TEV) protease, tissue plasminogen activator (tPA), a zinc-dependent endopeptidase, a matrix metalloproteinase (MMP), a serralysin, an astacin, an adamalysin, a disintegrin, an ADAM, a caspase, a cathespsin, a calpain, and the like.
Nucleic Acids Encoding Fusion Proteins
Using standard methods available in the art, a nucleic acid (typically DNA) molecule is constructed that encodes a fusion protein employed in a modified or unmodified arrangement for enhancing expression of a target protein of interest. One or more additional domains may also be incorporated into a protein, such as a standard epitope tag used to facilitate detection and/or purification of the protein. A nucleic acid molecule encoding a desired fusion protein can be inserted into any of a variety cloning vectors available in the art for the purpose of replicating the recombinant structural gene for the fusion protein. For expressing a fusion protein, a nucleic acid molecule encoding the fusion protein can be inserted into any of a variety of expression vectors available in the art. An expression vector with the inserted nucleic acid encoding the fusion protein is then introduced into compatible host cells that permit expression of the fusion protein from the expression vector. In the case of an unmodified arrangement, a vector may also contain a copy of functional structural gene encoding the unmodified target protein of interest if the host cell does not possess a functional gene for the target protein of interest.
Expression vectors of the invention include expression vector molecules comprising a nucleic acid segment encoding a protein expression enhancing polypeptide described herein and one or more cloning sites (for example, unique restriction enzyme sites) located 5′ or 3′ to the protein expression enhancing polypeptide coding sequence into which a nucleic acid molecule encoding another domain of the fusion protein may be inserted: in a modified arrangement, a nucleic acid encoding a target protein of interest may be inserted to form the desired fusion protein (modified target protein); whereas in an unmodified arrangement, a nucleic acid encoding a target protein binding domain may be inserted to form a fusion protein that is capable of binding to and enhancing expression of an unmodified target protein of interest. An expression vector may also possess multiple cloning sites that permit the insertion of one or more additional nucleic acid segments encoding one or more other desired domains (for example, an epitope tag, Fc region, etc.) to construct and express a desired fusion protein. The final nucleic acid fusion construct encoding a desired fusion is operably linked to a promoter on the expression vector. Engineering cloning sites into a vector molecule and operably linking an inserted nucleic acid segment encoding a desired protein to a promoter and other signals required for expression of the protein in a compatible host cell are within the skill in the art.
While a description herein for assembling a nucleic acid construct encoding a fusion protein of the invention may suggest a particular stepwise order to the linking of various nucleic acid molecules followed by insertion of the fully assembled nucleic acid construct into an expression vector, it is understood and appreciated that the exact order of linking segments of nucleic acid molecules to produce a nucleic acid construct encoding a desired fusion protein is within the discretion, skill, and experience of a practitioner in this art. Moreover, although it is possible to first link all segments together to form a nucleic acid molecule encoding a fusion protein prior to insertion into an expression vector, in some cases, a nucleic acid segment encoding one or more domains may already properly reside within an expression vector so that it is practical to insert one or more nucleic acid segments adjacent to the segment(s) already residing in the expression vector and thereby assemble within the expression vector an operably linked structural gene for a desired fusion protein of the invention.
Expression vectors encoding a fusion protein of the invention may be transfected into any of a variety of host cells that are compatible for expressing the fusion protein from the particular expression vector. Although some steps in the process of constructing a recombinant structural gene encoding a fusion protein of the invention may be conducted in either prokaryotic or eukaryotic cells, the preferred host cell for enhanced expression of fusion proteins according to the invention are eukaryotic cells. Eukaryotic host cells useful in the invention include, but are not limited to, a mammalian host cell, an insect host cell, a plant host cell, a fungal host cell, a eukaryotic algal host cell, a nematode host cell, a protozoan host cell, and a fish host cell. Mammalian host cells useful for expressing a fusion protein of the invention include, but are not limited to, a Chinese Hamster Ovary (CHO) cell, a COS cell, a Vero cell, an SP2/0 cell, an NS/0 myeloma cell, a human embryonic kidney (HEK293) cell, a baby hamster kidney (BHK) cell, a HeLa cell, a human B cell, a CV-1/EBNA cell, an L cell, a 3T3 cell, an HEPG2 cell, a PerC6 cell, and an MDCK cell. Fungal host cells useful for expressing a J domain fusion protein of the invention include, but are not limited to, Aspergillus, Neurospora, Saccharomyces, Pichia, Hansenula, Schizosaccharomyces, Kluyveromyces, Yarrowia, and Candida. A particularly useful Saccharomyces host cell is a Saccharomyces cerevisiae cell.
Using methods available in the art, nucleic acid molecules encoding a fusion protein of the invention may be introduced into cells of a plant or non-human animal for the purpose of expressing the fusion protein in levels that permit easy purification of the fusion protein or as a gene therapy to provide the plant, human, or non-human animal with the benefit of the function provided by the protein of interest within the expressed fusion protein. Such methods can be used to provide transgenic plants or animals that express the fusion protein encoded by the transferred nucleic acid (transgene) encoding the fusion protein. In the case of plants and non-human animals, techniques are available for incorporating expressible nucleic acid encoding a protein into the germline so that progeny of the transgenic organism also can express the fusion protein. A variety of vectors and methods are available for introducing nucleic acid into cells of a plant or non-human animal including, but not limited to, syringe injection of naked DNA into cells, ballistic transfer (for example, using a gene gun), liposomes, and virus-derived vector molecules.
A gene therapy for treating a human subject according to the invention may employ a recombinant gene encoding a fusion protein that comprises an expression enhancing polypeptide in either a modified or unmodified arrangement described herein. Such gene therapy is especially useful in diseases in which an improperly folded protein species results in loss or substantial loss of function as to cause a clinically recognized pathological condition. Examples of diseases in which an improperly folded protein species resulting in loss of function has been demonstrated or implicated include, but are not limited to, prion-associated disease (transmissible spongiform encephalopathy), Alzheimer's disease; Parkinson's disease; Huntington's disease; cystic fibrosis (CF), and al-antitrypsin (AAT) deficiency.
In a gene therapy employing a modified arrangement of the invention, a recombinant gene is constructed encoding a fusion protein comprising a protein expression enhancing polypeptide linked to a target protein of interest. The recombinant gene is inserted into a vector, which in turn is integrated into the genome of somatic cells of a human subject. In most cases, it is not necessary for the recombinant vector to be taken up and integrated into the genome of all somatic cells, but only a sub-population of cells that may be relevant to a particular disease. The fusion protein expressed from the integrated recombinant gene in the somatic cells of the human subject treats the disease by restoring a function of the endogenous target protein of interest that is otherwise missing, has been lost, or is so diminished as to cause a clinically recognized disease in a human subject.
In a gene therapy employing an unmodified arrangement of the invention, a recombinant gene is constructed encoding a fusion protein comprising a protein expression enhancing polypeptide linked to a target protein binding domain that has an affinity for and binds a target protein of interest. The recombinant gene is inserted into a vector, which in turn is integrated into the genome of somatic cells of a human subject. Again, in most cases, it is not necessary for the recombinant vector to be taken up and integrated into that genome of all somatic cells, but only a sub-population of cells that may be relevant to a particular disease. Expression of the fusion protein from the integrated recombinant gene in the cells of the human subject enhances expression of the endogenous target protein of interest so that the protein can provide the cells with the required function provided by the target protein to avoid a clinically recognized disease. If the endogenous gene for the endogenous target protein of interest is not functional or has been deleted, then a recombinant gene encoding the target protein of interest must also be constructed and inserted into a vector for integration into the genome of a human subject for expression along with the fusion protein.
Any of a variety of vectors, agents, and methods may be used to introduce nucleic acid molecules into the somatic cells of a human subject including, but not limited to, modified viruses (e.g., a modified adenovirus, a modified lentivirus), virus-associated virus (e.g., an adenovirus-associated virus), naked DNA (such as naked plasmid DNA), compacted DNA in nanoparticles, and liposomes (e.g., using various cationic lipids).
Fusion Proteins Comprising a Protein Expression Enhancing Polypeptide and a Target Protein of Interest in a Modified Arrangement
A fusion protein in a modified arrangement of the invention comprises a protein expression enhancing polypeptide (or PEEP, comprising an isolated J domain, an active J domain polypeptide fragment, or J domain analog polypeptide as described herein) linked to a target protein of interest. Preferably, the protein expression enhancing polypeptide is linked to the amino (N) terminus or carboxy (C) terminus of the target protein of interest. The protein expression enhancing polypeptide may also be spaced from the protein of interest by one or more intervening polypeptide sequences such as linkers, enzyme cleavage sites, epitope tags, and the like. Insertion of a protein expression enhancing polypeptide within a target protein of interest is possible, however as a practical matter this requires more complicated recombinant DNA engineering and has a high likelihood of interfering with the proper folding, desired function, or other properties of the target protein of interest, and is therefore generally less preferred. A target protein of interest that may be used to make a fusion protein of a modified arrangement according to the invention may be any protein or polypeptide that has a desirable property, including soluble proteins that normally reside in an intracellular location; membrane-associated proteins (including transmembrane proteins); secreted proteins; and genetically engineered, non-naturally occurring, proteins. Such engineered, non-naturally occurring proteins may include, but are not limited to, recombinant soluble forms of natural membrane-associated proteins, for example, the extracellular domain of a transmembrane protein (for example, integrins, complement regulatory proteins). Another example of engineered, non-naturally occurring proteins that may be used as a target protein component of a fusion protein in a modified arrangement are recombinant fusion proteins comprising a recombinant soluble receptor molecule in which an extracellular binding domain of a cell surface receptor is fused to an immunoglobulin Fc domain or immunoglobulin scaffold. A non-limiting example of such a non-naturally occurring fusion protein is etanercept in which the extracellular domain of the p75 human TNFα receptor molecule is linked to the hinge and Fc domain of an IgG1 immunoglobulin. Other proteins that may be used as a target protein of interest in a fusion protein of a modified arrangement of the invention include, but are not limited to, antibodies and antigen-binding portions thereof, cytokines, peptide hormones, enzymes (e.g., thrombin, lactase, proteases, transferases, kinases, etc.), and morphogenetic proteins.
Fusion Proteins Comprising a Protein Enhancing Expression Polypeptide and a Target Protein Binding Domain in an Unmodified Arrangement
A protein expression enhancing polypeptide (comprising an isolated J domain, active J domain polypeptide fragment, or J domain analog polypeptide as described herein) may also be used in an unmodified arrangement to enhance expression of a target protein of interest at its intended location. In an unmodified arrangement according to this invention, a fusion protein comprises a protein expression enhancing polypeptide linked to a target protein binding domain that has an affinity for and binds a target protein of interest. Thus, in an unmodified arrangement of the invention, the target protein of interest is not a component of a fusion protein and therefore retains its unaltered primary structure (amino acid sequence). While not intending to be bound by any particular mechanism, the binding of a target protein of interest to a target protein binding domain of the fusion protein appears to bring the target protein of interest into relatively close proximity to the protein expression enhancing polypeptide (also present in the fusion protein) to provide an enhanced level of expression of the target protein at its intended cellular or extracellular location as compared to the level of expression of the target protein in the absence of the fusion protein. This may involve increased recruitment of chaperone proteins or other post-translational cellular mechanisms involved in protein folding, compartmentalization, or secretion, or may involve increase avoidance of cellular degradation pathways. The effect is evidenced by a significant increase in the appearance of expressed protein in the desired intracellular or extracellular location.
Target Protein Binding Domains Useful in an Unmodified Arrangement
A fusion protein in an unmodified arrangement of the invention comprises a target protein binding domain that binds a target protein of interest for which an elevation of expression in its proper cellular or extracellular location is desired. A target protein binding domain of a target protein-binding fusion protein of the invention may be any protein or binding domain thereof that is known to bind to a target protein. The more specific the binding affinity of a protein or binding domain thereof is for a target protein, the less likely other proteins may potentially interfere with the enhancement in the level of expression desired for the target protein of interest.
Examples of target protein binding domains include antigen binding sites isolated from natural and genetically engineered antibodies and antigen binding fragments thereof, wherein the antigen binding site of an antibody or antigen binding fragment binds a target protein for which an elevation of expression is desired. In this context, antibodies and antigen binding fragments can easily be raised that bind a target protein of interest using standard methods available in the art. A variety of genetically engineered antibody formats are known in the art that may be used as a source of a target protein binding domain of a fusion protein in an unmodified arrangement of the invention. Such formats include, but not limited to, Fab fragments, F(ab′)2 fragments, single chain Fv (scFv) antibodies, and single domain antibodies (dAb). See, for example, a review of the variety of functional genetically engineered antibody binding formats available in the art in Marvin et al., Acta Pharmacol. Sin., 26(6): 649-658 (2005); Kufer et al, Trends Biotechnol., 22(5): 238-244 (2004); Kontermann, Acta Pharmacol. Sin., 26(1): 1-9 (2005), and Chan et al., Nat. Rev, 10: 301-316 (2010).
Particularly useful in the invention are antibody molecules or fragments in which an antigen binding domain directed to a target protein is provided in a single polypeptide because such polypeptides can be easily linked to a protein expression enhancing polypeptide to form a fusion protein of the invention using standard in vitro DNA methods. For example, a single chain Fv antibody (scFv) comprises both VH and VL domains of an antigen binding site linked in a single polypeptide. Another source of a single chain antigen binding site is a single domain antibody (dAb) in which the entire antigen binding site is present in a single heavy chain variable domain. See, for example, Ward et al., Nature, 341: 544-546 (1989); Muyldermans et al., Protein Eng., 7: 1129-1135 (1994); Vu et al., Mol. Immunol., 34: 1121-1131 (1997); Muyldermans et al., Trends Biochem. Sci., 26: 230-235 (2001); Nguyen et al., Immunogenetics, 54: 39-47 (2002).
For a target protein that possesses an immunoglobulin Fc domain, a target protein binding domain may be an antibody or antigen (Fc domain) binding fragment thereof as discussed above. An alternative to an antibody or antigen binding domain thereof is any of a variety of non-immunoglobulin proteins and polypeptides that are known to specifically bind Fc domains. Proteins that possess Fc binding domains include, but are not limited to, Protein A, Protein G, gE protein of herpes simplex virus type 1 (HSV-1), and the like. A number of synthetic peptides also have been identified that bind Fc domains. See, for example, DeLano et al., Science, 287:1279-1283 (2000); Yang et al., J. Peptide Res., 66(Suppl. 1): 120-137 (2006). As shown in the Examples below, such Fc-binding proteins and peptides are readily employed as target binding domains for fusion proteins of the invention directed to target proteins of interest comprising an Fc domain.
In the case in which a target protein of interest is a receptor or functional portion thereof that binds a protein ligand, the protein ligand may be used as a target binding domain in a fusion protein of the invention. Functional portions of receptors include, but are not limited to, the extracellular domain of a membrane-associated receptor that includes a functional ligand binding domain. Typically, such extracellular portions comprising a functional ligand binding domain are referred to as “truncated receptors” because the transmembrane and cytoplasmic domains of the receptor have been removed. According to the invention, the expression of such truncated receptor molecules may be elevated by co-expression with a fusion protein of the invention comprising a protein ligand of the receptor. Accordingly, particularly suited for use as a target binding domain of a fusion protein in a modified arrangement of the invention are ligand proteins that are single polypeptides, such as certain cytokine polypeptides (for example, IL8, IL13, and the like) as shown in the Examples below. Other protein ligands that may be used in a fusion protein to bind a target receptor protein or ligand binding portion thereof, include polypeptide co-receptors, polypeptide co-repressors, and polypeptide co-factors.
In the case in which the target protein is a protein ligand (for example, a cytokine) that is bound by a known receptor molecule, a target protein binding domain of a fusion protein in an unmodified arrangement of the invention may comprise the cognate receptor or extracellular ligand binding portion of the receptor that binds the target protein.
BAG domains have been suggested in the art as fusion partners for enhancement of expression of target proteins. BAG domains of a variety of BAG proteins have been determined. See, for example, Takayama et al., Nat. Cell Biol., 3: E237-E241 (2001). A BAG domain has the key defining features of a BAG domain of any member of the BAG protein family. Accordingly, a BAG domain comprises a polypeptide domain of a BAG protein that is typically 85-124 amino acids in length, binds the ATPase domain of Hsp70 chaperone proteins, and is characterized by three anti-parallel α-helices (I, II, III, IV), wherein helices III and IV interact with the ATPase domain of Hsp70 chaperone proteins. Recently, it has been reported that when desired recombinant proteins are linked to a BAG domain, the resulting fusion proteins are expressed at levels that are greater than those of the protein alone. See, International Publication No. WO 2012/087835 A2.
From the Examples, below, BAG domains employed in an unmodified arrangement did not provide significant enhancement of the level of expression of target proteins of interest. In contrast, the protein expression enhancing polypeptides described herein significantly enhance levels of expression of target proteins of interest in both modified and unmodified arrangements. As shown in the Examples below, fusion proteins comprising a protein expression enhancing polypeptide (such as an isolated J domain, an active J domain fragment, or a J domain analog polypeptide, e.g., of formula I or particular 10-12 amino acid cognates thereof disclosed herein) linked to a target protein of interest (in a modified arrangement of the invention) were expressed at significantly greater levels than that of control cells (no fusion protein). Other studies showed that fusion proteins comprising a protein expression enhancing polypeptide described herein linked to target protein binding domains (in an unmodified arrangement) were effective in providing significantly greater levels of expression of unmodified target proteins of interest as compared to the levels in the absence of such fusion proteins (control) or fusion proteins comprising a BAG domain linked to a target protein binding domain. Accordingly, protein expression enhancing polypeptides as described herein provide a new family of polypeptides for use in enhancing expression of target proteins of interest in both modified and unmodified arrangements.
Gene Therapy Approaches for Treating Cystic Fibrosis
Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) protein, a cAMP-regulated chloride channel and channel regulator. The deletion of phenylalanine at position 508 (Δ508F) in CFTR is the most common mutation that changes the conformation of the CFTR protein, which is then rapidly degraded by the endoplasmic reticulum (ER) quality systems. A general consensus is that only partial recovery of the wild-type CFTR protein function is required to provide a beneficial treatment to CF patients. Therefore, a number of gene therapy trials with CFTR have been attempted, but have not yet been successful owing to inefficient delivery of a gene for CFTR and to immunogenicity of the vehicle (e.g., viral vector). In view of the fact that proper protein folding of wild-type CFTR is known to be difficult, it would be very useful if protein folding of the CFTR protein could be improved.
Over twenty clinical trials of a gene therapy to treat cystic fibrosis (CF) have been conducted since the identity and isolation of the CFTR gene over twenty years ago. See a review of gene therapy for cystic fibrosis in Davies et al., Proc. Am. Thor. Soc., 7: 408-414 (2010). Such clinical trials have already established proof of concept to provide replacement cystic fibrosis transmembrane conductance regulator (CFTR) protein, however the sustainability of effective levels of expression of the replacement CFTR protein in the cells of human subjects remains among the most persistent challenges in the development of an effective gene therapy to treat CF. The CFTR wild-type protein is a protein well-known for its instability. Over 90% of CF patients possess at least one copy of a mutated gene for CFTR (CFTRΔ508F) in which the absence of a phenylalanine at position 508 results in a highly unstable protein that is rapidly degraded in cells. This suggests a fusion gene therapy approach for treating CF that would lead to increased CFTR function or restored CFTR function to those afflicted with CF. Such a gene therapy provides a nucleic acid encoding a fusion protein in either a modified or unmodified arrangement of the invention.
As shown in the Examples below, fusion proteins in which either a wild-type CFTR protein or the CFTRΔ508F protein is fused to a protein expression enhancing polypeptide (such as J domain) in a modified arrangement were expressed in significantly higher levels than either unfused protein. This suggests that a J domain fusion gene therapy approach for treating CF that would lead to increased CFTR function or restored CFTR function to those afflicted with CF. Accordingly, the modified arrangement of the invention provides new forms of gene therapies that use fusion proteins that are expressed at significantly higher levels and therefore are more effective than past therapies to replace or restore missing or lost protein functions that are associated with various diseases.
For an unmodified arrangement, a fusion protein comprises a protein expression enhancing polypeptide linked to a binding domain that binds the wild-type CFTR protein or the CFTRΔ508F protein. A number of proteins are known to contain PDZ domains that bind to the highly conserved, carboxy terminal, PDZ binding region of CFTR. A protein that can be used as a source of a PDZ domain for use as a target protein binding domain in a fusion protein in an unmodified arrangement of the invention includes, but is not limited to, any of the members of the NHERF family of PDZ adapter proteins including, but not limited to, of NHERF1 (also known as NHERF, EBP50, or SLC9A3R1), NHERF2 (also known as E3KARP or SLC9A3R2), and PDZK1 (also known as CAP70 or NHERF3). See, for example, Haggie et al., J. Biol. Chem., 279(7): 5494-5500 (2004); Guggino, W. B., Proc. Am. Thorac. Soc., 1: 28-32 (2004); and Singh et al., J. Clin. Investig., 119(3): 540-550 (2009). Accordingly, a PDZ domain of a PDZ protein may be particularly useful as a target protein binding domain in a fusion protein designed to target either or both CFTRΔ508F and wild-type CFTR proteins in a gene therapy of the invention.
Accordingly, the invention provides new forms of gene therapies that provide fusion proteins that significantly elevate the levels of expression of an endogenous unstable protein (such as the unstable CFTRΔ508F) and/or the levels of expression of a desired heterologous protein (such as a wild-type CFTR) and therefore are more effective than past therapies to replace or restore missing or lost protein functions that are associated with various diseases.
Additional embodiments and features of the invention will be apparent from the following non-limiting examples.
EXAMPLES
Example 1. Compositions and Methods for Enhancing Expression of Target Proteins of Interest Using a Modified Arrangement
Expression vector plasmids were constructed for expressing a target protein of interest linked to protein expression enhancing polypeptide described herein, which in turn may be linked to an standard epitope tag, which is usually attached at the carboxy (C) terminus or amino (N) terminus of the protein construct for easy identification or isolation using a corresponding anti-tag antibody and standard immunoblot assays.
A DNA linker molecule having a nucleotide sequence containing various restriction enzyme sites was produced by annealing two single-stranded DNA molecules having the sequences shown below (5′ to 3′):







(SEQ ID NO: 187)







AGCTTGGTACCGGATCCGAATTCGATATCGCGGCCGCTCTCGAGTCTAGA


 


GGGCC


and


 







(SEQ ID NO: 188)







CTCTAGACTCGAGAGCGGCCGCGATATCGAATTCGGATCCGGTACCA.






The annealed linker molecule was then inserted into plasmid pcDNA3 (catalogue no. V790-20, Invitrogen) digested with HindIII and ApaI to yield plasmid pcDNA′.

DNA molecules encoding the V5 epitope tag (GKPIPNPLLGLDST (SEQ ID NO:47)) or the Flag epitope tag (DYKDDDDK (SEQ ID NO:111)) were inserted into plasmid pcDNA′. A double-stranded DNA molecule having the coding sequence for the V5 epitope tag along with an N-terminal methionine, i.e., ATGGGTAAGCCTATCCCTAACCCTCTCCTCGGTCTCGATTCTACG (SEQ ID NO:189), was inserted into pcDNA′ digested with XhoI and XbaI to yield plasmid V5(C)-pcDNA′ or with HindIII and KpnI to yield plasmid V5(N)-pcDNA′.
A DNA molecule having the coding sequence for the Flag epitope tag, i.e., GATTACAAGGATGACGATGACAAG (SEQ ID NO:190), was inserted into plasmid pcDNA′ digested with XhoI and XbaI to yield plasmid Flag(N)-pcDNA′.
Preparation of DNA Molecules
DNA molecules encoding protein sequences were obtained by polymerase chain reaction (PCR), gene synthesis, or annealing of complementary DNA molecules using standard protocols. A DNA molecule encoding the amino acid sequence of an immunoglobulin Fc region was produced by standard oligonucleotide synthesis. A DNA molecule having a DNA sequence GGAGGCGGAAGTGGT GGGAGCGGTGGAAGCGGAGGC (SEQ ID NO:191) encoding the glycine-serine linker sequence GGGSGGSGGSGG (SEQ ID NO:121), was produced by annealing complementary single strands synthesized by standard methods.
Preparation of Expression Vector Plasmids for Expressing J Domain Fusion Proteins
To express C-terminally V5-tagged IL13Rα2 receptor protein (see, FIG. 1A), a DNA molecule encoding an IL13Rα2 receptor protein was inserted into plasmid V5(C)-pcDNA′ digested with HindIII and KpnI.
To express the fusion protein in which a J domain or BAG domain is attached to the N-terminus of IL13Rα2 receptor protein (see, FIG. 3A), a truncated IL13Rα2 receptor protein with its signal sequence deleted was inserted into plasmid V5(C)-pcDNA′ digested with NotI and XhoI.
To express a V5-tagged, truncated TNR1 receptor protein (see, FIG. 5A), a DNA molecule encoding a truncated (extracellular domain only) TNR1 receptor protein was inserted into plasmid V5(C)-pcDNA′ digested with HindIII and KpnI.
To express a V5-tagged α1 anti-trypsin (“α1AT”) (see, FIG. 4A), a DNA molecule encoding an α1 anti-trypsin was inserted into plasmid V5(C)-pcDNA′ digested with HindIII and KpnI To express an N-terminally V5-tagged p53 protein (see, FIG. 7A), a DNA molecule encoding a p53 protein was inserted into plasmid V5(N)-pcDNA′ digested with Nod and XhoI.
To express V-tagged CFTR and V5-tagged mutant CFTRΔ508F (see, FIG. 8A), a DNA molecule encoding a CFTR protein or a CFTRΔ508F protein was inserted into plasmid V5(N)-pcDNA′ digested with NotI and XhoI.
For expressing fusion proteins comprising a protein of interest fused to a J domain, DNA molecules encoding J domains were subcloned into the EcoRI site of plasmid V5(C)-pcDNA′ or the EcoRV plasmid V5(N)-pcDNA′ to yield plasmid vectors J-V5(C)-pcDNA′ or V5(N)-J-pcDNA′, respectively. Fusion proteins were produced using Hsp40, SV40, and CSP J domains.
To express fusion proteins comprising a protein of interest fused to a BAG domain, DNA molecules encoding a BAG domain were subcloned into EcoRI and EcoRV sites of plasmid V5(C)-pcDNA′ or plasmid V5(N)-pcDNA′ to yield plasmid vectors BAG-V5(C)-pcDNA′ or V5(N)-BAG-pcDNA′, respectively. Fusion proteins were produced using BAG3, BAG4, BAG5, and BAG6 domains as indicated below.
DNA molecules encoding IL13Rα2, TNFR1, α1AT, p53, or CFTR (wild type or Δ508F mutant) were then inserted in frame with the J domain (or, in some instances, a BAG domain) sequence in one or more of the expression vectors to express the resulting fusion protein, which also possessed an N-terminal or C-terminal V5 epitope tag for convenient identification of the encoded protein.
Expression and Detection of Proteins in HEK293 Cells
Expression vector plasmids encoding various protein constructs were transfected into HEK293 cells with X-tremeGENE HP transfection reagent (catalogue no. 06365752001, Roche). As indicated in the examples below, a separate plasmid expressing the green fluorescent protein (GFP) was co-transfected with each expression vector plasmid encoding a fusion protein of the invention to monitor the transfection efficiency. Cultures of transfectant cells were incubated for two days, and culture medium and/or cell lysates were analyzed for expressed proteins using dot blot or Western immunoblot assays. Samples of culture media were centrifuged to remove debris prior to analysis. For cell lysates, cells were lysed in lysis buffer (10 mM Tris-HCl, pH8.0, 150 mM NaCl, 10 mM EDTA, 2% SDS) containing 2 mM PMSF. After brief sonication, the sample was analyzed for express proteins using dot blot or Western immunoblot assays. For Western blot analysis, samples were boiled in SDS-sample buffer and run on polyacrylamide electrophoresis, followed by transfer of separated protein bands to membrane (PVDF membrane).
The expression of GFP as an internal transfection control was detected using an anti-GFP antibody. Expressed proteins in dot blots and Western blots were detected using a chemiluminescent signal. Briefly, blots were reacted with a primary antibody that binds the particular epitope tag (e.g., V5 or Flag) carried by the proteins. After rinsing away unreacted primary antibody, a secondary, enzyme-linked antibody (e.g., horse radish peroxidase linked anti-IgG antibody) was allowed to react with primary antibody molecules bound to the blots. After rinsing, manufacturer's chemiluminescent reagent was added. Chemiluminescent signals in blots were captured on x-ray film. Where indicated, the images of the chemiluminescent signals were scanned with a densitometer and analyzed using the NIH ImageJ image processing program.
Assays for Protein Activities
Standard assays are available for detecting activities of the proteins of interest used in preparing J domain fusion proteins described herein.
A binding assay for IL13Rα2 binding function is described in “Identification of distinct roles for a dileucine and a tyrosine internalization motif in the interleukin (IL)-13 binding component IL13 receptor alpha 2 chain,” J. Biol. Chem., 276(27): 25114-25120 (2001).
A binding assay for TNFR binding function is described in “Recombinant 55-kDa tumor necrosis factor (TNF) receptor: Stoichiometry of binding to TNF alpha and TNF beta and inhibition of TNF activity,” J. Biol. Chem., 266(27): 18324-18329 (1991)
An assay for α1-antitrypsin (α1AT) activity is described in “Alpha 1-antitrypsin and protease complexation is induced by lipopolysaccharide, interleukin-1beta, and tumor necrosis factor-alpha in monocytes,” Am. J. Respir. Crit. Care Med., 157(1): 246-255 (1998).
An assay for p53 activity is described in “Influenza virus infection increases p53 activity: role of p53 activity in cell death and viral replication,” J. Virol., 79(14): 8802-8811 (2005).
An assay for CFTR activity is described in “Pharmacology of CFTR chloride channel activity,” Physiol. Rev., 79(1 Suppl.): S109-S144 (1999).
Example 2. Enhancement of Expression of Target Proteins in a Modified Arrangement
FIG. 1A shows general diagrams of constructs for a C-terminally V5 epitope-tagged, full-length IL13Rα2 protein (“IL13Rα2WT”) and for a C-terminally V5 epitope-tagged fusion protein comprising IL13Rα2 fused to a BAG or to a J domain.
The V5-tagged IL13Rα2WT protein comprises an amino acid sequence for a full-length IL13Rα2 protein linked at the C terminus to a V5 epitope tag, which in turn is linked to twelve C-terminal amino acid residues from the cloning site of the expression vector. The amino acid sequence for the V5-tagged IL13Rα2WT is shown in the table below.







TABLE 2







Amino Acid Sequence of a V5-Tagged IL13Rα2WT Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2WT domain
SEQ ID NO: 192
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


(full-length)

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD




HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDTGTGSEFDIAA




ALEGKPIPNPLLGLDSTSRGPYSIVSPKC


 


IL13Rα2FL
residues 1-380
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI



of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 192
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDT


 


Linker
residues 381-393
GTGSEFDIAAALE



of SEQ ID



NO: 192


 


V5 epitope
residues 394-407
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 192


 


C-terminal
residues 408-419
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 192









The V5-tagged IL13Rα2WT-BAG3 domain fusion protein comprises an amino (N)-terminal amino acid sequence for a full-length IL13Rα2 protein linked to a BAG domain from the BAG3 protein, which in turn is linked to a V5 epitope tag, which in turn is linked to twelve C-terminal amino acid residues from the cloning site of the expression vector. The amino acid sequence for the IL13Rα2WT-BAG3 domain fusion protein is shown in the table below.







TABLE 3







Amino Acid Sequence of an


IL13Rα2WT-BAG3 Domain Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2WT-BAG3
SEQ ID NO: 193
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


fusion protein

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD




HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDTGTGSEFHPGV




LKVEAILEKVQGLEQAVDNFEGKKTDKKYL




MIEEYLTKELLALDSVDPEGRADVRQARRD




GVRKVQTILEKLEQKAIDDIAAALEGKPIP




NPLLGLDSTSRGPYSIVSPKC


 


IL13Rα2WT domain
residues 1-380
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


(full-length)
of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 193
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDT


 


Linker
residues 381-386
GTGSEF



of SEQ ID



NO: 193


 


BAG domain
residues 387-468
HPGVLKVEAILEKVQGLEQAVDNFEGKKTD


(from BAG3)
of SEQ ID
KKYLMIEEYLTKELLALDSVDPEGRADVRQ



NO: 193
ARRDGVRKVQTILEKLEQKAID


 


Linker
residues 469-475
DIAAALE



of SEQ ID



NO: 193


 


V5 epitope
residues 476-489
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 193


 


C-terminal
residues 490-501
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 193









The V5-tagged IL13Rα2WT-BAG4 domain fusion protein comprises an amino (N)-terminal amino acid sequence for a full-length IL13Rα2 protein linked to a BAG domain from the BAG4 protein, which in turn is linked to a V5 epitope tag, which in turn is linked to twelve C-terminal amino acid residues from the cloning site of the expression vector. The amino acid sequence for the IL13Rα2WT-BAG4 domain fusion protein is shown in the table below.







TABLE 4







Amino Acid Sequence of an


IL13Rα2WT-BAG4 Domain Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2WT-
SEQ ID NO: 194
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


BAG4 Domain

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD


Fusion Protein

HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDTGTGSEFESTP




PSIKKIIHVLEKVQYLEQEVEEFVGKKTDK




AYWLLEEMLTKELLELDSVETGGQDSVRQA




RKEAVCKIQAILEKLEKKGLDIAAALEGKP




IPNPLLGLDSTSRGPYSIVSPKC


 


IL13Rα2WT
residues 1-380
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


(full-length)
of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 194
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDT


 


Linker
residues 381-386
GTGSEF



of SEQ ID



NO: 194


 


BAG domain
residues 387-470
ESTPPSIKKIIHVLEKVQYLEQEVEEFVGK


(from BAG4)
of SEQ ID
KTDKAYWLLEEMLTKELLELDSVETGGQDS



NO: 194
VRQARKEAVCKIQAILEKLEKKGL


 


Linker
residues 471-477
DIAAALE



of SEQ ID



NO: 194


 


V5 epitope
residues 478-491
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 194


 


C-terminal
residues 492-503
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 194









The V5-tagged IL13Rα2WT-BAG5 domain fusion protein comprises an amino (N)-terminal amino acid sequence for a full-length IL13Rα2 protein linked to a BAG domain from the BAG5 protein, which in turn is linked to a V5 epitope tag, which in turn is linked to twelve C-terminal amino acid residues from the cloning site of the expression vector. The amino acid sequence for the IL13Rα2WT-BAG5 domain fusion protein is shown in the table below.







TABLE 5







Amino Acid Sequence of an


IL13Rα2WT-BAG5 Domain Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2WT-
SEQ ID NO: 195
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


BAG5 domain

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD


fusion protein

HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDTGTGSEFEHPS




HKAVWNVLGNLSEIQGEVLSFDGNRTDKNY




IRLEELLTKQLLALDAVDPQGEEKCKAARK




QAVRLAQNILSYLDLKSDEDIAAALEGKPI




PNPLLGLDSTSRGPYSIVSPKC


 


IL13Rα2WT
residues 1-380
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


(full-length)
of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 195
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDT


 


Linker
residues 381-386
GTGSEF



of SEQ ID



NO: 195


 


BAG domain
residues 387-469
EHPSHKAVWNVLGNLSEIQGEVLSFDGNRT


(from BAG5)
of SEQ ID
DKNYIRLEELLTKQLLALDAVDPQGEEKCK



NO: 195
AARKQAVRLAQNILSYLDLKSDE


 


Linker
residues 470-476
DIAAALE



of SEQ ID



NO: 195


 


V5 epitope
residues 477-490
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 195


 


C-terminal
residues 491-502
SRGPYSIVSPKC


residues
of SEQ ID



NO: 195









The V5-tagged IL13Rα2WT-BAG6 domain fusion protein comprises an amino (N)-terminal amino acid sequence for a full-length IL13Rα2 protein linked to a BAG domain from the BAG6 protein, which in turn is linked to a V5 epitope tag, which in turn is linked to twelve C-terminal amino acid residues from the cloning site of the expression vector. The amino acid sequence for the IL13Rα2WT-BAG6 domain fusion protein is shown in the table below.







TABLE 6







Amino Acid Sequence of an


IL13Rα2WT-BAG6 Domain Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2WT-BAG6
SEQ ID NO: 196
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


domain fusion

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD


protein

HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDTGTGSEFMPAK




RRKTMQGEGPQLLLSEAVSRAAKAAGARPL




TSPESLSRDLEAPEVQESYRQQLRSDIQKR




LQEDPNYSPQRFPNAQRAFADDPDIAAALE




GKPIPNPLLGLDSTSRGPYSIVSPKC


 


IL13Rα2WT
residues 1-380
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


(full-length)
of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 196
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDT


 


Linker
residues 381-386
GTGSEF



of SEQ ID



NO: 196


 


BAG domain
residues 387-473
MPAKRRKTMQGEGPQLLLSEAVSRAAKAAG


(from BAG6)
of SEQ ID
ARPLTSPESLSRDLEAPEVQESYRQQLRSD



NO: 196
IQKRLQEDPNYSPQRFPNAQRAFADDP


 


Linker
residues 474-480
DIAAALE



of SEQ ID



NO: 196


 


V5 epitope
residues 481-494
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 196


 


C-terminal
residues 495-506
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 196









The V5-tagged IL13Rα2WT-Hsp40 J domain fusion protein comprises an amino (N)-terminal amino acid sequence for a full-length IL13Rα2 protein linked to a J domain from the Hsp40 protein, which in turn is linked to a V5 epitope tag, which in turn is linked to twelve C-terminal amino acid residues from the cloning site of the expression vector. The amino acid sequence for the IL13Rα2-Hsp40 J domain fusion protein is shown in the table below.







TABLE 7







Amino Acid Sequence of an


IL13Rα2WT-Hsp40 J Domain Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2WT-Hsp40
SEQ ID NO: 197
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


J domain fusion

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD


protein

HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDTGTGSEFMGKD




YYQTLGLARGASDEEIKRAYRRQALRYHPD




KNKEPGAEEKFKEIAEAYDVLSDPRKREIF




DRYDIAAALEGKPIPNPLLGLDSTSRGPYS




IVSPKC


 


IL13Rα2WT domain
residues 1-380
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


(full-length)
of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 197
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDT


 


Linker
residues 381-386
GTGSEF



of SEQ ID



NO: 197


 


Hsp40 J domain
residues 387-453
MGKDYYQTLGLARGASDEEIKRAYRRQALR



of SEQ ID
YHPDKNKEPGAEEKFKEIAEAYDVLSDPRK



NO: 197
REIFDRY


 


Linker
residues 454-460
DIAAALE



of SEQ ID



NO: 197


V5 epitope
residues 461-474
GKPIPNPLLGLDST



of SEQ ID



NO: 197


 


C-terminal
residues 475-486
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 197









The V5-tagged IL13Rα2WT-SV40 J domain fusion protein comprises an amino (N)-terminal amino acid sequence for a full-length IL13Rα2 protein linked to a J domain from the SV40 J protein, which in turn is linked to a V5 epitope tag, which in turn is linked to twelve C-terminal amino acid residues from the cloning site of the expression vector. The amino acid sequence for the IL13Rα2-SV40 J domain fusion protein is shown in the table below.







TABLE 8







Amino Acid Sequence of an


IL13Rα2WT-SV40 J Domain Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2WT-SV40 J
SEQ ID NO: 198
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


domain fusion

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD


protein

HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDTGTGSEFMDKV




LNREESLQLMDLLGLERSAWGNIPLMRKAY




LKKCKEFHPDKGGDEEKMKKMNTLYKKMED




GVKYAHQPDFGGFWDADIAAALEGKPIPNP




LLGLDSTSRGPYSIVSPKC


 


IL13Rα2WT domain
residues 1-380
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


(full-length)
of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 198
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDT


 


Linker
residues 381-386
GTGSEF



of SEQ ID



NO: 198


 


SV40 J domain
residues 387-466
MDKVLNREESLQLMDLLGLERSAWGNIPLM



of SEQ ID
RKAYLKKCKEFHPDKGGDEEKMKKMNTLYK



NO: 198
KMEDGVKYAHQPDFGGFWDA


 


Linker
residues 467-473
DIAAALE



of SEQ ID



NO: 198


 


V5 epitope
residues 474-487
GKPIPNPLLGLDST



of SEQ ID



NO: 198


 


C-terminal
residues 488-499
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 198









The V5-tagged IL13Rα2WT-CSP J domain fusion protein comprises an amino (N)-terminal amino acid sequence for a full-length IL13Rα2 protein linked to a J domain from the CSP protein, which in turn is linked to a V5 epitope tag, which in turn is linked to twelve C-terminal amino acid residues from the cloning site of the expression vector. The amino acid sequence for the IL13Rα2WT-CSP J domain fusion protein is shown in the table below.







TABLE 9







Amino Acid Sequence of an


IL13Rα2WT-CSP J Domain Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2WT-CSP J
SEQ ID NO: 199
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


domain fusion

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD


protein

HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDTGTGSEFMADQ




RQRSLSTSGESLYHVLGLDKNATSDDIKKS




YRKLALKYHPDKNPDNPEAADKFKEINNAH




AILTDATKRNIYDKYGSLGLYVDIAAALEG




KPIPNPLLGLDSTSRGPYSIVSPKC


 


IL13Rα2 domain
residues 1-380
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI



of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 199
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKTLLRFWLPFGFILILVIFVTG




LLLRKPNTYPKMIPEFFCDT


 


Linker
residues 381-386
GTGSEF



of SEQ ID



NO: 199


 


CSP J domain
residues 387-472
MADQRQRSLSTSGESLYHVLGLDKNATSDD



of SEQ ID
IKKSYRKLALKYHPDKNPDNPEAADKFKEI



NO: 199
NNAHAILTDATKRNIYDKYGSLGLYV


 


Linker
residues 473-479
DIAAALE



of SEQ ID



NO: 199


 


V5 epitope tag
residues 480-493
GKPIPNPLLGLDST



of SEQ ID



NO: 199


 


C-terminal
residues 494-505
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 199









Using the expression vectors described above, the level of expression IL13Rα2-V5 was compared with that of various IL13Rα2 fusion proteins comprising a BAG domain or J domain in transfected HEK293 cells. The expression level of various fusion proteins in cells are shown in the Western blot in FIG. 1B. The first row shows lanes of the gel loaded with equal amounts of cell lysate protein. The second row shows expression of GFP as an internal transfection control. As shown in the first row of FIG. 1B, only a faint band was detected for the V5-tagged IL13Rα2, which was used to represent expression of the wild-type (WT) IL13Rα2 protein, indicating poor expression. Fusion proteins comprising IL13Rα2 and a BAG domain (BAG3, BAG4, BAG5, BAG6) were expressed at slightly higher levels. In contrast, fusion proteins comprising IL13Rα2 and any of the J domains were all expressed at dramatically higher levels than either the V5 tagged IL13Rα2 or the fusion proteins comprising IL13Rα2 and a BAG domain. The results of a densitometry analysis of the signals in FIG. 1B are shown in FIG. 1C. The fusion proteins comprising IL13Rα2 and any of the J domains were expressed at a level as much as 25-fold higher than the V5 epitope tagged IL13Rα2 (taken as 100%). See, bar graphs in FIG. 1C.
Truncated Form of IL13Rα2 Expression and Secretion
IL13Rα2 is a membrane receptor protein that binds to interleukin-13 (IL13) and mediates allergic inflammation. Binding of IL13 to the membrane-associated IL13Rα2 receptor transduces a signal to the cytoplasm that sets off an inflammatory response. Such a response is particularly detrimental in the case of asthma. A portion of the expressed, membrane-associated IL13Rα2 molecules is cleaved on the cell surface, releasing a soluble truncated form of IL13Rα2 (IL13Rα2TF) into the extracellular space. The truncated form of IL13Rα2 retains the ability to bind IL13 but cannot transmit a signal to the cell due to the absence of the transmembrane and cytoplasmic regions found in the full-length, membrane-associates protein. Accordingly, the truncated form of IL13Rα2 has been employed as a decoy receptor to treat asthma by binding to IL13 molecules without transducing a signal to the cell to set off an inflammatory response. For such therapeutic applications, a genetically engineered, truncated form of IL13Rα2 has been expressed in mammalian cells and purified as a secreted protein from culture medium. However, the production of the truncated form of IL13Rα2 is inefficient due to difficulties in expression and secretion of the protein.
The ability of a J domain to enhance expression of a soluble, truncated form of IL13Rα2 (IL13Rα2TF) was studied. In order to confirm if conjugation of a J domain to a truncated form of IL13Rα2 enhances expression of the secreted protein, plasmids that expressed an IL13Rα2TF or a fusion protein comprising IL13Rα2TF and an N-terminal J domain from Erdj3 were constructed. The proteins also possessed the V5 epitope tag for easy identification. See, diagrams of constructs in FIG. 2A.
The amino acid sequence for a V5 tagged IL13Rα2TF used in this experiment is shown in the table below.







TABLE 10





Amino Acid Sequence of a V5-Tagged IL13Rα2TF Fusion Protein.

















Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2TF
SEQ ID NO: 200
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


protein

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD




HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKGTGSEFDIAAALEGKPIPNPL




LGLDSTSRGPYSIVSPKC


 


IL13Rα2TF
residues 1-339
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI



of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 200
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKK


 


Linker
residues 340-352
GTGSEFDIAAALE



of SEQ ID



NO: 200


 


V5 epitope
residues 353-366
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 200


 


Linker
residues 367-378
SRGPYSIVSPKC



of SEQ ID



NO: 200









The amino acid sequence for a J domain fusion protein comprising an N-terminal J domain of the Erdj3 J protein, a mature (i.e., no signal sequence) and truncated IL13Rα2 (IL13Rα2TF), and the V5 epitope tag is shown in the table below.







TABLE 11







Amino Acid Sequence of a V5-Tagged Erdj3 J


domain-IL13Rα2TF Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Erdj3 J domain-
SEQ ID NO: 201
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


IL13Rα2TF fusion

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


protein

PQAQEKFQDLGAAYEVLSDSEKRDIAAASD




TEIKVNPPQDFEIVDPGYLGYLYLQWQPPL




SLDHFKECTVEYELKYRNIGSETWKTIITK




NLHYKDGFDLNKGIEAKIHTLLPWQCTNGS




EVQSSWAETTYWISPQGIPETKVQDMDCVY




YNWQYLLCSWKPGIGVLLDTNYNLFYWYEG




LDHALQCVDYIKADGQNIGCRFPYLEASDY




KDFYICVNGSSENKPIRSSYFTFQLQNIVK




PLPPVYLTFTRESSCEIKLKWSIPLGPIPA




RCFDYEIEIREDDTTLVTATVENETYTLKT




TNETRQLCFVVRSKVNIYCSDDGIWSEWSD




KQCWEGEDLSKKLEGKPIPNPLLGLDSTSR




GPYSIVSPKC


 


Erdj3 J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL



of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 201
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-88
DIAAA



of SEQ ID



NO: 201


 


IL13Rα2TF
residues 89-402
SDTEIKVNPPQDFEIVDPGYLGYLYLQWQP


(with mature N-
of SEQ ID
PLSLDHFKECTVEYELKYRNIGSETWKTII


terminus)
NO: 201
TKNLHYKDGFDLNKGIEAKIHTLLPWQCTN




GSEVQSSWAETTYWISPQGIPETKVQDMDC




VYYNWQYLLCSWKPGIGVLLDTNYNLFYWY




EGLDHALQCVDYIKADGQNIGCRFPYLEAS




DYKDFYICVNGSSENKPIRSSYFTFQLQNI




VKPLPPVYLTFTRESSCEIKLKWSIPLGPI




PARCFDYEIEIREDDTTLVTATVENETYTL




KTTNETRQLCFVVRSKVNIYCSDDGIWSEW




SDKQCWEGEDLSKK


 


Linker
residues 403-404
LE



of SEQ ID



NO: 201


 


V5 epitope
residues 405-418
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 201


 


C-terminal
residues 419-430
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 201









The amino acid sequence for a BAG domain fusion protein comprising a signal sequence, a BAG domain of BAG3, a mature (i.e., no signal sequence) and truncated IL13Rα2 (IL13Rα2TF), and the V5 epitope tag is shown in the table below.







TABLE 12







Amino Acid Sequence of a V5-Tagged BAG


domain-IL13Rα2TF Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





BAG domain-
SEQ ID NO: 202
MGVKVLFALICIAVAEAGTGSEFHPGVLKV


IL13Rα2TF fusion

EAILEKVQGLEQAVDNFEGKKTDKKYLMIE


protein

EYLTKELLALDSVDPEGRADVRQARRDGVR




KVQTILEKLEQKAIDDIAAASDTEIKVNPP




QDFEIVDPGYLGYLYLQWQPPLSLDHFKEC




TVEYELKYRNIGSETWKTIITKNLHYKDGF




DLNKGIEAKIHTLLPWQCTNGSEVQSSWAE




TTYWISPQGIPETKVQDMDCVYYNWQYLLC




SWKPGIGVLLDTNYNLFYWYEGLDHALQCV




DYIKADGQNIGCRFPYLEASDYKDFYICVN




GSSENKPIRSSYFTFQLQNIVKPLPPVYLT




FTRESSCEIKLKWSIPLGPIPARCFDYEIE




IREDDTTLVTATVENETYTLKTTNETRQLC




FVVRSKVNIYCSDDGIWSEWSDKQCWEGED




LSKKLEGKPIPNPLLGLDSTSRGPYSIVSP




KC


 


Signal Sequence
residues 1-17
MGVKVLFALICIAVAEA



of SEQ ID



NO: 202


 


Linker
residues 18-23
GTGSEF



of SEQ ID



NO: 202


 


BAG domain
residues 24-105
HPGVLKVEAILEKVQGLEQAVDNFEGKKTD


(from BAG3)
of SEQ ID
KKYLMIEEYLTKELLALDSVDPEGRADVRQ



NO: 202
ARRDGVRKVQTILEKLEQKAID


 


Linker
residues 106-110
DIAAA



of SEQ ID



NO: 202


 


IL13Rα2TF
residues 111-424
SDTEIKVNPPQDFEIVDPGYLGYLYLQWQP


(with mature N-
of SEQ ID
PLSLDHFKECTVEYELKYRNIGSETWKTII


terminus)
NO: 202
TKNLHYKDGFDLNKGIEAKIHTLLPWQCTN




GSEVQSSWAETTYWISPQGIPETKVQDMDC




VYYNWQYLLCSWKPGIGVLLDTNYNLFYWY




EGLDHALQCVDYIKADGQNIGCRFPYLEAS




DYKDFYICVNGSSENKPIRSSYFTFQLQNI




VKPLPPVYLTFTRESSCEIKLKWSIPLGPI




PARCFDYEIEIREDDTTLVTATVENETYTL




KTTNETRQLCFVVRSKVNIYCSDDGIWSEW




SDKQCWEGEDLSKK


 


Linker
residues 425-426
LE



of SEQ ID



NO: 202


 


V5 epitope
residues 427-440
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 202


 


C-terminal
residues 441-452
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 202









The expression plasmids were transfected into HEK293 cells. Samples of cell lysates and culture media from two-day cultures of the transfected cells were analyzed by immunoblotting with anti-V5 antibody for expression of IL13Rα2TF or IL13Rα2TF-J domain fusion protein. As shown in FIG. 2B, the expression of the IL13Rα2TF protein was barely detected in cell lysates (lane 2), and no detection was observed in the medium. In contrast, the level of expression of the IL13Rα2TF-J domain fusion protein was dramatically higher both inside the cell (cell lysate samples) and also as secreted into the medium. See, FIG. 2B. A similar effect was observed when the J domain was attached to the C-terminus of the truncated form of IL13Rα2 (data not shown).
Another experiment was performed to better quantify the secreted proteins using a dot blot immunoassay. HEK293 cells were transfected with an expression vector plasmid for expressing IL13Rα2TF, a BAG domain fused to IL13Rα2TF (BAG-IL13RαTF), or a J domain fused to IL13Rα2TF (J-IL13RαTF). Transfected cells were cultured for two days, and samples of cell culture media were analyzed for secreted proteins using a dot blot immunoassay. The results are shown in FIGS. 3A and 3B. FIG. 3A shows x-ray film images of chemiluminescent signals for V5-tagged proteins secreted into culture media. As shown in FIG. 3A, although the fusion protein comprising a BAG domain linked to IL13Rα2TF (lane 3) may have provided some minor enhancement in the level of secreted protein compared to the unfused IL13Rα2TF (lane 2), a fusion protein comprising a J domain linked to IL13Rα2TF (lane 3) exhibited a significantly enhanced level of secreted protein relative to either the unfused IL13Rα2TF (lane 2) or the or the BAG domain-IL13Rα2TF fusion protein (lane 3). The results of a densitometry analysis of the signals of the dot blots in FIG. 3A using the NIH ImageJ image processing program are shown in FIG. 3B. The bar graphs in FIG. 3B clearly show the significantly higher level of expression of secreted J domain-IL13Rα2TF fusion protein (bar graph 4) compared to either the IL13Rα2TF (bar graph 2) or the BAG domain-IL13Rα2TF fusion protein (bar graph 3). Use of the J domain fusion resulted in an approximate 3.5-fold increase in the amount of IL13Rα2TF being secreted by the transformed cells, compared to the expression level of cells transformed to express the IL13Rα2TF protein alone.
J Domain-α1 Anti-Trypsin Fusion Protein in a Modified Arrangement in Human Cells
The α1 anti-trypsin (α1AT) protein is secreted from the liver, and circulates in blood vessels. The function of α1AT is to protect tissues, particularly lung tissue, from excess proteases. The lung is damaged by proteases in a disease called α1 anti-trypsin deficiency. Subjects affected by α1 anti-trypsin deficiency may develop emphysema, asthma, and/or chronic obstructive pulmonary disease (COPD). Currently α1AT (purified from human serum) is used for the treatment of patients with al anti-trypsin deficiency. This treatment is expensive, and subjects that receive the human serum are at risk of contracting pathogens present in the human serum.
The effect of fusing a J domain to an α1 anti-trypsin (α1AT) was studied as a possible strategy for enhancing the levels of expression and secretion of a desired therapeutically useful protein in transfected cells. As shown in FIG. 4A, DNA constructs were prepared encoding a V5-tagged α1AT, a V5-tagged α1AT-BAG domain fusion protein, and a V5-tagged α1AT-J domain fusion protein.
The amino acid sequence of a V5-tagged α1AT protein is shown in the table below.







TABLE 13







Amino Acid Sequence of a V5-Tagged α1AT Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





α1AT protein
SEQ ID NO: 203
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD




AAQKTDTSHHDQDHPTFNKITPNLAEFAFS




LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQKGT




GSEFDIAAALEGKPIPNPLLGLDSTSRGPY




SIVSPKC


 


α1AT
residues 1-418
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD



of SEQ ID
AAQKTDTSHHDQDHPTFNKITPNLAEFAFS



NO: 203
LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQK


 


Linker
residues 419-431
GTGSEFDIAAALE



of SEQ ID



NO: 203


 


V5 epitope
residues 432-445
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 203


 


C-terminal
residues 446-457
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 203









The amino acid sequence of a BAG domain fusion protein comprising α1AT, the BAG domain of BAG3, and the V5 epitope tag is shown in the table below.







TABLE 14







Amino Acid Sequence of α1AT-BAG Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





α1AT-BAG domain
SEQ ID NO: 204
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD


fusion protein

AAQKTDTSHHDQDHPTFNKITPNLAEFAFS




LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQKGT




GSEFHPGVLKVEAILEKVQGLEQAVDNFEG




KKTDKKYLMIEEYLTKELLALDSVDPEGRA




DVRQARRDGVRKVQTILEKLEQKAIDDIAA




ALEGKPIPNPLLGLDSTSRGPYSIVSPKC


 


α1AT
residues 1-418
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD



of SEQ ID
AAQKTDTSHHDQDHPTFNKITPNLAEFAFS



NO: 204
LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQK


 


Linker
residues 419-424
GTGSEF



of SEQ ID



NO: 204


 


BAG domain
residues 425-506
HPGVLKVEAILEKVQGLEQAVDNFEGKKTD


(from BAG3)
of SEQ ID
KKYLMIEEYLTKELLALDSVDPEGRADVRQ



NO: 204
ARRDGVRKVQTILEKLEQKAID


 


Linker
residues 507-513
DIAAALE



of SEQ ID



NO: 204


 


V5 epitope
residues 514-527
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 204


 


C-terminal
residues 528-539
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 204









The amino acid sequence of a J domain fusion protein comprising α1AT, the Erdj3 J domain, and the V5 epitope tag is shown in the table below.







TABLE 15







Amino Acid Sequence of α1AT-J Domain Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





α1AT-Erdj3 J
SEQ ID NO: 205
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD


domain fusion

AAQKTDTSHHDQDHPTFNKITPNLAEFAFS


protein

LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQKGT




GSEFGRDFYKILGVPRSASIKDIKKAYRKL




ALQLHPDRNPDDPQAQEKFQDLGAAYEVLS




DSEKRDIAAALEGKPIPNPLLGLDSTSRGP




YSIVSPKC


 


α1AT
residues 1-418
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD



of SEQ ID
AAQKTDTSHHDQDHPTFNKITPNLAEFAFS



NO: 205
LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQK


 


Linker
residues 419-424
GTGSEF



of SEQ ID



NO: 205


 


Erdj3 J domain
residues 425-485
GRDFYKILGVPRSASIKDIKKAYRKLALQL



of SEQ ID
HPDRNPDDPQAQEKFQDLGAAYEVLSDSEK



NO: 205
R


 


Linker
residues 486-492
DIAAALE



of SEQ ID



NO: 205


 


V5 epitope
residues 493-506
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 205


 


C-terminal
residues 507-518
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 205









Expression vector plasmids encoding the above three recombinant α1AT protein constructs were transfected into HEK293 cells. Culture media from two-day cultures of transfected cells were harvested, and the level of the recombinant α1AT proteins secreted into the media determined by dot blot immunoassays. FIG. 4B shows x-ray film chemiluminescent signals of the dot blot assays. Although detectable amounts of both unfused α1AT (lane 2) and α1AT-BAG domain fusion protein (lane 3) were secreted into culture media, an even higher level of expression was obtained for secreted α1AT-J domain fusion protein (lane 3). The results of a densitometry analysis of the signals of the dot blots in FIG. 4B using the NIH ImageJ image processing program are shown in FIG. 4C. The bar graphs in FIG. 4C clearly show the significantly higher level of expression of secreted α1AT-J domain fusion protein (bar graph 4) compared to the level of expression of either α1AT (bar graph 2) or the α1AT-BAG domain fusion protein (bar graph 3). Use of the J domain fusion resulted in greater than a 1.5-fold increase in the amount of IL13Rα2TF being secreted by the transformed cells, compared to the expression level of cells transformed to express the α1AT protein alone or an α1AT-BAG fusion protein.
Truncated Form of TNFR1 Protein in a Modified Arrangement
One format for designing therapeutically active fusion proteins combines a binding domain, which specifically binds a desired target molecule, linked to an immunoglobulin Fc region, which endues the fusion protein with an enhanced in vivo half-life. An example of this class of drugs is etanercept, which binds and inhibits the effect of tumor necrosis factor (TNFα), which is a key protein of the immune system involved in a number of autoimmune diseases. For example, etanercept possesses a truncated form of a tumor necrosis factor α receptor (TNFR1TF) linked to an immunoglobulin Fc domain. The TNFR1 TF portion of etanercept provides specificity for the drug target (TNFα), and the Fc domain is believed to add stability and deliverability of the drug in vivo. Nevertheless, the Fc domain is also known to possess certain effector functions that may not be desired in treatment protocols for some diseases.
The effect of fusing a J domain to a truncated form of a receptor molecule was studied as a possible strategy for enhancing levels of expression and secretion of a desired receptor-based molecule. Such a J domain fusion protein may provide a possible alternative to prior drug designs involving truncated forms of receptor molecules linked to immunoglobulin Fc domains. The expression of a truncated form of a tumor necrosis factor receptor (TNFR1TF) with or without a J domain was studied using expression vector plasmids TNFR1TF-V5-pcDNA′ and TNFR1TF-J domain-V5-pcDNA′. The expression vectors add a V5 epitope tag to both proteins for easy detection with an anti-V5 antibody. See, diagrams of constructs in FIG. 5A.
The amino acid sequence of a V5-tagged TNFR1TF is shown in the table below.







TABLE 16







Amino Acid Sequence of a V5-Tagged TNFR1TF Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





TNFR1TF protein
SEQ ID NO: 206
MGLSTVPDLLLPLVLLELLVGIYPSGVIGL




VPHLGDREKRDSVCPQGKYIHPQNNSICCT




KCHKGTYLYNDCPGPGQDTDCRECESGSFT




ASENHLRHCLSCSKCRKEMGQVEISSCTVD




RDTVCGCRKNQYRHYWSENLFQCFNCSLCL




NGTVHLSCQEKQNTVCTCHAGFFLRENECV




SCSNCKKSLECTKLCLPQIENVKGTEDSGT




TGTGSEFDIAAALEGKPIPNPLLGLDSTSR




GPYSIVSPKC


 


TNFR1TF
residues 1-211
MGLSTVPDLLLPLVLLELLVGIYPSGVIGL



of SEQ ID
VPHLGDREKRDSVCPQGKYIHPQNNSICCT



NO: 206
KCHKGTYLYNDCPGPGQDTDCRECESGSFT




ASENHLRHCLSCSKCRKEMGQVEISSCTVD




RDTVCGCRKNQYRHYWSENLFQCFNCSLCL




NGTVHLSCQEKQNTVCTCHAGFFLRENECV




SCSNCKKSLECTKLCLPQIENVKGTEDSGT




T


 


Linker
residues 212-224
GTGSEFDIAAALE



of SEQ ID



NO: 206


 


V5 epitope
residues 225-238
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 206


 


C-terminal
residues 239-250
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 206









The amino acid sequence of a J domain fusion protein comprising TNFR1TF, the Erdj3 J domain, and the V5 epitope tag is shown in the table below.







TABLE 17







Amino Acid Sequence of a V5-Tagged TNFR1TF-Erdj3 J


Domain Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





TNFR1TF-J domain
SEQ ID NO: 207
MGLSTVPDLLLPLVLLELLVGIYPSGVIGL


fusion protein

VPHLGDREKRDSVCPQGKYIHPQNNSICCT




KCHKGTYLYNDCPGPGQDTDCRECESGSFT




ASENHLRHCLSCSKCRKEMGQVEISSCTVD




RDTVCGCRKNQYRHYWSENLFQCFNCSLCL




NGTVHLSCQEKQNTVCTCHAGFFLRENECV




SCSNCKKSLECTKLCLPQIENVKGTEDSGT




TGTGSEFGRDFYKILGVPRSASIKDIKKAY




RKLALQLHPDRNPDDPQAQEKFQDLGAAYE




VLSDSEKRDIAAALEGKPIPNPLLGLDSTS




RGPYSIVSPKC


 


TNFR1TF
residues 1-211
MGLSTVPDLLLPLVLLELLVGIYPSGVIGL



of SEQ ID
VPHLGDREKRDSVCPQGKYIHPQNNSICCT



NO: 207
KCHKGTYLYNDCPGPGQDTDCRECESGSFT




ASENHLRHCLSCSKCRKEMGQVEISSCTVD




RDTVCGCRKNQYRHYWSENLFQCFNCSLCL




NGTVHLSCQEKQNTVCTCHAGFFLRENECV




SCSNCKKSLECTKLCLPQIENVKGTEDSGT




T


 


Linker
residues 212-217
GTGSEF



of SEQ ID



NO: 207


 


Erdj3 J domain
residues 218-278
GRDFYKILGVPRSASIKDIKKAYRKLALQL



of SEQ ID
HPDRNPDDPQAQEKFQDLGAAYEVLSDSEK



NO: 207
R


 


Linker
residues 279-285
DIAAALE



of SEQ ID



NO: 207


 


V5 epitope
residues 286-299
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 207


 


C-terminal
residues 300-311
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 207









The expression plasmids were transfected into HEK293 cells. Samples of cell lysates and culture media from two-day cultures of transfected cells were analyzed by immunoblotting with anti-V5 antibody for expression of TNFR1TF or the TNFR1TF-J domain fusion protein. As shown in the dot blots in FIG. 5B, some TNFR1TF was detected in medium (lane 2), however, the level of the TNFR1TF-J domain fusion protein detected in the medium was significantly greater (lane 3). The results of a densitometry analysis of the signals of the dot blots in FIG. 5B using the NIH ImageJ image processing program are shown in FIG. 5C. Clearly, the level of expression of secreted TNFR1TF-J domain fusion protein (bar graph 3) was significantly higher than that of the (unfused) TNFR1TF protein (bar graph 2), i.e., about a 6-fold increase over the level of TNFR1TF alone.
Secretion of Fc-Fusion Proteins in a Modified Arrangement
In view of the above results showing that the level of expression of secreted truncated form of TNFR1 was enhanced by the conjugation of J domain (FIGS. 5B and 5C), it was of interest to examine whether a J domain would enhance expression of a protein of interest fused to an immunoglobulin Fc domain, such as a TNF1TF-Fc fusion protein. Such Fc-fusion molecules are a type of drug format illustrated by the drug etanercept (commercially available as ENBREL®), which is a TNF1TF-Fc fusion protein approved for treating a number of autoimmune diseases, such as severe rheumatoid arthritis, polyarticular juvenile idiopathic arthritis (JIA), psoriatic arthritis, ankylosing spondylitis, and plaque psoriasis.
For this study, a cDNA encoding each protein of interest (TNFR1TF, IL13Rα2TF, or α1AT) was augmented with a segment encoding a V5 epitope tag at the 3′ end, which was linked in turn to a segment encoding the constant domains of an immunoglobulin Fc region. For J-domain fusions, a cDNA encoding a J domain was linked in frame between the cDNA encoding each protein of interest and the segment encoding a V5 epitope tag. See, illustration of constructs in FIG. 6A. The corresponding expression vector plasmids were transfected into HEK293 cells. Culture media were assayed for secreted proteins by dot blot assay.
The amino acid sequence of the TNFR1TF-Fc fusion protein is shown in the table below.







TABLE 18







Amino Acid Sequence of a V5-Tagged TNFR1TF-Fc


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





TNFR1TF Fc
SEQ ID NO: 208
MGLSTVPDLLLPLVLLELLVGIYPSGVIGL


fusion protein

VPHLGDREKRDSVCPQGKYIHPQNNSICCT




KCHKGTYLYNDCPGPGQDTDCRECESGSFT




ASENHLRHCLSCSKCRKEMGQVEISSCTVD




RDTVCGCRKNQYRHYWSENLFQCFNCSLCL




NGTVHLSCQEKQNTVCTCHAGFFLRENECV




SCSNCKKSLECTKLCLPQIENVKGTEDSGT




TGTGSEFDIAAALEGKPIPNPLLGLDSTSR




PKSCDKTHTCPPCPAPELLGGPSVFLFPPK




PKDTLMISRTPEVTCVVVDVSHEDPEVKFN




WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK


 


TNFR1TF
residues 1-211
MGLSTVPDLLLPLVLLELLVGIYPSGVIGL



of SEQ ID
VPHLGDREKRDSVCPQGKYIHPQNNSICCT



NO: 208
KCHKGTYLYNDCPGPGQDTDCRECESGSFT




ASENHLRHCLSCSKCRKEMGQVEISSCTVD




RDTVCGCRKNQYRHYWSENLFQCFNCSLCL




NGTVHLSCQEKQNTVCTCHAGFFLRENECV




SCSNCKKSLECTKLCLPQIENVKGTEDSGT




T


 


Linker
residues 212-224
GTGSEFDIAAALE



of SEQ ID



NO: 208


 


V5 epitope
residues 225-238
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 208


 


Linker
residues 239-240
SR



of SEQ ID



NO: 208


 


Fc domain
residues 241-471
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 208
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









The amino acid sequence of a TNFR1TF-J domain-Fc fusion protein is shown in the table below.







TABLE 19







Amino Acid Sequence of a V5-Tagged TNFR1TF-Erdj3


J Domain-Fc Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





TNFR1TF-J domain
SEQ ID NO: 209
MGLSTVPDLLLPLVLLELLVGIYPSGVIGL


Fc fusion

VPHLGDREKRDSVCPQGKYIHPQNNSICCT


protein

KCHKGTYLYNDCPGPGQDTDCRECESGSFT




ASENHLRHCLSCSKCRKEMGQVEISSCTVD




RDTVCGCRKNQYRHYWSENLFQCFNCSLCL




NGTVHLSCQEKQNTVCTCHAGFFLRENECV




SCSNCKKSLECTKLCLPQIENVKGTEDSGT




TGTGSEFGRDFYKILGVPRSASIKDIKKAY




RKLALQLHPDRNPDDPQAQEKFQDLGAAYE




VLSDSEKRDIAAALEGKPIPNPLLGLDSTS




RPKSCDKTHTCPPCPAPELLGGPSVFLFPP




KPKDTLMISRTPEVTCVVVDVSHEDPEVKF




NWYVDGVEVHNAKTKPREEQYNSTYRVVSV




LTVLHQDWLNGKEYKCKVSNKALPAPIEKT




ISKAKGQPREPQVYTLPPSRDELTKNQVSL




TCLVKGFYPSDIAVEWESNGQPENNYKTTP




PVLDSDGSFFLYSKLTVDKSRWQQGNVFSC




SVMHEALHNHYTQKSLSLSPGK


 


TNFR1TF
residues 1-211
MGLSTVPDLLLPLVLLELLVGIYPSGVIGL



of SEQ ID
VPHLGDREKRDSVCPQGKYIHPQNNSICCT



NO: 209
KCHKGTYLYNDCPGPGQDTDCRECESGSFT




ASENHLRHCLSCSKCRKEMGQVEISSCTVD




RDTVCGCRKNQYRHYWSENLFQCFNCSLCL




NGTVHLSCQEKQNTVCTCHAGFFLRENECV




SCSNCKKSLECTKLCLPQIENVKGTEDSGT




T


 


Linker
residues 212-217
GTGSEF



of SEQ ID



NO: 209


 


Erdj3 J domain
residues 218-278
GRDFYKILGVPRSASIKDIKKAYRKLALQL



of SEQ ID
HPDRNPDDPQAQEKFQDLGAAYEVLSDSEK



NO: 209
R


 


Linker
residues 279-285
DIAAALE



of SEQ ID



NO: 209


 


V5 epitope
residues 286-299
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 209


 


Linker
residues 300-301
SR



of SEQ ID



NO: 209


 


Fc domain
residues 302-532
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 209
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









The amino acid sequence of an IL13Rα2TF-Fc fusion protein is shown in the table below.







TABLE 20







Amino Acid Sequence of a V5-Tagged IL13Rα2TF-Fc


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2TF-Fc
SEQ ID NO: 210
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


fusion protein

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD




HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKGTGSEFDIAAALEGKPIPNPL




LGLDSTSRPKSCDKTHTCPPCPAPELLGGP




SVFLFPPKPKDTLMISRTPEVTCVVVDVSH




EDPEVKFNWYVDGVEVHNAKTKPREEQYNS




TYRVVSVLTVLHQDWLNGKEYKCKVSNKAL




PAPIEKTISKAKGQPREPQVYTLPPSRDEL




TKNQVSLTCLVKGFYPSDIAVEWESNGQPE




NNYKTTPPVLDSDGSFFLYSKLTVDKSRWQ




QGNVFSCSVMHEALHNHYTQKSLSLSPGK


 


IL13Rα2TF
residues 1-339
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI



of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 210
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKK


 


Linker
residues 340-352
GTGSEFDIAAALE



of SEQ ID



NO: 210


 


V5 epitope
residues 353-366
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 210


 


Linker
residues 367-368
SR



of SEQ ID



NO: 210


 


Fc domain
residues 369-599
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 210
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









The amino acid sequence of an IL13Rα2TF-J domain-Fc fusion protein is shown in the table below.







TABLE 21







Amino Acid Sequence of a V5-Tagged IL13Rα2TF-Erdj3


J Domain-Fc Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2TF-J
SEQ ID NO: 211
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


domain-Fc fusion

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD


protein

HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKGTGSEFGRDFYKILGVPRSAS




IKDIKKAYRKLALQLHPDRNPDDPQAQEKF




QDLGAAYEVLSDSEKRDIAAALEGKPIPNP




LLGLDSTSRPKSCDKTHTCPPCPAPELLGG




PSVFLFPPKPKDTLMISRTPEVTCVVVDVS




HEDPEVKFNWYVDGVEVHNAKTKPREEQYN




STYRVVSVLTVLHQDWLNGKEYKCKVSNKA




LPAPIEKTISKAKGQPREPQVYTLPPSRDE




LTKNQVSLTCLVKGFYPSDIAVEWESNGQP




ENNYKTTPPVLDSDGSFFLYSKLTVDKSRW




QQGNVFSCSVMHEALHNHYTQKSLSLSPGK


 


IL13Rα2TF
residues 1-339
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI



of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 211
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKK


 


Linker
residues 340-345
GTGSEF



of SEQ ID



NO: 211


 


Erdj3 J domain
residues 346-406
GRDFYKILGVPRSASIKDIKKAYRKLALQL



of SEQ ID
HPDRNPDDPQAQEKFQDLGAAYEVLSDSEK



NO: 211
R


 


Linker
residues 407-413
DIAAALE



of SEQ ID



NO: 211


 


V5 epitope
residues 414-427
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 211


 


Linker
residues 428-429
SR



of SEQ ID



NO: 211


 


Fc domain
residues 430-660
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 211
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









The amino acid sequence of an α1AT-Fc fusion protein is shown in the table below.







TABLE 22







Amino Acid Sequence of V5-Tagged α1AT-Fc Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





α1AT protein-Fc
SEQ ID NO: 212
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD


fusion protein

AAQKTDTSHHDQDHPTFNKITPNLAEFAFS




LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQKGT




GSEFDIAAALEGKPIPNPLLGLDSTSRPKS




CDKTHTCPPCPAPELLGGPSVFLFPPKPKD




TLMISRTPEVTCVVVDVSHEDPEVKFNWYV




DGVEVHNAKTKPREEQYNSTYRVVSVLTVL




HQDWLNGKEYKCKVSNKALPAPIEKTISKA




KGQPREPQVYTLPPSRDELTKNQVSLTCLV




KGFYPSDIAVEWESNGQPENNYKTTPPVLD




SDGSFFLYSKLTVDKSRWQQGNVFSCSVMH




EALHNHYTQKSLSLSPGK


 


α1AT
residues 1-418
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD



of SEQ ID
AAQKTDTSHHDQDHPTFNKITPNLAEFAFS



NO: 212
LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQK


 


Linker
residues 419-431
GTGSEFDIAAALE



of SEQ ID



NO: 212


 


V5 epitope
residues 432-445
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 212


 


Linker
residues 446-447
SR



of SEQ ID



NO: 212


 


Fc domain
residues 448-678
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 212
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









The amino acid sequence of an α1AT-J domain-Fc fusion protein is shown in the table below.







TABLE 23







Amino Acid Sequence of a V5-Tagged α1 AT-Erdj3


J Domain-Fc Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





α1AT-J domain-Fc
SEQ ID NO: 213
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD


fusion protein

AAQKTDTSHHDQDHPTFNKITPNLAEFAFS




LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQKGT




GSEFGRDFYKILGVPRSASIKDIKKAYRKL




ALQLHPDRNPDDPQAQEKFQDLGAAYEVLS




DSEKRDIAAALEGKPIPNPLLGLDSTSRPK




SCDKTHTCPPCPAPELLGGPSVFLFPPKPK




DTLMISRTPEVTCVVVDVSHEDPEVKFNWY




VDGVEVHNAKTKPREEQYNSTYRVVSVLTV




LHQDWLNGKEYKCKVSNKALPAPIEKTISK




AKGQPREPQVYTLPPSRDELTKNQVSLTCL




VKGFYPSDIAVEWESNGQPENNYKTTPPVL




DSDGSFFLYSKLTVDKSRWQQGNVFSCSVM




HEALHNHYTQKSLSLSPGK


 


α1AT
residues 1-418
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD



of SEQ ID
AAQKTDTSHHDQDHPTFNKITPNLAEFAFS



NO: 213
LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQK


 


Linker
residues 419-424
GTGSEF



of SEQ ID



NO: 213


 


Erdj3 J domain
residues 425-485
GRDFYKILGVPRSASIKDIKKAYRKLALQL



of SEQ ID
HPDRNPDDPQAQEKFQDLGAAYEVLSDSEK



NO: 213
R


 


Linker
residues 486-492
DIAAALE



of SEQ ID



NO: 213


 


V5 epitope
residues 493-506
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 213


 


Linker
residues 507-508
SR



of SEQ ID



NO: 213


 


Fc domain
residues 509-739
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 213
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









Each of the Fc fusion proteins (TNFRI-V5-Fc, IL13Rα2TF-Fc, α1AT-Fc) were expressed in culture media as shown in the dot blots in the middle lane of each panel in FIG. 6B. This level of expression of the Fc fusion proteins was greater than that for each of the proteins of interest alone (i.e., without fusion to an Fc domain; data not shown). However, significantly higher levels of expression were obtained in each case when a J domain was linked to the protein of interest segment within the Fc fusion proteins as shown in the dot blots in the right lane of each panel in FIG. 6B. The results of a densitometry analysis of the chemiluminescent signals of the dot blots in FIG. 6B are shown in the corresponding panels of FIG. 6C, where the significantly higher level of expression of the J domain fusion proteins is clearly evident.
Enhanced Expression of p53 Protein in a Modified Arrangement in Human Cells
Proteins such as IL13Rα2, TNFR, and α1AT are synthesized in the endoplasmic reticulum (ER) for delivery to the cell membrane or secretion from the cell. To determine the effect of the presence of a J domain on the expression of cytoplasmic proteins, the expression of a fusion of the p53 protein and J domain was studied. The p53 protein is a transcription factor that plays pivotal roles in genomic stability. More than half of cancer patients have some abnormalities in the pathway involving p53. Therefore, overexpression of p53 in a cancer patient has been attempted as a treatment for cancer.
A cDNA encoding p53 was inserted into expression plasmid V5(N)-pcDNA′ to yield plasmid V5(N)-p53-pcDNA′ to express a p53 protein containing an N-terminal V5 epitope tag. To express the p53-J domain fusion protein, a cDNA encoding a J domain of the SV40 large T antigen was then inserted into the V5(N)-p53-pcDNA′ vector between the V5 and p53 coding regions. See, diagrams of constructs in FIG. 7A.
The amino acid sequence of a V5-tagged p53 protein is shown in the table below.







TABLE 24







Amino Acid Sequence of a V5-Tagged p53 Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





p53 protein
SEQ ID NO: 214
MGKPIPNPLLGLDSTGTGSEFDIAAAMEEP




QSDPSVEPPLSQETFSDLWKLLPENNVLSP




LPSQAMDDLMLSPDDIEQWFTEDPGPDEAP




RMPEAAPPVAPAPAAPTPAAPAPAPSWPLS




SSVPSQKTYQGSYGFRLGFLHSGTAKSVTC




TYSPALNKMFCQLAKTCPVQLWVDSTPPPG




TRVRAMAIYKQSQHMTEVVRRCPHHERCSD




SDGLAPPQHLIRVEGNLRVEYLDDRNTFRH




SVVVPYEPPEVGSDCTTIHYNYMCNSSCMG




GMNRRPILTIITLEDSSGNLLGRNSFEVRV




CACPGRDRRTEEENLRKKGEPHHELPPGST




KRALPNNTSSSPQPKKKPLDGEYFTLQIRG




RERFEMFRELNEALELKDAQAGKEPGGSRA




HSSHLKSKKGQSTSRHKKLMFKTEGPDSDA




AALESRGPYSIVSPKC


 


V5 epitope
residues 1-15
MGKPIPNPLLGLDST


domain
of SEQ ID



NO: 214


 


Linker
residues 16-26
GTGSEFDIAAA



of SEQ ID



NO: 214


 


p53
residues 27-422
MEEPQSDPSVEPPLSQETFSDLWKLLPENN



of SEQ ID
VLSPLPSQAMDDLMLSPDDIEQWFTEDPGP



NO: 214
DEAPRMPEAAPPVAPAPAAPTPAAPAPAPS




WPLSSSVPSQKTYQGSYGFRLGFLHSGTAK




SVTCTYSPALNKMFCQLAKTCPVQLWVDST




PPPGTRVRAMAIYKQSQHMTEVVRRCPHHE




RCSDSDGLAPPQHLIRVEGNLRVEYLDDRN




TFRHSVVVPYEPPEVGSDCTTIHYNYMCNS




SCMGGMNRRPILTIITLEDSSGNLLGRNSF




EVRVCACPGRDRRTEEENLRKKGEPHHELP




PGSTKRALPNNTSSSPQPKKKPLDGEYFTL




QIRGRERFEMFRELNEALELKDAQAGKEPG




GSRAHSSHLKSKKGQSTSRHKKLMFKTEGP




DSDAAA


 


C-terminal
residues 423-436
LESRGPYSIVSPKC


vector residues
of SEQ ID



NO: 214









The amino acid sequence of a J domain fusion protein comprising the V5 epitope tag, the SV40 J domain, and the p53 protein is shown in the table below.







TABLE 25







Amino Acid Sequence of a V5-Tagged SV40 J Domain-p53


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





p53-SV40 J
SEQ ID NO: 215
MGKPIPNPLLGLDSTGTGSEFMDKVLNREE


domain fusion

SLQLMDLLGLERSAWGNIPLMRKAYLKKCK


protein

EFHPDKGGDEEKMKKMNTLYKKMEDGVKYA




HQPDFGGFWDADIAAAMEEPQSDPSVEPPL




SQETFSDLWKLLPENNVLSPLPSQAMDDLM




LSPDDIEQWFTEDPGPDEAPRMPEAAPPVA




PAPAAPTPAAPAPAPSWPLSSSVPSQKTYQ




GSYGFRLGFLHSGTAKSVTCTYSPALNKMF




CQLAKTCPVQLWVDSTPPPGTRVRAMAIYK




QSQHMTEVVRRCPHHERCSDSDGLAPPQHL




IRVEGNLRVEYLDDRNTFRHSVVVPYEPPE




VGSDCTTIHYNYMCNSSCMGGMNRRPILTI




ITLEDSSGNLLGRNSFEVRVCACPGRDRRT




EEENLRKKGEPHHELPPGSTKRALPNNTSS




SPQPKKKPLDGEYFTLQIRGRERFEMFREL




NEALELKDAQAGKEPGGSRAHSSHLKSKKG




QSTSRHKKLMFKTEGPDSDAAALESRGPYS




IVSPKC


 


V5 epitope
residues 1-15
MGKPIPNPLLGLDST


domain
of SEQ ID



NO: 215


 


Linker
residues 16-21
GTGSEF



of SEQ ID



NO: 215


 


SV40 J domain
residues 22-101
MDKVLNREESLQLMDLLGLERSAWGNIPLM



of SEQ ID
RKAYLKKCKEFHPDKGGDEEKMKKMNTLYK



NO: 215
KMEDGVKYAHQPDFGGFWDA


 


Linker
residues 102-106
DIAAA



of SEQ ID



NO: 215


 


p53
residues 107-502
MEEPQSDPSVEPPLSQETFSDLWKLLPENN



of SEQ ID
VLSPLPSQAMDDLMLSPDDIEQWFTEDPGP



NO: 215
DEAPRMPEAAPPVAPAPAAPTPAAPAPAPS




WPLSSSVPSQKTYQGSYGFRLGFLHSGTAK




SVTCTYSPALNKMFCQLAKTCPVQLWVDST




PPPGTRVRAMAIYKQSQHMTEVVRRCPHHE




RCSDSDGLAPPQHLIRVEGNLRVEYLDDRN




TFRHSVVVPYEPPEVGSDCTTIHYNYMCNS




SCMGGMNRRPILTIITLEDSSGNLLGRNSF




EVRVCACPGRDRRTEEENLRKKGEPHHELP




PGSTKRALPNNTSSSPQPKKKPLDGEYFTL




QIRGRERFEMFRELNEALELKDAQAGKEPG




GSRAHSSHLKSKKGQSTSRHKKLMFKTEGP




DSDAAA


 


Linker
residues 503-516
LESRGPYSIVSPKC



of SEQ ID



NO: 215









Plasmids V5(N)-p53-pcDNA′ and V5(N)-J-p53-pcDNA′ were transfected into MCF cells, and incubated for two days. Cells were lysed in lysis buffer, and protein was detected by Western immunoblot assay using anti-V5 antibody. As shown in FIG. 7B, the level of expression of the p53-J domain fusion protein (lane 3) was significantly greater than that of the p53 protein without a J domain. Accordingly, the results indicate that fusion with a J domain can enhance not only membrane-associated and secreted proteins, but cytoplasmic proteins as well.
CFTR Expression in a Modified Arrangement in Human Cells
Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) protein, a cAMP-regulated chloride channel and channel regulator. The deletion of phenylalanine at position 508 (Δ508F) in CFTR is the most common mutation that changes the conformation of the CFTR protein, which is then rapidly degraded by the ER quality systems. A general consensus is that only partial recovery of the wild-type CFTR protein function is required to provide a beneficial treatment to CF patients. Therefore, a number of gene therapy trials with CFTR have been attempted, but have not yet been successful owing to inefficient delivery of a gene for CFTR and to immunogenicity of the vehicle (e.g., viral vector). In view of the fact that proper protein folding of wild-type CFTR is known to be difficult, it would be very useful if protein folding of the CFTR protein could be improved.
The cftr gene or its Phe508 deletion mutant (cftrΔ508F) was inserted into plasmid V5(N)-pcDNA′. A DNA coding for the BAG domain of the BAG3 protein or a DNA coding for the J domain from the Hsp40 J protein was inserted in the plasmids between V5 and the cftr coding sequences to yield plasmids to express a wild-type CFTR or mutant CFTR (Δ508F) protein linked to an N-terminal V5 epitope tag or to express a wild-type or mutant CFTR protein fused at its N-terminus to a BAG or J domain, which in turn was fused to an N-terminal V5 epitope tag. Diagrams of the various constructs used in this experiment are shown in FIG. 8A.
The amino acid sequence a V5-tagged wild-type CFTR (CFTR WT) is shown in the table below.







TABLE 26







Amino Acid Sequence of a V5-Tagged CFTR Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged CFTR
SEQ ID NO: 216
MGKPIPNPLLGLDSTGTGSEFDIAAAMQRS


protein

PLEKASVVSKLFFSWTRPILRKGYRQRLEL




SDIYQIPSVDSADNLSEKLEREWDRELASK




KNPKLINALRRCFFWRFMFYGIFLYLGEVT




KAVQPLLLGRIIASYDPDNKEERSIAIYLG




IGLCLLFIVRTLLLHPAIFGLHHIGMQMRI




AMFSLIYKKTLKLSSRVLDKISIGQLVSLL




SNNLNKFDEGLALAHFVWIAPLQVALLMGL




IWELLQASAFCGLGFLIVLALFQAGLGRMM




MKYRDQRAGKISERLVITSEMIENIQSVKA




YCWEEAMEKMIENLRQTELKLTRKAAYVRY




FNSSAFFFSGFFVVFLSVLPYALIKGIILR




KIFTTISFCIVLRMAVTRQFPWAVQTWYDS




LGAINKIQDFLQKQEYKTLEYNLTTTEVVM




ENVTAFWEEGFGELFEKAKQNNNNRKTSNG




DDSLFFSNFSLLGTPVLKDINFKIERGQLL




AVAGSTGAGKTSLLMVIMGELEPSEGKIKH




SGRISFCSQFSWIMPGTIKENIIFGVSYDE




YRYRSVIKACQLEEDISKFAEKDNIVLGEG




GITLSGGQRARISLARAVYKDADLYLLDSP




FGYLDVLTEKEIFESCVCKLMANKTRILVT




SKMEHLKKADKILILHEGSSYFYGTFSELQ




NLQPDFSSKLMGCDSFDQFSAERRNSILTE




TLHRFSLEGDAPVSWTETKKQSFKQTGEFG




EKRKNSILNPINSIRKFSIVQKTPLQMNGI




EEDSDEPLERRLSLVPDSEQGEAILPRISV




ISTGPTLQARRRQSVLNLMTHSVNQGQNIH




RKTTASTRKVSLAPQANLTELDIYSRRLSQ




ETGLEISEEINEEDLKECFFDDMESIPAVT




TWNTYLRYITVHKSLIFVLIWCLVIFLAEV




AASLVVLWLLGNTPLQDKGNSTHSRNNSYA




VIITSTSSYYVFYIYVGVADTLLAMGFFRG




LPLVHTLITVSKILHHKMLHSVLQAPMSTL




NTLKAGGILNRFSKDIAILDDLLPLTIFDF




IQLLLIVIGAIAVVAVLQPYIFVATVPVIV




AFIMLRAYFLQTSQQLKQLESEGRSPIFTH




LVTSLKGLWTLRAFGRQPYFETLFHKALNL




HTANWFLYLSTLRWFQMRIEMIFVIFFIAV




TFISILTTGEGEGRVGIILTLAMNIMSTLQ




WAVNSSIDVDSLMRSVSRVFKFIDMPTEGK




PTKSTKPYKNGQLSKVMIIENSHVKKDDIW




PSGGQMTVKDLTAKYTEGGNAILENISFSI




SPGQRVGLLGRTGSGKSTLLSAFLRLLNTE




GEIQIDGVSWDSITLQQWRKAFGVIPQKVF




IFSGTFRKNLDPYEQWSDQEIWKVADEVGL




RSVIEQFPGKLDFVLVDGGCVLSHGHKQLM




CLARSVLSKAKILLLDEPSAHLDPVTYQII




RRTLKQAFADCTVILCEHRIEAMLECQQFL




VIEENKVRQYDSIQKLLNERSLFRQAISPS




DRVKLFPHRNSSKCKSKPQIAALKEETEEE




VQDTRL


 


V5 epitope
residues 1-15
MGKPIPNPLLGLDST


domain
of SEQ ID



NO: 216


 


Linker
residues 16-26
GTGSEFDIAAA



of SEQ ID



NO: 216


 


CFTR
residues 27-1506
MQRSPLEKASVVSKLFFSWTRPILRKGYRQ



of SEQ ID
RLELSDIYQIPSVDSADNLSEKLEREWDRE



NO: 216
LASKKNPKLINALRRCFFWRFMFYGIFLYL




GEVTKAVQPLLLGRIIASYDPDNKEERSIA




IYLGIGLCLLFIVRTLLLHPAIFGLHHIGM




QMRIAMFSLIYKKTLKLSSRVLDKISIGQL




VSLLSNNLNKFDEGLALAHFVWIAPLQVAL




LMGLIWELLQASAFCGLGFLIVLALFQAGL




GRMMMKYRDQRAGKISERLVITSEMIENIQ




SVKAYCWEEAMEKMIENLRQTELKLTRKAA




YVRYFNSSAFFFSGFFVVFLSVLPYALIKG




IILRKIFTTISFCIVLRMAVTRQFPWAVQT




WYDSLGAINKIQDFLQKQEYKTLEYNLTTT




EVVMENVTAFWEEGFGELFEKAKQNNNNRK




TSNGDDSLFFSNFSLLGTPVLKDINFKIER




GQLLAVAGSTGAGKTSLLMVIMGELEPSEG




KIKHSGRISFCSQFSWIMPGTIKENIIFGV




SYDEYRYRSVIKACQLEEDISKFAEKDNIV




LGEGGITLSGGQRARISLARAVYKDADLYL




LDSPFGYLDVLTEKEIFESCVCKLMANKTR




ILVTSKMEHLKKADKILILHEGSSYFYGTF




SELQNLQPDFSSKLMGCDSFDQFSAERRNS




ILTETLHRFSLEGDAPVSWTETKKQSFKQT




GEFGEKRKNSILNPINSIRKFSIVQKTPLQ




MNGIEEDSDEPLERRLSLVPDSEQGEAILP




RISVISTGPTLQARRRQSVLNLMTHSVNQG




QNIHRKTTASTRKVSLAPQANLTELDIYSR




RLSQETGLEISEEINEEDLKECFFDDMESI




PAVTTWNTYLRYITVHKSLIFVLIWCLVIF




LAEVAASLVVLWLLGNTPLQDKGNSTHSRN




NSYAVIITSTSSYYVFYIYVGVADTLLAMG




FFRGLPLVHTLITVSKILHHKMLHSVLQAP




MSTLNTLKAGGILNRFSKDIAILDDLLPLT




IFDFIQLLLIVIGAIAVVAVLQPYIFVATV




PVIVAFIMLRAYFLQTSQQLKQLESEGRSP




IFTHLVTSLKGLWTLRAFGRQPYFETLFHK




ALNLHTANWFLYLSTLRWFQMRIEMIFVIF




FIAVTFISILTTGEGEGRVGIILTLAMNIM




STLQWAVNSSIDVDSLMRSVSRVFKFIDMP




TEGKPTKSTKPYKNGQLSKVMIIENSHVKK




DDIWPSGGQMTVKDLTAKYTEGGNAILENI




SFSISPGQRVGLLGRTGSGKSTLLSAFLRL




LNTEGEIQIDGVSWDSITLQQWRKAFGVIP




QKVFIFSGTFRKNLDPYEQWSDQEIWKVAD




EVGLRSVIEQFPGKLDFVLVDGGCVLSHGH




KQLMCLARSVLSKAKILLLDEPSAHLDPVT




YQIIRRTLKQAFADCTVILCEHRIEAMLEC




QQFLVIEENKVRQYDSIQKLLNERSLFRQA




ISPSDRVKLFPHRNSSKCKSKPQIAALKEE




TEEEVQDTRL









The amino acid sequence of a V5-tagged BAG-CFTR (wild-type) protein is shown in the table below.







TABLE 27







Amino Acid Sequence of a V5-Tagged BAG Domain-CFTR


Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged BAG
SEQ ID NO: 217
MGKPIPNPLLGLDSTGTGSEFHPGVLKVEA


domain-CFTR

ILEKVQGLEQAVDNFEGKKTDKKYLMIEEY


fusion protein

LTKELLALDSVDPEGRADVRQARRDGVRKV




QTILEKLEQKAIDDIAAAMQRSPLEKASVV




SKLFFSWTRPILRKGYRQRLELSDIYQIPS




VDSADNLSEKLEREWDRELASKKNPKLINA




LRRCFFWRFMFYGIFLYLGEVTKAVQPLLL




GRIIASYDPDNKEERSIAIYLGIGLCLLFI




VRTLLLHPAIFGLHHIGMQMRIAMFSLIYK




KTLKLSSRVLDKISIGQLVSLLSNNLNKFD




EGLALAHFVWIAPLQVALLMGLIWELLQAS




AFCGLGFLIVLALFQAGLGRMMMKYRDQRA




GKISERLVITSEMIENIQSVKAYCWEEAME




KMIENLRQTELKLTRKAAYVRYFNSSAFFF




SGFFVVFLSVLPYALIKGIILRKIFTTISF




CIVLRMAVTRQFPWAVQTWYDSLGAINKIQ




DFLQKQEYKTLEYNLTTTEVVMENVTAFWE




EGFGELFEKAKQNNNNRKTSNGDDSLFFSN




FSLLGTPVLKDINFKIERGQLLAVAGSTGA




GKTSLLMVIMGELEPSEGKIKHSGRISFCS




QFSWIMPGTIKENIIFGVSYDEYRYRSVIK




ACQLEEDISKFAEKDNIVLGEGGITLSGGQ




RARISLARAVYKDADLYLLDSPFGYLDVLT




EKEIFESCVCKLMANKTRILVTSKMEHLKK




ADKILILHEGSSYFYGTFSELQNLQPDFSS




KLMGCDSFDQFSAERRNSILTETLHRFSLE




GDAPVSWTETKKQSFKQTGEFGEKRKNSIL




NPINSIRKFSIVQKTPLQMNGIEEDSDEPL




ERRLSLVPDSEQGEAILPRISVISTGPTLQ




ARRRQSVLNLMTHSVNQGQNIHRKTTASTR




KVSLAPQANLTELDIYSRRLSQETGLEISE




EINEEDLKECFFDDMESIPAVTTWNTYLRY




ITVHKSLIFVLIWCLVIFLAEVAASLVVLW




LLGNTPLQDKGNSTHSRNNSYAVIITSTSS




YYVFYIYVGVADTLLAMGFFRGLPLVHTLI




TVSKILHHKMLHSVLQAPMSTLNTLKAGGI




LNRFSKDIAILDDLLPLTIFDFIQLLLIVI




GAIAVVAVLQPYIFVATVPVIVAFIMLRAY




FLQTSQQLKQLESEGRSPIFTHLVTSLKGL




WTLRAFGRQPYFETLFHKALNLHTANWFLY




LSTLRWFQMRIEMIFVIFFIAVTFISILTT




GEGEGRVGIILTLAMNIMSTLQWAVNSSID




VDSLMRSVSRVFKFIDMPTEGKPTKSTKPY




KNGQLSKVMIIENSHVKKDDIWPSGGQMTV




KDLTAKYTEGGNAILENISFSISPGQRVGL




LGRTGSGKSTLLSAFLRLLNTEGEIQIDGV




SWDSITLQQWRKAFGVIPQKVFIFSGTFRK




NLDPYEQWSDQEIWKVADEVGLRSVIEQFP




GKLDFVLVDGGCVLSHGHKQLMCLARSVLS




KAKILLLDEPSAHLDPVTYQIIRRTLKQAF




ADCTVILCEHRIEAMLECQQFLVIEENKVR




QYDSIQKLLNERSLFRQAISPSDRVKLFPH




RNSSKCKSKPQIAALKEETEEEVQDTRL


 


V5 epitope
residues 1-15
MGKPIPNPLLGLDST


domain
of SEQ ID



NO: 217


 


Linker
residues 16-21
GTGSEF



of SEQ ID



NO: 217


 


BAG domain
residues 22-103
HPGVLKVEAILEKVQGLEQAVDNFEGKKTD


(from BAG3)
of SEQ ID
KKYLMIEEYLTKELLALDSVDPEGRADVRQ



NO: 217
ARRDGVRKVQTILEKLEQKAID


 


Linker
residues 104-108
DIAAA



of SEQ ID



NO: 217


 


CFTR
residues 109-1588
MQRSPLEKASVVSKLFFSWTRPILRKGYRQ



of SEQ ID
RLELSDIYQIPSVDSADNLSEKLEREWDRE



NO: 217
LASKKNPKLINALRRCFFWRFMFYGIFLYL




GEVTKAVQPLLLGRIIASYDPDNKEERSIA




IYLGIGLCLLFIVRTLLLHPAIFGLHHIGM




QMRIAMFSLIYKKTLKLSSRVLDKISIGQL




VSLLSNNLNKFDEGLALAHFVWIAPLQVAL




LMGLIWELLQASAFCGLGFLIVLALFQAGL




GRMMMKYRDQRAGKISERLVITSEMIENIQ




SVKAYCWEEAMEKMIENLRQTELKLTRKAA




YVRYFNSSAFFFSGFFVVFLSVLPYALIKG




IILRKIFTTISFCIVLRMAVTRQFPWAVQT




WYDSLGAINKIQDFLQKQEYKTLEYNLTTT




EVVMENVTAFWEEGFGELFEKAKQNNNNRK




TSNGDDSLFFSNFSLLGTPVLKDINFKIER




GQLLAVAGSTGAGKTSLLMVIMGELEPSEG




KIKHSGRISFCSQFSWIMPGTIKENIIFGV




SYDEYRYRSVIKACQLEEDISKFAEKDNIV




LGEGGITLSGGQRARISLARAVYKDADLYL




LDSPFGYLDVLTEKEIFESCVCKLMANKTR




ILVTSKMEHLKKADKILILHEGSSYFYGTF




SELQNLQPDFSSKLMGCDSFDQFSAERRNS




ILTETLHRFSLEGDAPVSWTETKKQSFKQT




GEFGEKRKNSILNPINSIRKFSIVQKTPLQ




MNGIEEDSDEPLERRLSLVPDSEQGEAILP




RISVISTGPTLQARRRQSVLNLMTHSVNQG




QNIHRKTTASTRKVSLAPQANLTELDIYSR




RLSQETGLEISEEINEEDLKECFFDDMESI




PAVTTWNTYLRYITVHKSLIFVLIWCLVIF




LAEVAASLVVLWLLGNTPLQDKGNSTHSRN




NSYAVIITSTSSYYVFYIYVGVADTLLAMG




FFRGLPLVHTLITVSKILHHKMLHSVLQAP




MSTLNTLKAGGILNRFSKDIAILDDLLPLT




IFDFIQLLLIVIGAIAVVAVLQPYIFVATV




PVIVAFIMLRAYFLQTSQQLKQLESEGRSP




IFTHLVTSLKGLWTLRAFGRQPYFETLFHK




ALNLHTANWFLYLSTLRWFQMRIEMIFVIF




FIAVTFISILTTGEGEGRVGIILTLAMNIM




STLQWAVNSSIDVDSLMRSVSRVFKFIDMP




TEGKPTKSTKPYKNGQLSKVMIIENSHVKK




DDIWPSGGQMTVKDLTAKYTEGGNAILENI




SFSISPGQRVGLLGRTGSGKSTLLSAFLRL




LNTEGEIQIDGVSWDSITLQQWRKAFGVIP




QKVFIFSGTFRKNLDPYEQWSDQEIWKVAD




EVGLRSVIEQFPGKLDFVLVDGGCVLSHGH




KQLMCLARSVLSKAKILLLDEPSAHLDPVT




YQIIRRTLKQAFADCTVILCEHRIEAMLEC




QQFLVIEENKVRQYDSIQKLLNERSLFRQA




ISPSDRVKLFPHRNSSKCKSKPQIAALKEE




TEEEVQDTRL









The amino acid sequences a J domain fusion comprising the V5 epitope tag, the SV40 J domain, and the CFTR wild-type protein is shown in the table below.







TABLE 28







Amino Acid Sequence of a V5-Tagged SV40 J Domain-CFTR


Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged SV40 J
SEQ ID NO: 218
MGKPIPNPLLGLDSTGTGSEFMDKVLNREE


domain-CFTR

SLQLMDLLGLERSAWGNIPLMRKAYLKKCK


fusion protein

EFHPDKGGDEEKMKKMNTLYKKMEDGVKYA




HQPDFGGFWDADIAAAMQRSPLEKASVVSK




LFFSWTRPILRKGYRQRLELSDIYQIPSVD




SADNLSEKLEREWDRELASKKNPKLINALR




RCFFWRFMFYGIFLYLGEVTKAVQPLLLGR




IIASYDPDNKEERSIAIYLGIGLCLLFIVR




TLLLHPAIFGLHHIGMQMRIAMFSLIYKKT




LKLSSRVLDKISIGQLVSLLSNNLNKFDEG




LALAHFVWIAPLQVALLMGLIWELLQASAF




CGLGFLIVLALFQAGLGRMMMKYRDQRAGK




ISERLVITSEMIENIQSVKAYCWEEAMEKM




IENLRQTELKLTRKAAYVRYFNSSAFFFSG




FFVVFLSVLPYALIKGIILRKIFTTISFCI




VLRMAVTRQFPWAVQTWYDSLGAINKIQDF




LQKQEYKTLEYNLTTTEVVMENVTAFWEEG




FGELFEKAKQNNNNRKTSNGDDSLFFSNFS




LLGTPVLKDINFKIERGQLLAVAGSTGAGK




TSLLMVIMGELEPSEGKIKHSGRISFCSQF




SWIMPGTIKENIIFGVSYDEYRYRSVIKAC




QLEEDISKFAEKDNIVLGEGGITLSGGQRA




RISLARAVYKDADLYLLDSPFGYLDVLTEK




EIFESCVCKLMANKTRILVTSKMEHLKKAD




KILILHEGSSYFYGTFSELQNLQPDFSSKL




MGCDSFDQFSAERRNSILTETLHRFSLEGD




APVSWTETKKQSFKQTGEFGEKRKNSILNP




INSIRKFSIVQKTPLQMNGIEEDSDEPLER




RLSLVPDSEQGEAILPRISVISTGPTLQAR




RRQSVLNLMTHSVNQGQNIHRKTTASTRKV




SLAPQANLTELDIYSRRLSQETGLEISEEI




NEEDLKECFFDDMESIPAVTTWNTYLRYIT




VHKSLIFVLIWCLVIFLAEVAASLVVLWLL




GNTPLQDKGNSTHSRNNSYAVIITSTSSYY




VFYIYVGVADTLLAMGFFRGLPLVHTLITV




SKILHHKMLHSVLQAPMSTLNTLKAGGILN




RFSKDIAILDDLLPLTIFDFIQLLLIVIGA




IAVVAVLQPYIFVATVPVIVAFIMLRAYFL




QTSQQLKQLESEGRSPIFTHLVTSLKGLWT




LRAFGRQPYFETLFHKALNLHTANWFLYLS




TLRWFQMRIEMIFVIFFIAVTFISILTTGE




GEGRVGIILTLAMNIMSTLQWAVNSSIDVD




SLMRSVSRVFKFIDMPTEGKPTKSTKPYKN




GQLSKVMIIENSHVKKDDIWPSGGQMTVKD




LTAKYTEGGNAILENISFSISPGQRVGLLG




RTGSGKSTLLSAFLRLLNTEGEIQIDGVSW




DSITLQQWRKAFGVIPQKVFIFSGTFRKNL




DPYEQWSDQEIWKVADEVGLRSVIEQFPGK




LDFVLVDGGCVLSHGHKQLMCLARSVLSKA




KILLLDEPSAHLDPVTYQIIRRTLKQAFAD




CTVILCEHRIEAMLECQQFLVIEENKVRQY




DSIQKLLNERSLFRQAISPSDRVKLFPHRN




SSKCKSKPQIAALKEETEEEVQDTRL


 


V5 epitope
residues 1-15
MGKPIPNPLLGLDST


domain
of SEQ ID



NO: 218


 


Linker
residues 16-21
GTGSEF



of SEQ ID



NO: 218


 


SV40 J domain
residues 22-101
MDKVLNREESLQLMDLLGLERSAWGNIPLM



of SEQ ID
RKAYLKKCKEFHPDKGGDEEKMKKMNTLYK



NO: 218
KMEDGVKYAHQPDFGGFWDA


 


Linker
residues 102-106
DIAAA



of SEQ ID



NO: 218


 


CFTR
residues 107-1586
MQRSPLEKASVVSKLFFSWTRPILRKGYRQ



of SEQ ID
RLELSDIYQIPSVDSADNLSEKLEREWDRE



NO: 218
LASKKNPKLINALRRCFFWRFMFYGIFLYL




GEVTKAVQPLLLGRIIASYDPDNKEERSIA




IYLGIGLCLLFIVRTLLLHPAIFGLHHIGM




QMRIAMFSLIYKKTLKLSSRVLDKISIGQL




VSLLSNNLNKFDEGLALAHFVWIAPLQVAL




LMGLIWELLQASAFCGLGFLIVLALFQAGL




GRMMMKYRDQRAGKISERLVITSEMIENIQ




SVKAYCWEEAMEKMIENLRQTELKLTRKAA




YVRYFNSSAFFFSGFFVVFLSVLPYALIKG




IILRKIFTTISFCIVLRMAVTRQFPWAVQT




WYDSLGAINKIQDFLQKQEYKTLEYNLTTT




EVVMENVTAFWEEGFGELFEKAKQNNNNRK




TSNGDDSLFFSNFSLLGTPVLKDINFKIER




GQLLAVAGSTGAGKTSLLMVIMGELEPSEG




KIKHSGRISFCSQFSWIMPGTIKENIIFGV




SYDEYRYRSVIKACQLEEDISKFAEKDNIV




LGEGGITLSGGQRARISLARAVYKDADLYL




LDSPFGYLDVLTEKEIFESCVCKLMANKTR




ILVTSKMEHLKKADKILILHEGSSYFYGTF




SELQNLQPDFSSKLMGCDSFDQFSAERRNS




ILTETLHRFSLEGDAPVSWTETKKQSFKQT




GEFGEKRKNSILNPINSIRKFSIVQKTPLQ




MNGIEEDSDEPLERRLSLVPDSEQGEAILP




RISVISTGPTLQARRRQSVLNLMTHSVNQG




QNIHRKTTASTRKVSLAPQANLTELDIYSR




RLSQETGLEISEEINEEDLKECFFDDMESI




PAVTTWNTYLRYITVHKSLIFVLIWCLVIF




LAEVAASLVVLWLLGNTPLQDKGNSTHSRN




NSYAVIITSTSSYYVFYIYVGVADTLLAMG




FFRGLPLVHTLITVSKILHHKMLHSVLQAP




MSTLNTLKAGGILNRFSKDIAILDDLLPLT




IFDFIQLLLIVIGAIAVVAVLQPYIFVATV




PVIVAFIMLRAYFLQTSQQLKQLESEGRSP




IFTHLVTSLKGLWTLRAFGRQPYFETLFHK




ALNLHTANWFLYLSTLRWFQMRIEMIFVIF




FIAVTFISILTTGEGEGRVGIILTLAMNIM




STLQWAVNSSIDVDSLMRSVSRVFKFIDMP




TEGKPTKSTKPYKNGQLSKVMIIENSHVKK




DDIWPSGGQMTVKDLTAKYTEGGNAILENI




SFSISPGQRVGLLGRTGSGKSTLLSAFLRL




LNTEGEIQIDGVSWDSITLQQWRKAFGVIP




QKVFIFSGTFRKNLDPYEQWSDQEIWKVAD




EVGLRSVIEQFPGKLDFVLVDGGCVLSHGH




KQLMCLARSVLSKAKILLLDEPSAHLDPVT




YQIIRRTLKQAFADCTVILCEHRIEAMLEC




QQFLVIEENKVRQYDSIQKLLNERSLFRQA




ISPSDRVKLFPHRNSSKCKSKPQIAALKEE




TEEEVQDTRL









The amino acid sequence of a V5-tagged CFTR (Δ508F) protein is shown in the table below.







TABLE 29







Amino Acid Sequence of a V5-Tagged CFTR(Δ508F) Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged
SEQ ID NO: 219
MGKPIPNPLLGLDSTGTGSEFDIAAAMQRS


CFTR(Δ508F)

PLEKASVVSKLFFSWTRPILRKGYRQRLEL


protein

SDIYQIPSVDSADNLSEKLEREWDRELASK




KNPKLINALRRCFFWRFMFYGIFLYLGEVT




KAVQPLLLGRIIASYDPDNKEERSIAIYLG




IGLCLLFIVRTLLLHPAIFGLHHIGMQMRI




AMFSLIYKKTLKLSSRVLDKISIGQLVSLL




SNNLNKFDEGLALAHFVWIAPLQVALLMGL




IWELLQASAFCGLGFLIVLALFQAGLGRMM




MKYRDQRAGKISERLVITSEMIENIQSVKA




YCWEEAMEKMIENLRQTELKLTRKAAYVRY




FNSSAFFFSGFFVVFLSVLPYALIKGIILR




KIFTTISFCIVLRMAVTRQFPWAVQTWYDS




LGAINKIQDFLQKQEYKTLEYNLTTTEVVM




ENVTAFWEEGFGELFEKAKQNNNNRKTSNG




DDSLFFSNFSLLGTPVLKDINFKIERGQLL




AVAGSTGAGKTSLLMVIMGELEPSEGKIKH




SGRISFCSQFSWIMPGTIKENIIGVSYDEY




RYRSVIKACQLEEDISKFAEKDNIVLGEGG




ITLSGGQRARISLARAVYKDADLYLLDSPF




GYLDVLTEKEIFESCVCKLMANKTRILVTS




KMEHLKKADKILILHEGSSYFYGTFSELQN




LQPDFSSKLMGCDSFDQFSAERRNSILTET




LHRFSLEGDAPVSWTETKKQSFKQTGEFGE




KRKNSILNPINSIRKFSIVQKTPLQMNGIE




EDSDEPLERRLSLVPDSEQGEAILPRISVI




STGPTLQARRRQSVLNLMTHSVNQGQNIHR




KTTASTRKVSLAPQANLTELDIYSRRLSQE




TGLEISEEINEEDLKECFFDDMESIPAVTT




WNTYLRYITVHKSLIFVLIWCLVIFLAEVA




ASLVVLWLLGNTPLQDKGNSTHSRNNSYAV




IITSTSSYYVFYIYVGVADTLLAMGFFRGL




PLVHTLITVSKILHHKMLHSVLQAPMSTLN




TLKAGGILNRFSKDIAILDDLLPLTIFDFI




QLLLIVIGAIAVVAVLQPYIFVATVPVIVA




FIMLRAYFLQTSQQLKQLESEGRSPIFTHL




VTSLKGLWTLRAFGRQPYFETLFHKALNLH




TANWFLYLSTLRWFQMRIEMIFVIFFIAVT




FISILTTGEGEGRVGIILTLAMNIMSTLQW




AVNSSIDVDSLMRSVSRVFKFIDMPTEGKP




TKSTKPYKNGQLSKVMIIENSHVKKDDIWP




SGGQMTVKDLTAKYTEGGNAILENISFSIS




PGQRVGLLGRTGSGKSTLLSAFLRLLNTEG




EIQIDGVSWDSITLQQWRKAFGVIPQKVFI




FSGTFRKNLDPYEQWSDQEIWKVADEVGLR




SVIEQFPGKLDFVLVDGGCVLSHGHKQLMC




LARSVLSKAKILLLDEPSAHLDPVTYQIIR




RTLKQAFADCTVILCEHRIEAMLECQQFLV




IEENKVRQYDSIQKLLNERSLFRQAISPSD




RVKLFPHRNSSKCKSKPQIAALKEETEEEV




QDTRL


 


V5 epitope
residues 1-15
MGKPIPNPLLGLDST


domain
of SEQ ID



NO: 219


 


Linker
residues 16-26
GTGSEFDIAAA



of SEQ ID



NO: 219


 


CFTR(Δ508F)
residues 27-1505
MQRSPLEKASVVSKLFFSWTRPILRKGYRQ



of SEQ ID
RLELSDIYQIPSVDSADNLSEKLEREWDRE



NO: 219
LASKKNPKLINALRRCFFWRFMFYGIFLYL




GEVTKAVQPLLLGRIIASYDPDNKEERSIA




IYLGIGLCLLFIVRTLLLHPAIFGLHHIGM




QMRIAMFSLIYKKTLKLSSRVLDKISIGQL




VSLLSNNLNKFDEGLALAHFVWIAPLQVAL




LMGLIWELLQASAFCGLGFLIVLALFQAGL




GRMMMKYRDQRAGKISERLVITSEMIENIQ




SVKAYCWEEAMEKMIENLRQTELKLTRKAA




YVRYFNSSAFFFSGFFVVFLSVLPYALIKG




IILRKIFTTISFCIVLRMAVTRQFPWAVQT




WYDSLGAINKIQDFLQKQEYKTLEYNLTTT




EVVMENVTAFWEEGFGELFEKAKQNNNNRK




TSNGDDSLFFSNFSLLGTPVLKDINFKIER




GQLLAVAGSTGAGKTSLLMVIMGELEPSEG




KIKHSGRISFCSQFSWIMPGTIKENIIGVS




YDEYRYRSVIKACQLEEDISKFAEKDNIVL




GEGGITLSGGQRARISLARAVYKDADLYLL




DSPFGYLDVLTEKEIFESCVCKLMANKTRI




LVTSKMEHLKKADKILILHEGSSYFYGTFS




ELQNLQPDFSSKLMGCDSFDQFSAERRNSI




LTETLHRFSLEGDAPVSWTETKKQSFKQTG




EFGEKRKNSILNPINSIRKFSIVQKTPLQM




NGIEEDSDEPLERRLSLVPDSEQGEAILPR




ISVISTGPTLQARRRQSVLNLMTHSVNQGQ




NIHRKTTASTRKVSLAPQANLTELDIYSRR




LSQETGLEISEEINEEDLKECFFDDMESIP




AVTTWNTYLRYITVHKSLIFVLIWCLVIFL




AEVAASLVVLWLLGNTPLQDKGNSTHSRNN




SYAVIITSTSSYYVFYIYVGVADTLLAMGF




FRGLPLVHTLITVSKILHHKMLHSVLQAPM




STLNTLKAGGILNRFSKDIAILDDLLPLTI




FDFIQLLLIVIGAIAVVAVLQPYIFVATVP




VIVAFIMLRAYFLQTSQQLKQLESEGRSPI




FTHLVTSLKGLWTLRAFGRQPYFETLFHKA




LNLHTANWFLYLSTLRWFQMRIEMIFVIFF




IAVTFISILTTGEGEGRVGIILTLAMNIMS




TLQWAVNSSIDVDSLMRSVSRVFKFIDMPT




EGKPTKSTKPYKNGQLSKVMIIENSHVKKD




DIWPSGGQMTVKDLTAKYTEGGNAILENIS




FSISPGQRVGLLGRTGSGKSTLLSAFLRLL




NTEGEIQIDGVSWDSITLQQWRKAFGVIPQ




KVFIFSGTFRKNLDPYEQWSDQEIWKVADE




VGLRSVIEQFPGKLDFVLVDGGCVLSHGHK




QLMCLARSVLSKAKILLLDEPSAHLDPVTY




QIIRRTLKQAFADCTVILCEHRIEAMLECQ




QFLVIEENKVRQYDSIQKLLNERSLFRQAI




SPSDRVKLFPHRNSSKCKSKPQIAALKEET




EEEVQDTRL









The amino acid sequence of a V5-tagged BAG domain-CFTR (Δ508F) fusion protein is shown in the table below.







TABLE 30







Amino Acid Sequence of a V5-Tagged BAG Domain-CFTR(Δ508F)


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged BAG
SEQ ID NO: 220
MGKPIPNPLLGLDSTGTGSEFHPGVLKVEA


domain-

ILEKVQGLEQAVDNFEGKKTDKKYLMIEEY


CFTR(Δ508F)

LTKELLALDSVDPEGRADVRQARRDGVRKV


fusion protein

QTILEKLEQKAIDDIAAAMQRSPLEKASVV




SKLFFSWTRPILRKGYRQRLELSDIYQIPS




VDSADNLSEKLEREWDRELASKKNPKLINA




LRRCFFWRFMFYGIFLYLGEVTKAVQPLLL




GRIIASYDPDNKEERSIAIYLGIGLCLLFI




VRTLLLHPAIFGLHHIGMQMRIAMFSLIYK




KTLKLSSRVLDKISIGQLVSLLSNNLNKFD




EGLALAHFVWIAPLQVALLMGLIWELLQAS




AFCGLGFLIVLALFQAGLGRMMMKYRDQRA




GKISERLVITSEMIENIQSVKAYCWEEAME




KMIENLRQTELKLTRKAAYVRYFNSSAFFF




SGFFVVFLSVLPYALIKGIILRKIFTTISF




CIVLRMAVTRQFPWAVQTWYDSLGAINKIQ




DFLQKQEYKTLEYNLTTTEVVMENVTAFWE




EGFGELFEKAKQNNNNRKTSNGDDSLFFSN




FSLLGTPVLKDINFKIERGQLLAVAGSTGA




GKTSLLMVIMGELEPSEGKIKHSGRISFCS




QFSWIMPGTIKENIIGVSYDEYRYRSVIKA




CQLEEDISKFAEKDNIVLGEGGITLSGGQR




ARISLARAVYKDADLYLLDSPFGYLDVLTE




KEIFESCVCKLMANKTRILVTSKMEHLKKA




DKILILHEGSSYFYGTFSELQNLQPDFSSK




LMGCDSFDQFSAERRNSILTETLHRFSLEG




DAPVSWTETKKQSFKQTGEFGEKRKNSILN




PINSIRKFSIVQKTPLQMNGIEEDSDEPLE




RRLSLVPDSEQGEAILPRISVISTGPTLQA




RRRQSVLNLMTHSVNQGQNIHRKTTASTRK




VSLAPQANLTELDIYSRRLSQETGLEISEE




INEEDLKECFFDDMESIPAVTTWNTYLRYI




TVHKSLIFVLIWCLVIFLAEVAASLVVLWL




LGNTPLQDKGNSTHSRNNSYAVIITSTSSY




YVFYIYVGVADTLLAMGFFRGLPLVHTLIT




VSKILHHKMLHSVLQAPMSTLNTLKAGGIL




NRFSKDIAILDDLLPLTIFDFIQLLLIVIG




AIAVVAVLQPYIFVATVPVIVAFIMLRAYF




LQTSQQLKQLESEGRSPIFTHLVTSLKGLW




TLRAFGRQPYFETLFHKALNLHTANWFLYL




STLRWFQMRIEMIFVIFFIAVTFISILTTG




EGEGRVGIILTLAMNIMSTLQWAVNSSIDV




DSLMRSVSRVFKFIDMPTEGKPTKSTKPYK




NGQLSKVMIIENSHVKKDDIWPSGGQMTVK




DLTAKYTEGGNAILENISFSISPGQRVGLL




GRTGSGKSTLLSAFLRLLNTEGEIQIDGVS




WDSITLQQWRKAFGVIPQKVFIFSGTFRKN




LDPYEQWSDQEIWKVADEVGLRSVIEQFPG




KLDFVLVDGGCVLSHGHKQLMCLARSVLSK




AKILLLDEPSAHLDPVTYQIIRRTLKQAFA




DCTVILCEHRIEAMLECQQFLVIEENKVRQ




YDSIQKLLNERSLFRQAISPSDRVKLFPHR




NSSKCKSKPQIAALKEETEEEVQDTRL


 


V5 epitope
residues 1-15
MGKPIPNPLLGLDST


domain
of SEQ ID



NO: 220


 


Linker
residues 16-21
GTGSEF



of SEQ ID



NO: 220


 


BAG domain
residues 22-103
HPGVLKVEAILEKVQGLEQAVDNFEGKKTD


(from BAG3)
of SEQ ID
KKYLMIEEYLTKELLALDSVDPEGRADVRQ



NO: 220
ARRDGVRKVQTILEKLEQKAID


 


Linker
residues 104-108
DIAAA



of SEQ ID



NO: 220


 


CFTR(Δ508F)
residues 109-1587
MQRSPLEKASVVSKLFFSWTRPILRKGYRQ



of SEQ ID
RLELSDIYQIPSVDSADNLSEKLEREWDRE



NO: 220
LASKKNPKLINALRRCFFWRFMFYGIFLYL




GEVTKAVQPLLLGRIIASYDPDNKEERSIA




IYLGIGLCLLFIVRTLLLHPAIFGLHHIGM




QMRIAMFSLIYKKTLKLSSRVLDKISIGQL




VSLLSNNLNKFDEGLALAHFVWIAPLQVAL




LMGLIWELLQASAFCGLGFLIVLALFQAGL




GRMMMKYRDQRAGKISERLVITSEMIENIQ




SVKAYCWEEAMEKMIENLRQTELKLTRKAA




YVRYFNSSAFFFSGFFVVFLSVLPYALIKG




IILRKIFTTISFCIVLRMAVTRQFPWAVQT




WYDSLGAINKIQDFLQKQEYKTLEYNLTTT




EVVMENVTAFWEEGFGELFEKAKQNNNNRK




TSNGDDSLFFSNFSLLGTPVLKDINFKIER




GQLLAVAGSTGAGKTSLLMVIMGELEPSEG




KIKHSGRISFCSQFSWIMPGTIKENIIGVS




YDEYRYRSVIKACQLEEDISKFAEKDNIVL




GEGGITLSGGQRARISLARAVYKDADLYLL




DSPFGYLDVLTEKEIFESCVCKLMANKTRI




LVTSKMEHLKKADKILILHEGSSYFYGTFS




ELQNLQPDFSSKLMGCDSFDQFSAERRNSI




LTETLHRFSLEGDAPVSWTETKKQSFKQTG




EFGEKRKNSILNPINSIRKFSIVQKTPLQM




NGIEEDSDEPLERRLSLVPDSEQGEAILPR




ISVISTGPTLQARRRQSVLNLMTHSVNQGQ




NIHRKTTASTRKVSLAPQANLTELDIYSRR




LSQETGLEISEEINEEDLKECFFDDMESIP




AVTTWNTYLRYITVHKSLIFVLIWCLVIFL




AEVAASLVVLWLLGNTPLQDKGNSTHSRNN




SYAVIITSTSSYYVFYIYVGVADTLLAMGF




FRGLPLVHTLITVSKILHHKMLHSVLQAPM




STLNTLKAGGILNRFSKDIAILDDLLPLTI




FDFIQLLLIVIGAIAVVAVLQPYIFVATVP




VIVAFIMLRAYFLQTSQQLKQLESEGRSPI




FTHLVTSLKGLWTLRAFGRQPYFETLFHKA




LNLHTANWFLYLSTLRWFQMRIEMIFVIFF




IAVTFISILTTGEGEGRVGIILTLAMNIMS




TLQWAVNSSIDVDSLMRSVSRVFKFIDMPT




EGKPTKSTKPYKNGQLSKVMIIENSHVKKD




DIWPSGGQMTVKDLTAKYTEGGNAILENIS




FSISPGQRVGLLGRTGSGKSTLLSAFLRLL




NTEGEIQIDGVSWDSITLQQWRKAFGVIPQ




KVFIFSGTFRKNLDPYEQWSDQEIWKVADE




VGLRSVIEQFPGKLDFVLVDGGCVLSHGHK




QLMCLARSVLSKAKILLLDEPSAHLDPVTY




QIIRRTLKQAFADCTVILCEHRIEAMLECQ




QFLVIEENKVRQYDSIQKLLNERSLFRQAI




SPSDRVKLFPHRNSSKCKSKPQIAALKEET




EEEVQDTRL









The amino acid of a V5-tagged J domain-CFTR (Δ508F) fusion protein is shown in the table below.







TABLE 31







Amino Acid Sequence of a V5-Tagged SV40 J Domain-CFTR(Δ508F)


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged, SV40
SEQ ID NO: 221
MGKPIPNPLLGLDSTGTGSEFMDKVLNREE


J domain-

SLQLMDLLGLERSAWGNIPLMRKAYLKKCK


CFTR(Δ508F)

EFHPDKGGDEEKMKKMNTLYKKMEDGVKYA


fusion protein

HQPDFGGFWDADIAAAMQRSPLEKASVVSK




LFFSWTRPILRKGYRQRLELSDIYQIPSVD




SADNLSEKLEREWDRELASKKNPKLINALR




RCFFWRFMFYGIFLYLGEVTKAVQPLLLGR




IIASYDPDNKEERSIAIYLGIGLCLLFIVR




TLLLHPAIFGLHHIGMQMRIAMFSLIYKKT




LKLSSRVLDKISIGQLVSLLSNNLNKFDEG




LALAHFVWIAPLQVALLMGLIWELLQASAF




CGLGFLIVLALFQAGLGRMMMKYRDQRAGK




ISERLVITSEMIENIQSVKAYCWEEAMEKM




IENLRQTELKLTRKAAYVRYFNSSAFFFSG




FFVVFLSVLPYALIKGIILRKIFTTISFCI




VLRMAVTRQFPWAVQTWYDSLGAINKIQDF




LQKQEYKTLEYNLTTTEVVMENVTAFWEEG




FGELFEKAKQNNNNRKTSNGDDSLFFSNFS




LLGTPVLKDINFKIERGQLLAVAGSTGAGK




TSLLMVIMGELEPSEGKIKHSGRISFCSQF




SWIMPGTIKENIIGVSYDEYRYRSVIKACQ




LEEDISKFAEKDNIVLGEGGITLSGGQRAR




ISLARAVYKDADLYLLDSPFGYLDVLTEKE




IFESCVCKLMANKTRILVTSKMEHLKKADK




ILILHEGSSYFYGTFSELQNLQPDFSSKLM




GCDSFDQFSAERRNSILTETLHRFSLEGDA




PVSWTETKKQSFKQTGEFGEKRKNSILNPI




NSIRKFSIVQKTPLQMNGIEEDSDEPLERR




LSLVPDSEQGEAILPRISVISTGPTLQARR




RQSVLNLMTHSVNQGQNIHRKTTASTRKVS




LAPQANLTELDIYSRRLSQETGLEISEEIN




EEDLKECFFDDMESIPAVTTWNTYLRYITV




HKSLIFVLIWCLVIFLAEVAASLVVLWLLG




NTPLQDKGNSTHSRNNSYAVIITSTSSYYV




FYIYVGVADTLLAMGFFRGLPLVHTLITVS




KILHHKMLHSVLQAPMSTLNTLKAGGILNR




FSKDIAILDDLLPLTIFDFIQLLLIVIGAI




AVVAVLQPYIFVATVPVIVAFIMLRAYFLQ




TSQQLKQLESEGRSPIFTHLVTSLKGLWTL




RAFGRQPYFETLFHKALNLHTANWFLYLST




LRWFQMRIEMIFVIFFIAVTFISILTTGEG




EGRVGIILTLAMNIMSTLQWAVNSSIDVDS




LMRSVSRVFKFIDMPTEGKPTKSTKPYKNG




QLSKVMIIENSHVKKDDIWPSGGQMTVKDL




TAKYTEGGNAILENISFSISPGQRVGLLGR




TGSGKSTLLSAFLRLLNTEGEIQIDGVSWD




SITLQQWRKAFGVIPQKVFIFSGTFRKNLD




PYEQWSDQEIWKVADEVGLRSVIEQFPGKL




DFVLVDGGCVLSHGHKQLMCLARSVLSKAK




ILLLDEPSAHLDPVTYQIIRRTLKQAFADC




TVILCEHRIEAMLECQQFLVIEENKVRQYD




SIQKLLNERSLFRQAISPSDRVKLFPHRNS




SKCKSKPQIAALKEETEEEVQDTRL


 


V5 epitope
residues 1-15
MGKPIPNPLLGLDST


domain
of SEQ ID



NO: 221


 


Linker
residues 16-21
GTGSEF



of SEQ ID



NO: 221


 


SV40 J domain
residues 22-101
MDKVLNREESLQLMDLLGLERSAWGNIPLM



of SEQ ID
RKAYLKKCKEFHPDKGGDEEKMKKMNTLYK



NO: 221
KMEDGVKYAHQPDFGGFWDA


 


Linker
residues 102-106
DIAAA



of SEQ ID



NO: 221


 


CFTR(Δ508F)
residues 107-1585
MQRSPLEKASVVSKLFFSWTRPILRKGYRQ



of SEQ ID
RLELSDIYQIPSVDSADNLSEKLEREWDRE



NO: 221
LASKKNPKLINALRRCFFWRFMFYGIFLYL




GEVTKAVQPLLLGRIIASYDPDNKEERSIA




IYLGIGLCLLFIVRTLLLHPAIFGLHHIGM




QMRIAMFSLIYKKTLKLSSRVLDKISIGQL




VSLLSNNLNKFDEGLALAHFVWIAPLQVAL




LMGLIWELLQASAFCGLGFLIVLALFQAGL




GRMMMKYRDQRAGKISERLVITSEMIENIQ




SVKAYCWEEAMEKMIENLRQTELKLTRKAA




YVRYFNSSAFFFSGFFVVFLSVLPYALIKG




IILRKIFTTISFCIVLRMAVTRQFPWAVQT




WYDSLGAINKIQDFLQKQEYKTLEYNLTTT




EVVMENVTAFWEEGFGELFEKAKQNNNNRK




TSNGDDSLFFSNFSLLGTPVLKDINFKIER




GQLLAVAGSTGAGKTSLLMVIMGELEPSEG




KIKHSGRISFCSQFSWIMPGTIKENIIGVS




YDEYRYRSVIKACQLEEDISKFAEKDNIVL




GEGGITLSGGQRARISLARAVYKDADLYLL




DSPFGYLDVLTEKEIFESCVCKLMANKTRI




LVTSKMEHLKKADKILILHEGSSYFYGTFS




ELQNLQPDFSSKLMGCDSFDQFSAERRNSI




LTETLHRFSLEGDAPVSWTETKKQSFKQTG




EFGEKRKNSILNPINSIRKFSIVQKTPLQM




NGIEEDSDEPLERRLSLVPDSEQGEAILPR




ISVISTGPTLQARRRQSVLNLMTHSVNQGQ




NIHRKTTASTRKVSLAPQANLTELDIYSRR




LSQETGLEISEEINEEDLKECFFDDMESIP




AVTTWNTYLRYITVHKSLIFVLIWCLVIFL




AEVAASLVVLWLLGNTPLQDKGNSTHSRNN




SYAVIITSTSSYYVFYIYVGVADTLLAMGF




FRGLPLVHTLITVSKILHHKMLHSVLQAPM




STLNTLKAGGILNRFSKDIAILDDLLPLTI




FDFIQLLLIVIGAIAVVAVLQPYIFVATVP




VIVAFIMLRAYFLQTSQQLKQLESEGRSPI




FTHLVTSLKGLWTLRAFGRQPYFETLFHKA




LNLHTANWFLYLSTLRWFQMRIEMIFVIFF




IAVTFISILTTGEGEGRVGIILTLAMNIMS




TLQWAVNSSIDVDSLMRSVSRVFKFIDMPT




EGKPTKSTKPYKNGQLSKVMIIENSHVKKD




DIWPSGGQMTVKDLTAKYTEGGNAILENIS




FSISPGQRVGLLGRTGSGKSTLLSAFLRLL




NTEGEIQIDGVSWDSITLQQWRKAFGVIPQ




KVFIFSGTFRKNLDPYEQWSDQEIWKVADE




VGLRSVIEQFPGKLDFVLVDGGCVLSHGHK




QLMCLARSVLSKAKILLLDEPSAHLDPVTY




QIIRRTLKQAFADCTVILCEHRIEAMLECQ




QFLVIEENKVRQYDSIQKLLNERSLFRQAI




SPSDRVKLFPHRNSSKCKSKPQIAALKEET




EEEVQDTRL









To study the expression of the various CFTR protein constructs, the plasmids were transfected to HEK293 cells. Samples of cell lysates from two-day cultures of transfected cells were analyzed by immunoblotting with anti-V5 antibody. As shown in FIG. 8B, neither the wild-type CFTR protein nor the mutant CFTR (Δ508F) protein expressed well in transfected cells. Fusion of either protein with a BAG3 domain (BAG-CFTR WT, BAG-CFTR Δ508F) provided some enhancement of expression. In contrast, fusion with a J domain significantly enhanced the level of expression of both wild-type and mutant proteins (J-CFTR WT, J-CFTR Δ508F). See, FIG. 8B
Conclusion of Results
The results of the above experiments clearly show that fusion with a J domain significantly enhances the level of expression of a protein of interest, including therapeutically useful proteins.
Example 3. Compositions and Methods for Enhancing Expression of Target Proteins of Interest Using an Unmodified Arrangement
Expression vector plasmids were constructed for expressing fusion proteins for enhancing expression of specific proteins (target proteins). As described below, fusion proteins were usually linked to a standard epitope tag for easy identification or isolation using a corresponding anti-tag antibody and standard immunoblot (such as dot blot, Western blot) assays.
A DNA linker molecule having a nucleotide sequence containing various restriction enzyme sites for cloning heterologous DNA molecules was produced by annealing two single-stranded DNA molecules having the sequences shown below (5′ to 3′):







(SEQ ID NO: 187)







AGCTTGGTACCGGATCCGAATTCGATATCGCGGCCGCTCTCGAGTCTA


 


GAGGGCC


and


 







(SEQ ID NO: 188)







CTCTAGACTCGAGAGCGGCCGCGATATCGAATTCGGATCCGGTACCA.






The annealed linker molecule was then inserted into plasmid pcDNA3 (catalogue no. V790-20, Invitrogen) digested with HindIII and ApaI downstream of a CMV promoter to yield the expression vector plasmid pcDNA′ for use in mammalian host cells.

DNA molecules encoding the V5 epitope tag (GKPIPNPLLGLDST; SEQ ID NO:110) or the Flag epitope tag (DYKDDDDK; SEQ ID NO:111) were synthesized and inserted into plasmid pcDNA′ digested with HindIII and KpnI. A double-stranded DNA molecule having the coding sequence for the V5 epitope tag with an N-terminal methionine, i.e., ATGGGTAAGCCTATCCCTAACCCTCTCCTCGGTCTCGATTCTACG (SEQ ID NO:189), was inserted into pcDNA′ digested with XhoI and XbaI to yield plasmid V5-pcDNA′.
A DNA molecule having the coding sequence for the Flag epitope tag, i.e., GATTACAAGGATGACGATGACAAG (SEQ ID NO:190), was inserted into plasmid pcDNA′ digested with XhoI and XbaI to yield plasmid Flag-pcDNA′.
To express IL13Rα2 receptor protein, a DNA molecule encoding an IL13Rα2 receptor protein was inserted into plasmid V5-pcDNA′ digested with HindIII and KpnI.
To express TNR1 receptor protein, a DNA molecule encoding a TNRI receptor protein was inserted into plasmid V5-pcDNA′ digested with HindIII and KpnI.
To express α1 anti-trypsin (“α1AT”), a DNA molecule encoding an α1 anti-trypsin was inserted into plasmid V5-pcDNA′ digested with HindIII and KpnI.
A DNA molecule encoding an Fc region polypeptide of a human IgG1 molecule was synthesized and inserted into V5-pcDNA′ digested with XbaI and ApaI.
Unless indicated otherwise, a DNA molecule encoding a particular protein expression enhancing polypeptide was cloned into plasmid Flag-pcDNA′ digested with EcoRI and EcoRV to insert a DNA segment encoding the J domain of an Erdj3 J protein, or digested with KpnI and BamHI to insert a DNA segment encoding the J domain of an Erdj5 J protein, to yield plasmid (J domain)-Flag-pcDNA′, wherein “(J domain)” refers to the particular protein expression enhancing polypeptide specified in the examples below.
Unless indicated otherwise, each DNA molecule encoding a target binding domain for a corresponding target protein in the examples below was inserted into plasmid Flag-pcDNA′ digested with NotI and XhoI.
Expression and Detection of Target Proteins in HEK293 Cells
Expression vector plasmids encoding various protein constructs were transfected into HEK293 cells with X-tremeGENE HP transfection reagent (catalogue no. 06365752001, Roche). As indicated in the examples below, a separate plasmid expressing the green fluorescent protein (GFP) was co-transfected with each expression vector plasmid encoding a fusion protein of the invention to monitor the transfection efficiency. Cultures of transfectant cells were incubated for two days, and cells were lysed in lysis buffer (10 mM Tris-HCl, pH8.0, 150 mM NaCl, 10 mM EDTA, 2% SDS) containing 2 mM PMSF. After brief sonication, the sample was analyzed for express proteins using dot blot or Western immunoblot assays. For Western blot analysis, samples were boiled in SDS-sample buffer and run on polyacrylamide electrophoresis, followed by transfer of separated protein bands to membrane (PVDF membrane). The expression of GFP as an internal transfection control was detected using an anti-GFP antibody.
Expressed proteins in dot and Western blots were detected using a chemiluminescent signal. Briefly, blots were reacted with a primary antibody that binds the particular epitope tag (e.g., V5 or Flag) carried by the proteins. After rinsing away unreacted primary antibody, a secondary, enzyme-linked antibody (e.g., horse radish peroxidase linked anti-IgG antibody) was allowed to react with primary antibody molecules bound to the blots. After rinsing, manufacturer's chemiluminescent reagent was added. Chemiluminescent signals in blots were captured on x-ray film. Where indicated, the images of the chemiluminescent signals were scanned with a densitometer and analyzed using the NIH ImageJ image processing program.
Cells expressing humanized anti-IL-8 antibody (CHO DP-12 clone, clone No. 1933; catalog No. CRL-12444) and plasmid p6G425V11N35A.choSD (catalog No. 209552) were purchased from the American Type Culture Collection (Manassas, Va.).
Example 4. Enhanced Expression of Secreted IL13Rα2TF Protein in an Unmodified Arrangement
The IL13 receptor, IL13Rα2 is a membrane protein that binds to interleukin-13 (IL13) and mediates allergic inflammation. The IL13Rα2 receptor protein is known to be an unstable protein in a mammalian cell due to the difficulties of protein folding (Genetic Engineering & Biotechnology News, 28(5) (2008)). Part of the expressed IL13Rα2 proteins is digested on the cell surface and shed into the extracellular space. This truncated form of IL13Rα2 (also referred to as “IL13Rα2TF”) still possesses the ability to bind IL13, but cannot transmit a signal to the cell owing to the absence of transmembrane and cytoplasmic regions of the full-length IL13Rα2 protein. Therefore, the truncated form of IL13Rα2 has been used as a type of decoy receptor to treat asthma by binding IL13 molecules without transducing a signal to the cell to set off an inflammatory response (Zhang, et al., J. Biol. Chem., 272(14): 9474-80 (1997)). A genetically engineered truncated form of IL13Rα2 has been expressed in bacteria, however the protein aggregated into inclusion bodies, from which the protein was purified (Tang et al., Molec. Immunol. 39: 719-727 (2003)). However, it is known that one limitation to the expression of the IL13Rα2TF protein by transfected cells has been ascribed to inefficient folding of into their proper functional conformations. When proteins cannot fold into their proper conformation they are ushered to the proteasome for degradation and scavenging of amino acids. Accordingly, production of IL13Rα2TF molecules in transfected cells has recognized attendant limitations of expression and secretion of the protein (Lee et al., Cell Technol. for Cell Products, 29-39 (2007)).
This experiment studied the enhancement in the level of and secretion of the IL13Rα2TF protein using an alternative arrangement to the “modified” arrangement described in Examples 1-3 in which a target protein of interest is modified by fusion to a protein expression enhancing polypeptide of the invention. In an “unmodified” arrangement, a target protein of interest is “unmodified” in that it is not fused to a protein expression enhancing polypeptide of the invention, but instead is co-expressed with a fusion protein comprising a protein expression enhancing polypeptide linked to a target protein binding domain. FIG. 9A shows a schematic diagram of this unmodified arrangement for enhancing expression of a target protein of interest. According to this scheme, a target protein of interest is bound by a target protein binding domain of the fusion protein, which also comprises a protein expression enhancing polypeptide domain. Presumably, binding of the target protein to the fusion protein brings the target protein into close proximity to the protein expression enhancing polypeptide domain, which in turn leads to enhanced expression of the target protein of interest.
FIG. 9B shows a diagram of a nucleic acid construct in which a cDNA encoding an IL13Rα2TF protein is augmented at its 3′ end with a nucleic acid encoding a V5 epitope tag. FIG. 9C shows a diagram of a nucleic acid construct for a fusion protein of the invention. For this experiment, the fusion protein according to the invention comprised a J domain of the Erdj3 J protein as a protein expression enhancing polypeptide linked to an IL13 protein as a target binding domain.
The amino acid sequence of the V5-tagged IL13Rα2TF protein is shown in the table below.







TABLE 32







Amino Acid Sequence of a V5-Tagged IL13Rα2TF Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged
SEQ ID NO: 222
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


IL13Rα2TF

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD


protein

HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKGTGSEFDIAAALEGKPIPNPL




LGLDSTSRGPYSIVSPKC


 


IL13Rα2TF
residues 1-339
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI



of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 222
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKK


 


Linker
residues 340-352
GTGSEFDIAAALE



of SEQ ID



NO: 222


 


V5 epitope
residues 353-366
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 222


 


C-terminal
residues 367-378
SRGPYSIVSPKC


vector residues
of SEQ ID



NO: 222









The amino acid sequence of the IL13 protein as used in this experiment included a Flag epitope tag, a signal sequence, and 13 additional C-terminal amino acid residues from the expression vector used to express the protein as shown in the table below.







TABLE 33







Amino Acid Sequence of a Flag-Tagged IL13 Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 223
MGVKVLFALICIAVAEAGTGSEFDIAAALT


IL13 protein

CLGGFASPGPVPPSTALRELIEELVNITQN




QKAPLCNGSMVWSINLTAGMYCAALESLIN




VSGCSAIEKTQRMLSGFCPHKVSAGQFSSL




HVRDTKIEVAQFVKDLLLHLKKLFREGQFN




LEGDYKDDDDKGSRGPYSIVSPKC


 


Signal Sequence
residues 1-17
MGVKVLFALICIAVAEA



of SEQ ID



NO: 223


 


Linker
residues 18-28
GTGSEFDIAAA



of SEQ ID



NO: 223


 


IL13
residues 29-150
LTCLGGFASPGPVPPSTALRELIEELVNIT



of SEQ ID
QNQKAPLCNGSMVWSINLTAGMYCAALESL



NO: 223
INVSGCSAIEKTQRMLSGFCPHKVSAGQFS




SLHVRDTKIEVAQFVKDLLLHLKKLFREGQ




FN


 


Linker
residues 151-153
LEG



of SEQ ID



NO: 223


 


Flag epitope
residues 154-161
DYKDDDDK


domain
of SEQ ID



NO: 223


 


C-terminal
residues 162-174
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 223









The amino acid sequence of a J domain-IL13 fusion protein included a Flag epitope tag as shown in the table below.







TABLE 34







Amino Acid Sequence of a Flag-Tagged Erdj3 J Domain-IL13


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 224
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


J domain-IL13

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


fusion protein

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG




GSGGSGGAAALTCLGGFASPGPVPPSTALR




ELIEELVNITQNQKAPLCNGSMVWSINLTA




GMYCAALESLINVSGCSAIEKTQRMLSGFC




PHKVSAGQFSSLHVRDTKIEVAQFVKDLLL




HLKKLFREGQFNLEGDYKDDDDKGSRGPYS




IVSPKC


 


Erdj3 J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL



of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 224
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DIGGGSGGSGGSGGAAA



of SEQ ID



NO: 224


 


IL13
residues 101-222
LTCLGGFASPGPVPPSTALRELIEELVNIT



of SEQ ID
QNQKAPLCNGSMVWSINLTAGMYCAALESL



NO: 224
INVSGCSAIEKTQRMLSGFCPHKVSAGQFS




SLHVRDTKIEVAQFVKDLLLHLKKLFREGQ




FN


 


Linker
residues 223-225
LEG



of SEQ ID



NO: 224


 


Flag epitope
residues 226-233
DYKDDDDK


domain
of SEQ ID



NO: 224


 


C-terminal
residues 234-246
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 224









HEK293 cells were co-transfected with expression vectors for expressing the V5-tagged IL13Rα2TF and for expressing the J domain-IL13 fusion protein. Transfected cells were cultured for two days, and cell lysates and samples of cell media were harvested and analyzed by Western blot (immunoblot) assay using an anti-V5 antibody to detect secreted V5-tagged IL13Rα2TF. As shown in FIG. 10, cells transfected with an expression vector for expressing the IL13Rα2TF protein alone expressed some protein in the cells (middle panel, lane 2, from the left) but only a very little, if any, IL13Rα2TF protein was detected in culture medium (top panel, lane 2, from the left). Co-expression of the IL13Rα2TF protein and its IL13 protein ligand resulted in some detectable expression of IL13Rα2TF protein in the transfected cells (middle panel, lane 3, from the left) and in culture medium (top panel, lane 3, from the left). This result is consistent with earlier reports that co-expression of IL13Rα2TF with its IL13 ligand improves secretion of the IL13Rα2TF (Lee et al., Cell Technol. for Cell Products, 29-39 (2007)). However, co-expression IL13Rα2TF with a J domain-IL13 fusion protein according to the invention further enhanced the level of expression of IL13Rα2TF within the cells (middle panel, lane 4, from the left) and dramatically enhanced the level of expression of secreted IL13Rα2TF protein (top panel, lane 4, from the left) as compared to expression of IL13Rα2TF alone (top panel, lane 2, from the left) or co-expression of IL13Rα2TF and IL13 ligand (top panel, lane 3, from the left). The results indicate that both stability and secretion of the IL13Rα2TF protein were improved by co-expression with a J domain-IL13 fusion protein of the invention.
Example 5. Enhanced Expression of Secreted IL13Rα2TF-Fc Fusion Protein in an Unmodified Arrangement
As noted above, a truncated form of IL13Rα2 (IL13Rα2TF) comprises the extracellular domain of the IL13Rα2 receptor protein, including a functional IL13 ligand binding domain. However, the production of IL13Rα2TF is also inefficient owing to difficulties in expression and secretion of the protein. One strategy that has been employed to generate more stable forms of therapeutically relevant proteins, and especially receptor proteins, is to prepare a fusion protein in which all or a functional portion of a protein of interest is linked to the constant domains of an immunoglobulin Fc domain. Such an Fc fusion protein format has been used to design a family of potentially useful drugs that provide a desired therapeutically relevant activity and, owing to the Fc domain, also exhibit an increased in vivo serum half-life, which in turn should reduce dosing frequencies. Within such Fc fusion proteins, a “protein of interest” domain (for example, the extracellular, ligand-binding domain of a receptor protein) retains its desired functional property (for example, ligand binding).
This experiment examined the effect on the level of expression of an Fc fusion protein (target protein) when the Fc fusion protein was co-expressed with a fusion protein of the invention in an unmodified arrangement. An IL13Rα2TF-Fc fusion protein was used as a representative example of an Fc fusion protein drug. The IL13Rα2TF-Fc fusion protein also possessed a V5 epitope tag between the IL13Rα2TF (“protein of interest”) domain and the Fc domain for easy identification with an anti-V5 epitope antibody. See, an illustration of a DNA construct for the IL13Rα2TF-Fc fusion protein in FIG. 11A. For this experiment, examples of fusion proteins according to the invention comprised a J domain of a J protein as a protein expression enhancing polypeptide domain linked to Protein A, which binds immunoglobulin Fc domains, as a target binding domain. See, FIG. 11B.
The amino acid sequence for the V5-tagged IL13Rα2TF-Fc fusion protein used in this experiment is shown in the table below.







TABLE 35







Amino Acid Sequence of a V5-Tagged IL13Rα2TF-Fc


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged
SEQ ID NO: 225
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


IL13Rα2TF-Fc

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD


fusion protein

HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKGTGSEFDIAAALEGKPIPNPL




LGLDSTSRPKSCDKTHTCPPCPAPELLGGP




SVFLFPPKPKDTLMISRTPEVTCVVVDVSH




EDPEVKFNWYVDGVEVHNAKTKPREEQYNS




TYRVVSVLTVLHQDWLNGKEYKCKVSNKAL




PAPIEKTISKAKGQPREPQVYTLPPSRDEL




TKNQVSLTCLVKGFYPSDIAVEWESNGQPE




NNYKTTPPVLDSDGSFFLYSKLTVDKSRWQ




QGNVFSCSVMHEALHNHYTQKSLSLSPGK


 


IL13Rα2TF
residues 1-339
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI



of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 225
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKK


 


Linker
residues 340-352
GTGSEFDIAAALE



of SEQ ID



NO: 225


 


V5 epitope
residues 353-366
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 225


 


Linker
residues 367-368
SR



of SEQ ID



NO: 225


 


Fc domain
residues 369-599
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 225
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









In one aspect of this experiment, the level of expression of an IL13Rα2TF-Fc fusion protein was examined when co-expressed with a Protein A molecule. The Protein A molecule was tagged with a Flag epitope tag for easy identification with a standard anti-Flag antibody. The amino acid sequence for a Flag-tagged Protein A is shown in the table below.







TABLE 36







Amino Acid Sequence of a Flag-Tagged Protein A.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 226
MGVKVLFALICIAVAEAGTGSEFDIAAAAD


Protein A

NKFNKEQQNAFYEILNMPNLNEEQRNGFIQ


protein

SLKDDPSQSANVLGEAKKLNDSQAPKLEGD




YKDDDDKGSRGPYSIVSPKC


 


Signal Sequence
residues 1-17
MGVKVLFALICIAVAEA



of SEQ ID



NO: 226


 


Linker
residues 18-28
GTGSEFDIAAA



of SEQ ID



NO: 226


 


Protein A
residues 29-86
ADNKFNKEQQNAFYEILNMPNLNEEQRNGF



of SEQ ID
IQSLKDDPSQSANVLGEAKKLNDSQAPK



NO: 226


 


Linker
residues 87-89
LEG



of SEQ ID



NO: 226


 


Flag epitope
residues 90-97
DYKDDDDK


domain
of SEQ ID



NO: 226


 


C-terminal
residues 98-110
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 226









An example of a fusion protein for enhancing expression of the IL13Rα2TF-Fc fusion protein possessed the J domain from the Erdj3 protein linked to Protein A. A Flag epitope tag was linked to the C-terminus of the Protein A domain. See illustration of DNA construct in FIG. 11B. The amino acid sequence for the J domain-Protein A fusion protein is shown in the table below.







TABLE 37







Amino Acid Sequence of a Flag-Tagged Erdj3 J domain-Protein A


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 227
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


Protein A fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAAADNKFNKEQQNAFYEILNMP




NLNEEQRNGFIQSLKDDPSQSANVLGEAKK




LNDSQAPKLEGDYKDDDDKGSRGPYSIVSP




KC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 227
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DIGGGSGGSGGSGGAAA



of SEQ ID



NO: 227


 


Protein A
residues 101-158
ADNKFNKEQQNAFYEILNMPNLNEEQRNGF



of SEQ ID
IQSLKDDPSQSANVLGEAKKLNDSQAPK



NO: 227


 


Linker
residues 159-161
LEG



of SEQ ID



NO: 227


 


Flag epitope
residues 162-169
DYKDDDDK


domain
of SEQ ID



NO: 227


 


C-terminal
residues 170-182
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 227









Another example of a fusion protein for enhancing expression of the IL13Rα2TF-Fc fusion protein possessed the J domain from the Erdj5 protein linked to Protein A. A Flag epitope tag was linked to the C-terminus of the Protein A domain. See illustration of DNA construct in FIG. 11B. The amino acid sequence for the Flag-tagged Erdj5 J domain-Protein A fusion protein is shown in the table below.







TABLE 38







Amino Acid Sequence of a Flag-Tagged Erdj5 J domain-Protein A


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 228
MGVWLNKDDYIRDLKRIILCFLIVYMAILV


Erdj5 J domain-

GTDQDFYSLLGVSKTASSREIRQAFKKLAL


Protein A fusion

KLHPDKNPNNPNAHGDFLKINRAYEVLKDE


protein

DGSEFDIGGGSGGSGGSGGAAAADNKFNKE




QQNAFYEILNMPNLNEEQRNGFIQSLKDDP




SQSANVLGEAKKLNDSQAPKLEGDYKDDDD




KGSRGPYSIVSPKC


 


J domain
residues 1-91
MGVWLNKDDYIRDLKRIILCFLIVYMAILV


(from Erdj5)
of SEQ ID
GTDQDFYSLLGVSKTASSREIRQAFKKLAL



NO: 228
KLHPDKNPNNPNAHGDFLKINRAYEVLKDE




D


 


Linker
residues 92-112
GSEFDIGGGSGGSGGSGGAAA



of SEQ ID



NO: 228


 


Protein A
residues 113-170
ADNKFNKEQQNAFYEILNMPNLNEEQRNGF



of SEQ ID
IQSLKDDPSQSANVLGEAKKLNDSQAPK



NO: 228


 


Linker
residues 171-173
LEG



of SEQ ID



NO: 228


 


Flag epitope
residues 174-181
DYKDDDDK


domain
of SEQ ID



NO: 228


 


C-terminal
residues 182-194
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 228









HEK293 cells were transfected with expression vector plasmids to compare levels of expression in culture medium of IL13Rα2TF-Fc fusion protein expressed alone, IL13Rα2TF-Fc fusion protein co-expressed with Protein A (“Protein A Only”), IL13Rα2TF-Fc fusion protein co-expressed with the Erdj3 J domain-Protein A fusion protein (“J-Protein A”), and IL13Rα2TF-Fc fusion protein co-expressed with the Erdj5 J domain-Protein A fusion protein (“J2-Protein A”). Transfected cells were cultured for two days, and samples of cell media were harvested and analyzed by Western blot (immunoblot) assay using an anti-V5 antibody to detect secreted V5-tagged IL13Rα2TF-Fc fusion protein. FIG. 12A shows x-ray film images of chemiluminescent signals of the Western blot analysis of culture media. Lane 1 of FIG. 12A is culture medium of a “mock” culture of cells transfected with expression vector lacking a structural gene for expressing any protein (empty vector). When expressed alone (lane 2), some IL13Rα2TF-Fc fusion protein was detected in the medium. As shown in lane 3 of the FIG. 12A, co-expression with Protein A (Protein A Only) provided no significant enhancement in the level of IL13Rα2TF-Fc fusion protein secreted to the medium. However, co-expression with the either J domain-Protein A fusion protein significantly enhanced the level of expression of IL13Rα2TF-Fc fusion protein secreted into the medium (lanes 4 and 5 of FIG. 12A). Importantly, the fact that co-expression of IL13Rα2TF-Fc with Protein A alone did not affect the secretion of IL13Rα2TF-Fc (lane 3) indicates that: (1) the J domain of a J domain-Protein A fusion protein is essential for enhancing the level of expression of secreted IL13Rα2TF-Fc and (2) the Protein A domain of the J domain-Protein A fusion protein is essential for providing the target specificity for enhancing the level of expression of the secreted IL13Rα2TF-Fc target protein.
The results of a densitometry analysis of the chemiluminescent signals in the lanes of FIG. 12A using the NIH ImageJ image processing program are shown in the respective bar graphs in FIG. 12B. The bar graphs in FIG. 12B clearly show that co-expression of IL13Rα2TF-Fc with either J domain-Protein A fusion protein (bar graphs 4 and 5) significantly enhanced the level of expression of secreted IL13Rα2TF-Fc as compared to expression of IL13Rα2TF-Fc alone (bar graph 2) or co-expression of IL13Rα2TF-Fc with Protein A alone (bar graph 3).
That the enhanced level of expression of secreted IL13Rα2TF-Fc protein in FIGS. 12A and 12B was dependent on the specificity of the target binding domain of the J domain-Protein A fusion protein for the Fc domain is supported by the results shown in FIG. 12C. As shown in the Western blot analysis of culture media in FIG. 12C, no significant expression of secreted IL13Rα2TF (no Fc domain) was detected in culture media when transfected cells expressed the IL13Rα2TF protein alone (lane 1), co-expressed the IL13Rα2TF protein with the J-Protein A fusion protein (lane 2), or co-expressed the IL13Rα2TF protein with Protein A alone (Protein A Only, lane 3). The results of a densitometry analysis of the chemiluminescent signals in the lanes of FIG. 12C using the NIH ImageJ image processing program are shown in the respective bar graphs in FIG. 12D.
Example 6. Enhanced Expression of an Additional Secreted Fc Fusion Proteins in an Unmodified Arrangement
A series of experiments were performed to test and compare the effectiveness of a J domain-Protein A fusion protein of the invention to enhance several different Fc fusion proteins. The results are of a Western blot analysis of culture media from cultures of transfected cells are shown in FIG. 13.
Example 6.1. Enhanced Expression of a Secreted IL13Rα2TF-Fc Fusion Protein
Consistent with above results in Example 5, co-expression of the IL13Rα2TF-Fc protein with the Erdj3 J domain-Protein A fusion protein in transfected cells significantly enhanced the level of expression of IL13Rα2TF-Fc protein secreted into the culture medium (see, lane 2 of FIG. 13A-1) as compared to that observed for transfected cells expressing the IL13Rα2TF-Fc protein alone (lane 1 of FIG. 13A-1). The significant enhancement in the level of expression of secreted IL13Rα2TF-Fc protein is also clear from the results of a densitometry analysis of the chemiluminescent signals in FIG. 13A-1 using the NIH ImageJ image processing program are shown in the respective bar graphs in FIG. 13A-2.
Example 6.2. Enhanced Expression of a Secreted TNFRITF-Fc Fusion Protein
Tumor necrosis factor-α (TNF-α) is a major cytokine that binds the TNF-α receptor (TNFR1) and induces an inflammatory response that is involved in a number of autoimmune diseases, such as rheumatoid arthritis, Crohn's disease, and psoriasis. The truncated protein of the TNF-α receptor (TNFR1TF) is used as a decoy receptor to bind to TNF-α and thereby inhibit TNF-α activity. Etanercept (commercially available as ENBREL®, Amgen) is a TNF-α blocker in which a truncated form of TNFR is fused to an Fc domain (TNFR1TF-Fc). The TNFR1TF domain of the molecule provides the desired TNF-α binding specificity, and the immunoglobulin Fc domain is believed to add in vivo stability to the drug circulating in a patient.
The TNFR1TF-Fc fusion target protein used in this experiment also possessed a V5 epitope tag between the TNFR1 and Fc domains. The amino acid sequence for the TNFR1TF-Fc fusion protein used in this experiment is shown in the table below.







TABLE 39







Amino Acid Sequence of TNFR1TF-Fc Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged
SEQ ID NO: 229
MGLSTVPDLLLPLVLLELLVGIYPSGVIGL


TNFR1TF protein

VPHLGDREKRDSVCPQGKYIHPQNNSICCT




KCHKGTYLYNDCPGPGQDTDCRECESGSFT




ASENHLRHCLSCSKCRKEMGQVEISSCTVD




RDTVCGCRKNQYRHYWSENLFQCFNCSLCL




NGTVHLSCQEKQNTVCTCHAGFFLRENECV




SCSNCKKSLECTKLCLPQIENVKGTEDSGT




TGTGSEFDIAAALEGKPIPNPLLGLDSTSR




PKSCDKTHTCPPCPAPELLGGPSVFLFPPK




PKDTLMISRTPEVTCVVVDVSHEDPEVKFN




WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK


 


TNFRITF
residues 1-211
MGLSTVPDLLLPLVLLELLVGIYPSGVIGL



of SEQ ID
VPHLGDREKRDSVCPQGKYIHPQNNSICCT



NO: 229
KCHKGTYLYNDCPGPGQDTDCRECESGSFT




ASENHLRHCLSCSKCRKEMGQVEISSCTVD




RDTVCGCRKNQYRHYWSENLFQCFNCSLCL




NGTVHLSCQEKQNTVCTCHAGFFLRENECV




SCSNCKKSLECTKLCLPQIENVKGTEDSGT




T


 


Linker
residues 212-224
GTGSEFDIAAALE



of SEQ ID



NO: 229


 


V5 epitope
residues 225-238
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 229


 


Linker
residues 239-240
SR



of SEQ ID



NO: 229


 


Fc domain
residues 241-471
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 229
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









FIG. 13B-1 shows x-ray film images of chemiluminescent signals of a Western blot analysis of culture media from transfected cells expressing TNFR1TF-Fc fusion protein alone (lane 1) or co-expressing TNFR1TF-Fc fusion protein and the Erdj3 J domain-Protein A fusion protein described above (lane 2). The results show a significant enhancement in the level of expression of secreted TNFR1TF-Fc fusion protein in transfected cells co-expressing TNFR1TF-Fc fusion protein and the Erdj3 J domain-Protein A fusion protein as compared to the level of TNFR1TF-Fc fusion protein expressed in the absence of the J domain-Protein A fusion protein. The significant enhancement in the level of expression of secreted TNFR1TF-Fc fusion protein is also clear from the results of a densitometry analysis of the signals in the lanes in FIG. 13B-1 using the NIH ImageJ image processing program as shown in the respective bar graphs in FIG. 13B-2.
Example 6.3. Enhanced Expression of a Secreted α1AT-Fc Fusion Protein
The α1 anti-trypsin protein (α1AT) is secreted from the liver into the circulatory system. The function of α1AT is to protect tissues, particularly lung tissue, from excessive protease activities. The lung tissue of patients with α1 anti-trypsin deficiency can become severely damaged by proteases. Such patients may develop emphysema, asthma, and/or chronic obstructive pulmonary disease (COPD). Currently α1AT (purified from human serum) is used for the treatment of patients with α1 anti-trypsin deficiency. This treatment is expensive, and patients that receive the purified α1AT may be at risk of contracting pathogens present in the human serum.
The target α1AT-Fc fusion protein used in this experiment also possessed a V5 epitope tag between the α1AT and Fc domains. The amino acid sequence for the α1AT-Fc fusion protein (α1AT-Fc) used in this experiment is shown in the table below.







TABLE 40







Amino Acid Sequence of a V5-Tagged α1AT-Fc Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged α1AT-
SEQ ID NO: 230
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD


Fc fusion

AAQKTDTSHHDQDHPTFNKITPNLAEFAFS


protein

LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQKGT




GSEFDIAAALEGKPIPNPLLGLDSTSRPKS




CDKTHTCPPCPAPELLGGPSVFLFPPKPKD




TLMISRTPEVTCVVVDVSHEDPEVKFNWYV




DGVEVHNAKTKPREEQYNSTYRVVSVLTVL




HQDWLNGKEYKCKVSNKALPAPIEKTISKA




KGQPREPQVYTLPPSRDELTKNQVSLTCLV




KGFYPSDIAVEWESNGQPENNYKTTPPVLD




SDGSFFLYSKLTVDKSRWQQGNVFSCSVMH




EALHNHYTQKSLSLSPGK


 


α1AT
residues 1-418
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD



of SEQ ID
AAQKTDTSHHDQDHPTFNKITPNLAEFAFS



NO: 230
LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDEKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQK


 


Linker
residues 419-431
GTGSEFDIAAALE



of SEQ ID



NO: 230


 


V5 epitope
residues 432-445
GKPIPNPLLGLDST


domain
of SEQ ID



NO: 230


 


Linker
residues 446-447
SR



of SEQ ID



NO: 230


 


Fc domain
residues 448-678
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 230
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









FIG. 13C-1 shows X-ray film images of chemiluminescent signals of a Western blot analysis of culture media from transfected cells expressing α1AT-Fc fusion protein alone (lane 1) or co-expressing α1AT-Fc fusion protein and the Erdj3 J domain-Protein A fusion protein described above (lane 2). The results show a significant enhancement in the level of secreted α1AT-Fc fusion protein (lane 2) as compared to the level of α1AT-Fc fusion protein expressed in the absence of the J domain-Protein A fusion protein (lane 1). The significant enhancement in the level of expression of secreted α1AT-Fc fusion protein is also clear from the results of a densitometry analysis of the signals in the lanes in FIG. 13C-1 using the NIH ImageJ image processing program as shown in the respective bar graphs in FIG. 13C-2.
Example 7. Enhancement of Expression of Secreted IgG1 Antibody Molecules in an Unmodified Arrangement
The above studies showed that expression and secretion of Fc-fusion proteins were significantly enhanced by co-expression of a J domain-Protein A fusion protein. Protein A is a well-known example of a protein that binds to immunoglobulin Fc regions. This study examined whether fusion of other proteins that are known to bind immunoglobulin domains with a J domain of a J protein can enhance the expression level of a secreted target antibody.
In this study, a humanized IgG1 anti-IL8 antibody was used as a target antibody protein. The expression levels of the secreted anti-IL8 antibody were examined in the presence and absence of various J domain fusion proteins as explained below.
In one aspect of this experiment, the level of expression of the anti-IL8 antibody was examined when co-expressed with a Protein A molecule, which is known to bind the immunoglobulin Fc domain. The Protein A molecule was the same Flag-tagged Protein A described in Example 5, above.
In another aspect of this experiment, the level of expression of the anti-IL8 antibody was examined when co-expressed with a Protein L molecule, which is known to bind antibody light chains. As with the Protein A molecule described above, the Protein L molecule used in this experiment was tagged with a Flag epitope tag for easy identification with a standard anti-Flag antibody. The amino acid sequence for a Flag-tagged Protein L is shown in the table below.







TABLE 41







Amino Acid Sequence of a Flag-Tagged Protein L.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 231
MGVKVLFALICIAVAEAGTGSEFDIAAAVT


Protein L

IKANLIFADGKTQTAEFKGTFEEATAEAYR


protein

YADLLAKENGEYTADLEDGGYTINIKFAKE




TPETPEEPKEELEGDYKDDDDKGSRGPYSI




VSPKC


 


Signal Sequence
residues 1-17
MGVKVLFALICIAVAEA



of SEQ ID



NO: 231


 


Linker
residues 18-28
GTGSEFDIAAA



of SEQ ID



NO: 231


 


Protein L
residues 29-101
VTIKANLIFADGKTQTAEFKGTFEEATAEA



of SEQ ID
YRYADLLAKENGEYTADLEDGGYTINIKFA



NO: 231
KETPETPEEPKEE


 


Linker
residues 102-104
LEG



of SEQ ID



NO: 231


 


Flag epitope
residues 105-112
DYKDDDDK


domain
of SEQ ID



NO: 231


 


C-terminal
residues 113-125
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 231









The amino acid sequence of an Erjd3 J domain-Protein L fusion protein included a Flag epitope tag as shown in the table below.







TABLE 42







Amino Acid Sequence of a Flag-Tagged Erdj3 J domain-Protein L


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 232
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


Protein L fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAAVTIKANLIFADGKTQTAEFK




GTFEEATAEAYRYADLLAKENGEYTADLED




GGYTINIKFAKETPETPEEPKEELEGDYKD




DDDKGSRGPYSIVSPKC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 232
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DIGGGSGGSGGSGGAAA



of SEQ ID



NO: 232


 


Protein L
residues 101-173
VTIKANLIFADGKTQTAEFKGTFEEATAEA



of SEQ ID
YRYADLLAKENGEYTADLEDGGYTINIKFA



NO: 232
KETPETPEEPKEE


 


Linker
residues 174-176
LEG



of SEQ ID



NO: 232


 


Flag epitope
residues 177-184
DYKDDDDK


domain
of SEQ ID



NO: 232


 


C-terminal
residues 185-197
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 232









The amino acid sequence of the IL8 protein used in this experiment included a Flag epitope tag, a signal sequence, and 13 additional C-terminal amino acid residues from the expression vector used to express the protein as shown in the table below.







TABLE 43







Amino Acid Sequence of a Flag-Tagged IL8 Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged IL8
SEQ ID NO: 233
MGVKVLFALICIAVAEAGTGSEFDIAAASA


protein

KELRCQCIKTYSKPFHPKFIKELRVIESGP




HCANTEIIVKLSDGRELCLDPKENWVQRVV




EKFLKRAENSLEGDYKDDDDKGSRGPYSIV




SPKC


 


Signal Sequence
residues 1-17
MGVKVLFALICIAVAEA



of SEQ ID



NO: 233


 


Linker
residues 18-28
GTGSEFDIAAA



of SEQ ID



NO: 233


 


IL8
residues 29-100
SAKELRCQCIKTYSKPFHPKFIKELRVIES



of SEQ ID
GPHCANTEIIVKLSDGRELCLDPKENWVQR



NO: 233
VVEKFLKRAENS


 


Linker
residues 101-103
LEG



of SEQ ID



NO: 233


 


Flag epitope
residues 104-111
DYKDDDDK


domain
of SEQ ID



NO: 233


 


C-terminal
residues 112-124
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 233









The amino acid sequence of an Erdj3 J domain-IL8 fusion protein included a Flag epitope tag as shown in the table below.







TABLE 44







Amino Acid Sequence of a Flag-Tagged Erdj3 J domain-IL8


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 234
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


IL8 fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAASAKELRCQCIKTYSKPFHPK




FIKELRVIESGPHCANTEIIVKLSDGRELC




LDPKENWVQRVVEKFLKRAENSLEGDYKDD




DDKGSRGPYSIVSPKC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 234
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DI GGGSGGSGGSGG AAA



of SEQ ID



NO: 234


 


IL8
residues 101-172
SAKELRCQCIKTYSKPFHPKFIKELRVIES



of SEQ ID
GPHCANTEIIVKLSDGRELCLDPKENWVQR



NO: 234
VVEKFLKRAENS


 


Linker
residues 173-175
LEG



of SEQ ID



NO: 234


 


Flag epitope
residues 176-183
DYKDDDDK


domain
of SEQ ID



NO: 234


 


C-terminal
residues 184-196
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 234









HEK293 cells were transfected with an expression plasmid for expressing anti-IL8 antibody alone, co-expressing anti-IL8 antibody and Protein A (Protein A Only), co-expressing anti-IL8 antibody and an Erdj3 J domain-Protein A fusion protein of the invention (J-Protein A), co-expressing anti-IL8 antibody and Protein L (Protein L Only), co-expressing anti-IL8 antibody and an Erdj3 J domain-Protein L fusion protein of the invention (J-Protein L), co-expressing anti-IL8 antibody and its IL8 ligand (IL8), co-expressing an Erdj3 J domain-IL8 ligand fusion protein of the invention (J-IL8), expressing the Erdj3 J-Protein A fusion protein of the invention alone (J-Protein A), expressing the Erdj3 J domain-Protein L fusion protein of the invention alone (J-Protein L), and expressing the Erdj3 J domain-IL8 ligand fusion protein of the invention alone (J-IL8). Expression of the anti-IL8 antibody in culture media was analyzed by dot blot assay using an anti-human IgG antibody (anti-hIgG antibody, catalog no. AP112P, Millipore).
As shown in the dot blots of culture media in FIG. 14A, co-expression in transfected cells of the anti-IL8 antibody with a J domain-Protein A fusion protein (lane 4), with a J domain-Protein L fusion protein (lane 6), or with a J domain-IL8 fusion protein (lane 8) significantly enhanced the level of expression of anti-IL8 antibody secreted into the culture medium as compared to the level of the antibody expressed in transfected cells expressing the anti-IL8 antibody alone (lane 2), co-expressing with Protein A alone (lane 3, Protein A Only), co-expressing Protein L alone (lane 5, Protein L Only), or co-expressing IL8 ligand alone (lane 7). No signal was detected in culture media of transfected cells expressing the J domain-Protein A fusion protein alone (lane 9, J-Protein A), the J domain-Protein L fusion protein alone (lane 10, J-Protein L), or expressing the J domain-IL8 fusion protein alone (lane 10, J-IL8), indicating that all three fusion proteins specifically targeted and enhanced the co-expressed anti-IL8 antibody.
The results of a densitometry analysis of the signals in the lanes in FIG. 14A using the NIH ImageJ image processing program are shown in the respective bar graphs in FIG. 14B. The results of this series of experiments clearly show that co-expression of the targeted anti-IL8 antibody with a fusion protein of the invention comprising a protein expression enhancing polypeptide (here: Erdj3 J domain) linked to a target binding domain (here: Protein A, Protein L, or IL8) significantly enhanced the expression of secreted anti-IL8 antibody as compared to co-expression of the antibody with the unfused target binding domain protein alone (Protein G only, Protein L only, or IL8 only).
Example 8. Enhancement of Established Expression in CHO-DP12 Producing Cell Line Using an Unmodified Arrangement
This example examined whether a fusion protein of the invention could be used to improve the level of expression of a target protein already being produced in an established commercially relevant production cell line. For this experiment a CHO-DP12 cell line was used that stably expresses a humanized anti-IL8 IgG1 antibody as obtained from the American Type Culture Collection (accession no. CRL-124444, American Type Culture Collection, Manassas, Va.) along with an expression vector plasmid for expressing the anti-IL8 antibody (accession no. 209552, ATCC, Manassas, Va.). The fusion protein of the invention was that Erdj3 J domain-Protein A fusion protein described above. Cells of the CHO-DP12 production cell line were transfected with an expression vector carrying an operably linked structural gene encoding the Erdj3 J domain-Protein A fusion protein. The transfection efficiency was not as high with the CHO-DP12 cells as compared with HEK293 cells. Nevertheless, as shown in the dot blot assays in FIG. 15A, co-expression of the humanized antibody with the J domain-Protein A fusion protein significantly enhanced the level of expression of the antibody secreted into the culture medium (lane 3) as compared to the level of the antibody expressed in the absence of the J domain-Protein A fusion protein (lane 2, none).
The results of a densitometry analysis of the chemiluminescent signals in the dot blots in the lanes in FIG. 15A using the NIH ImageJ image processing program are shown in the respective bar graphs in FIG. 15B. The results indicate that co-expression of the antibody with the J domain-Protein A fusion protein (bar graph 3) significantly enhanced expression of the secreted antibody, providing an approximately four to five-fold greater enhancement in the level of expression, as compared to that obtained when the antibody was expressed in the absence of the J domain-Protein A fusion protein (bar graph 2).
The results indicate that a fusion protein of the invention can be employed to significantly enhance the level of production of a protein that is already being stably expressed in an established production cell line.
Example 9. Other Fusion Proteins for Enhancing Expression of Secreted Fc-Containing Molecules in an Unmodified Arrangement
Example 9.1. Fusion Proteins Comprising Fc Binding Domains from Additional Protein Species
This example provides a series of experiments to test various fusion proteins comprising a J domain (as a protein expression enhancing polypeptide domain) linked to any of a variety of polypeptides (as the target binding domain) that have been reported to bind the Fc region of antibody molecules. The various J domain fusion proteins were then tested and compared for their ability to enhance levels of expression of the IL13Rα2TF-Fc fusion protein as described in Example 5 above that was secreted into medium of transfected HEK293 cells.
The J-Protein A fusion protein of the invention used in this example is the Erdj3-Protein A fusion protein described in Example 5 above.
In another fusion protein used in the experiments described herein, the J domain from the Erdj3 J protein was linked to Protein G, which is known to bind certain immunoglobulin Fc domains. A Flag epitope tag was linked to the C-terminus of the Protein G domain as shown for the J-Protein A fusion protein in Example 5 and FIG. 11B. The amino acid sequence for a Flag-tagged J domain-Protein G fusion protein of the invention is shown in the table below.







TABLE 45







Amino Acid Sequence of a Flag-Tagged Erdj3 J domain-Protein G


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID N0: 235
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


Protein G fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAATYKLVINGKTLKGETTTEAV




DAATAEKVFKQYANDNGVDGEWTYDDATKT




FTVTEKPEVIDASELTPAVTLEGDYKDDDD




KGSRGPYSIVSPKC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 235
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DIGGGSGGSGGSGGAAA



of SEQ ID



NO: 235


 


Protein G
residues 101-170
TYKLVINGKTLKGETTTEAVDAATAEKVFK



of SEQ ID
QYANDNGVDGEWTYDDATKTFTVTEKPEVI



NO: 235
DASELTPAVT


 


Linker
residues 171-173
LEG



of SEQ ID



NO: 235


 


Flag epitope
residues 174-181
DYKDDDDK


domain
of SEQ ID



NO: 235


 


C-terminal
residues 182-194
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 235









In another fusion protein used in the experiments described herein, the J domain from the Erdj3 J protein was linked to a human FcR (hFcR) receptor protein, which is a receptor that binds certain immunoglobulin Fc domains. A Flag epitope tag was linked to the C-terminus of the hFcR domain as shown for the J-Protein A fusion protein in Example 5 and FIG. 11B. The amino acid sequence for a Flag-tagged J domain-hFcR fusion protein is shown in the table below.







TABLE 46







Amino Acid Sequence of a Flag-Tagged Erdj3 J Domain-hFcR


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 236
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


hFcR fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAAAVITLQPPWVSVFQEETVTL




HCEVLHLPGSSSTQWFLNGTATQTSTPSYR




ITSASVNDSGEYRCQRGLSGRSDPIQLEIH




RGWLLLQVSSRVFTEGEPLALRCHAWKDKL




VYNVLYYRNGKAFKFFHWNSNLTILKTNIS




HNGTYHCSGMGKLEGDYKDDDDKGSRGPYS




IVSPKC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 236
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DIGGGSGGSGGSGGAAA



of SEQ ID



NO: 236


 


hFcR
residues 101-252
AVITLQPPWVSVFQEETVTLHCEVLHLPGS



of SEQ ID
SSTQWFLNGTATQTSTPSYRITSASVNDSG



NO: 236
EYRCQRGLSGRSDPIQLEIHRGWLLLQVSS




RVFTEGEPLALRCHAWKDKLVYNVLYYRNG




KAFKFFHWNSNLTILKTNISHNGTYHCSGM




GK


 


Linker
residues 253-255
LEG



of SEQ ID



NO: 236


 


Flag epitope
residues 256-263
DYKDDDDK


domain
of SEQ ID



NO: 236


 


C-terminal
residues 264-276
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 236









In another fusion protein used in the experiments described herein, the J domain from the Erdj3 J protein was linked to the Macaca mulatta rhadinovirus FcR receptor protein (vFcR), which is a receptor that binds certain immunoglobulin Fc domains. A Flag epitope tag was linked to the C-terminus of the vFcR domain as shown for the J-Protein A fusion protein in Example 5 and FIG. 11B. The amino acid sequence for a Flag-tagged J domain-vFcR fusion protein is shown in the table below.







TABLE 47







Amino Acid Sequence of a Flag-Tagged Erdj3 J domain-vFcR


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 237
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


vFcR protein

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG




GSGGSGGAAAAKLTSVPTWCPPHPGDTYLL




TCRGTSTARDQRSTQWFRNNTLMRGSNFYG




RLVSVTPNATISDRYACQTKTTTRSNNIDF




RVSSSRLTLQERCSSYGYTYANNTRVLRCY




SGGNVTLRNVVFHLNGTAVINGTTTNIHTF




VLTEKTGGTYFCSAFLEGDYKDDDDKGSRG




PYSIVSPKC


 


Erdj3 J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL



of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 237
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DI GGGSGGSGGSGG AAA



of SEQ ID



NO: 237


 


vFcR
residues 101-255
AKLTSVPTWCPPHPGDTYLLTCRGTSTARD



of SEQ ID
QRSTQWFRNNTLMRGSNFYGRLVSVTPNAT



NO: 237
ISDRYACQTKTTTRSNNIDFRVSSSRLTLQ




ERCSSYGYTYANNTRVLRCYSGGNVTLRNV




VFHLNGTAVINGTTTNIHTFVLTEKTGGTY




FCSAF


 


Linker
residues 256-258
LEG



of SEQ ID



NO: 237


 


Flag epitope
residues 259-266
DYKDDDDK


domain
of SEQ ID



NO: 237


 


C-terminal
residues 267-279
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 237









In another fusion protein used in the experiments described herein, the J domain from the Erdj3 J protein was linked to a herpes simplex virus type 1 gI protein, which has no significant Fc binding activity. A Flag epitope tag was linked to the C-terminus of the gI domain as shown for the J-Protein A fusion protein in Example 5 and FIG. 11B. The amino acid sequence for a Flag-tagged J domain-gI fusion protein is shown in the table below.







TABLE 48







Amino Acid Sequence of a Flag-Tagged Erdj3 J Domain-gI


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 238
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


gI protein

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG




GSGGSGGAAALVVRGPTVSLVSNSFVDAGA




LGPDGVVEEDLLILGELRFVGDQVPHTTYY




DGVVELWHYPMGHKCPRVVHVVTVTACPRR




PAVAFALCRATDSTHSPAYPTLELNLAQQP




LLRVRRATRDYAGVYVLRVWVGDAPNASLF




VLGMAIAAEGTLAYNGSAHGSCDPKLLPYS




APRLAPASVYQPAPNPASTPSTTIPAPQAS




TTPFPTGDPKPQLEGDYKDDDDKGSRGPYS




IVSPKC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 238
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DIGGGSGGSGGSGGAAA



of SEQ ID



NO: 238


 


gI
residues 101-312
LVVRGPTVSLVSNSFVDAGALGPDGVVEED



of SEQ ID
LLILGELRFVGDQVPHTTYYDGVVELWHYP



NO: 238
MGHKCPRVVHVVTVTACPRRPAVAFALCRA




TDSTHSPAYPTLELNLAQQPLLRVRRATRD




YAGVYVLRVWVGDAPNASLFVLGMAIAAEG




TLAYNGSAHGSCDPKLLPYSAPRLAPASVY




QPAPNPASTPSTTIPAPQASTTPFPTGDPK




PQ


 


Linker
residues 313-315
LEG



of SEQ ID



NO: 238


 


Flag epitope
residues 316-323
DYKDDDDK


domain
of SEQ ID



NO: 238


 


C-terminal
residues 324-336
GSRGPYSIVSPKC


vector residues
of SEQ ID



NO: 238









In another fusion protein used in the experiments described herein, the J domain from the Erdj3 J protein was linked to a herpes simplex virus type 1 gE protein, which has a relatively weak affinity for the immunoglobulin Fc domain. A Flag epitope tag was linked to the C-terminus of the gE domain as shown for the J-Protein A fusion protein in Example 5 and FIG. 11B. The amino acid sequence for a Flag-tagged J domain-gE fusion protein is shown in the table below.







TABLE 49







Amino Acid Sequence of a Flag-Tagged Erdj3 J domain-gE


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 239
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


gE fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAAGTPKTSWRRVSVGEDVSLLP




APGPTGRGPTQKLLWAVEPLDGCGPLHPSW




VSLMPPKQVPETVVDAACMRAPVPLAMAYA




PPAPSATGGLRTDFVWQERAAVVNRSLVIH




GVRETDSGLYTLSVGDIKDPARQVASVVLV




VQPAPVPTPPPTPADYDEDDNDEGEDESLA




GTPASGTPRLPPPPAPPRSWPSAPEVSHVR




GVTVRMETPEAILFSPGETFSTNVSIHAIA




HDDQTYSMDVVWLRFDVPTSCAEMRIYESC




LYHPQLPECLSPADAPCAASTWTSRLAVRS




YAGCSRTNPPPRCSAEAHMEPVPGLAWQAA




SVNLEFRDASPQHSGLYLCVVYVNDHIHAW




GHITISTAAQYRNAVVEQPLPQRGADLAEL




EGDYKDDDDKGSRGPYSIVSPKC


 


Erdj3 J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL



of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 239
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DIGGGSGGSGGSGGAAA



of SEQ ID



NO: 239


 


gE
residues 101-479
GTPKTSWRRVSVGEDVSLLPAPGPTGRGPT



of SEQ ID
QKLLWAVEPLDGCGPLHPSWVSLMPPKQVP



NO: 239
ETVVDAACMRAPVPLAMAYAPPAPSATGGL




RTDFVWQERAAVVNRSLVIHGVRETDSGLY




TLSVGDIKDPARQVASVVLVVQPAPVPTPP




PTPADYDEDDNDEGEDESLAGTPASGTPRL




PPPPAPPRSWPSAPEVSHVRGVTVRMETPE




AILFSPGETFSTNVSIHAIAHDDQTYSMDV




VWLRFDVPTSCAEMRIYESCLYHPQLPECL




SPADAPCAASTWTSRLAVRSYAGCSRTNPP




PRCSAEAHMEPVPGLAWQAASVNLEFRDAS




PQHSGLYLCVVYVNDHIHAWGHITISTAAQ




YRNAVVEQPLPQRGADLAE


 


Linker
residues 480-482
LEG



of SEQ ID



NO: 239


 


Flag epitope
residues 483-490
DYKDDDDK


domain
of SEQ ID



NO: 239


 


C-terminal
residues 491-503
GSRGPYSIVSPKC


vector residues
of SEQ ID


NO: 239









HEK293 cells were transfected with expression vector plasmids to compare levels of expression in culture medium of the IL13Rα2TF-Fc fusion protein expressed alone, co-expressed with a J domain-Protein A fusion protein (as described above in Example 5), co-expressed with Protein A (“Protein A Only”, as described in Example 5), co-expressed with a J domain-Protein G fusion protein (J-Protein G), co-expressed with a J domain fusion protein in which a J domain is linked to a human FcR receptor protein (“J-hFcR”), co-expressed with a J domain fusion protein in which a J domain is linked to a viral FcR receptor protein (“J-vFcR”), co-expressed with a J domain fusion protein in which a J domain is linked to a herpes simplex virus type 1 gI protein (“J-gI”), co-expressed with a J domain fusion protein in which a J domain is linked to a herpes simplex virus type 1 gE protein (“J-gE”), and co-expressed with both J-gI and J-gE fusion proteins (“J-gI+J-gE”). Transfected cells were cultured for two days, and samples of cell media were harvested and analyzed by Western blot (immunoblot) assay using an anti-V5 antibody to detect secreted V5-tagged IL13Rα2TF.
FIG. 16A shows X-ray film images of chemiluminescent signals of a Western blot analysis of culture media from cultures of transfected cells. Lane 1 of FIG. 16A is medium from a culture of cells transfected with an expression vector to express the IL13Rα2TF-Fc fusion protein alone. When expressed alone, some IL13Rα2TF-Fc fusion protein was detected in the medium (lane 1 of FIG. 16A). Some IL13Rα2TF-Fc protein was also detected when expressed with Protein A only (lane 3 of FIG. 16A), as previously noted above with respect to the results described in Example 5 and FIG. 12A. Also as previously described in Example 5 and FIG. 12A above, co-expression of IL13Rα2TF-Fc fusion protein with a J domain-Protein A fusion protein significantly enhanced the level of expression of IL13Rα2TF-Fc fusion protein secreted into culture medium (lane 2 of FIG. 16A) as compared to the level of expression of IL13Rα2TF alone (lane 1 of FIG. 16A) or co-expression of IL13Rα2TF-Fc with Protein A alone (lane 3 of FIG. 16A). Co-expression of the IL13Rα2TF-Fc protein with a J domain-Protein G fusion protein also significantly enhanced the level of expression of secreted IL13Rα2TF-Fc protein (lane 4 of FIG. 16A) as compared to the level of expression of IL13Rα2TF alone (lane 1 of FIG. 16A) or co-expression of IL13Rα2TF-Fc with Protein A alone (lane 3 of FIG. 16A).
Viral proteins gI and gE from herpes simplex virus type 1 are known to form a heterodimer, wherein the gE protein weakly binds antibody molecules. In addition, whereas the gE protein alone weakly binds to antibody molecules, gI alone does not bind antibody molecules. Consistent with these prior findings, co-expression of the IL13Rα2TF-Fc fusion protein with a J domain-gI fusion protein (lane 7 of FIG. 16A) resulted in a relatively low level of expression of secreted IL13Rα2TF-Fc that was similar to that observed in cells expressing the IL13Rα2TF-Fc alone (lane 1 of FIG. 16A). In contrast, co-expression of the IL13Rα2TF-Fc fusion protein with a J domain-gE fusion protein significantly enhanced the level of expression of secreted IL13Rα2TF-Fc (lane 8 of FIG. 16A). A similar enhancement in the level of secreted IL13Rα2TF-Fc was observed when IL13Rα2TF-Fc was co-expressed with both J-gI and J-gE fusion proteins (lane 9 of FIG. 16A), indicating that the J-gI fusion protein does not significantly enhance the level of expression of secreted IL13Rα2TF-Fc, consistent with the previous finding that the gI protein does not bind Fc domains.
The human Fc binding receptor (hFcR) and the Macaca mulatta rhadinovirus Fc binding receptor (vFcR) are well characterized receptors for binding Fc regions of antibody molecules. J domain fusions comprising these FcR molecules were prepared and tested for the ability to enhance expression of the IL13Rα2TF-Fc fusion protein. As shown in FIG. 16A, co-expression of the IL13Rα2TF-Fc protein with either a J domain-hFcR fusion protein or a J domain-vFcR fusion protein not only failed to enhance expression of secreted IL13Rα2TF-Fc (lanes 5 and 6 of FIG. 16A), but actually appeared to suppress even a low level of expression of secreted protein observed in cells expressing the IL13Rα2TF-Fc protein alone (lane 1 of FIG. 16A). One possible explanation for such apparent suppression of even baseline secretion may be that the J domain-FcR fusion proteins employed in these experiments becomes caught in the endoplasmic reticulum (ER). Further work is required to find functional constructs containing FcR regions to target and enhance expression of proteins that possess an Fc region.
The results of a densitometry analysis of the chemiluminescent signals in the Western blot in FIG. 16A using the NIH ImageJ image processing program are shown in the respective bar graphs in FIG. 16B.
Example 9.2. Fusion Proteins Comprising Fc Targeting Peptides for Use in Enhancing Expression of Target Proteins in an Unmodified Arrangement
A variety of peptides are known that bind the Fc domain of immunoglobulin molecules. This experiment tested various fusion proteins comprising a J domain (as a protein expression enhancing polypeptide) linked to each of several representative Fc-binding peptides (as a target binding domain) for use in enhancing the level of expression of proteins that possess an Fc domain. The six peptides used to construct fusion proteins are shown in the table below.







TABLE 50







Amino Acid Sequences of Representative Peptides that Bind Fc Domains.









Peptide




Designation
Amino Acid Sequence
Reference





FcBP1
DCAWHLGELVWCT
DeLano et al., Science, 287: 1279-1283 (2000)



(SEQ ID NO: 240)



 


FcBP2
HWRGWV
Yang et al., J. Peptide Res., 66 (Suppl. 1): 120-137



(SEQ ID NO: 241)
(2006)


 


FcBP3
HVHYYW
Yang et al., J. Peptide Res., 66 (Suppl. 1): 120-137



(SEQ ID NO: 242)
(2006)


 


FcBP4
YYWLHH
Yang et al., J. Peptide Res., 66 (Suppl. 1): 120-137



(SEQ ID NO: 243)
(2006)


 


FcBP5
HVHYY
Yang et al., J. Peptide Res., 66 (Suppl. 1): 120-137



(SEQ ID NO: 244)
(2006)


 


FcBP6
YYWL
Yang et al., J. Peptide Res., 66 (Suppl. 1): 120-137



(SEQ ID NO: 245)
(2006)









Expression vector plasmids were prepared for expressing J domain fusion proteins comprising a J domain (from the Erdj3 protein) linked to each of the six peptides. The IL13Rα2TF-Fc fusion protein was used as a representative target protein comprising an Fc domain.
The amino acid sequence for a J domain fusion protein comprising a J domain of the Erdj3 J protein linked to the FcBP1 peptide used in this experiment included a Flag epitope tag and 13 additional C-terminal amino acid residues from the expression vector used to express the protein as shown in the table below.







TABLE 51







Amino Acid Sequence of a Flag-Tagged Erdj3 J Domain-FcBP1


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 246
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


FcBP1 fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAADCAWHLGELVWCTLEGDYKD




DDDKGSRGPYSIVSPKC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 246
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DIGGGSGGSGGSGGAAA



of SEQ ID




NO: 246



 


FcBP1
residues 101-113
DCAWHLGELVWCT



of SEQ ID




NO: 246



 


Linker
residues 114-116
LEG



of SEQ ID




NO: 246



 


Flag epitope
residues 117-124
DYKDDDDK


domain
of SEQ ID




NO: 246



 


C-terminal
residues 125-137
GSRGPYSIVSPKC


vector residues
of SEQ ID




NO: 246









The amino acid sequence for a J domain fusion protein comprising a J domain of the Erdj3 J protein linked to the FcBP2 peptide used in this experiment included a Flag epitope tag and 13 additional C-terminal amino acid residues from the expression vector used to express the protein as shown in the table below.







TABLE 52







Amino Acid Sequence of a Flag-Tagged Erdj3 J Domain-FcBP2


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 247
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


FcBP2 fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAAHWRGWVLEGDYKDDDDKGSR




GPYSIVSPKC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 247
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DIGGGSGGSGGSGGAAA



of SEQ ID




NO: 247



 


FcBP2
residues 101-106
HWRGWV



of SEQ ID




NO: 247



 


Linker
residues 107-109
LEG



of SEQ ID




NO: 247



 


Flag epitope
residues 110-117
DYKDDDDK


domain
of SEQ ID




NO: 247



 


C-terminal
residues 118-130
GSRGPYSIVSPKC


vector residues
of SEQ ID




NO: 247









The amino acid sequence for a J domain fusion protein comprising a J domain of the Erdj3 J protein linked to the FcBP3 peptide used in this experiment included a Flag epitope tag and 13 additional C-terminal amino acid residues from the expression vector used to express the protein as shown in the table below.







TABLE 53







Amino Acid Sequence of a Flag-Tagged Erdj3 J Domain-FcBP3


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 248
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


FcBP3 fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAAHVHYYWLEGDYKDDDDKGSR




GPYSIVSPKC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 248
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DI GGGSGGSGGSGG AAA



of SEQ ID




NO: 248



 


FcBP3
residues 101-106
HVHYYW



of SEQ ID




NO: 248



 


Linker
residues 107-109
LEG



of SEQ ID




NO: 248



 


Flag epitope
residues 110-117
DYKDDDDK


domain
of SEQ ID




NO: 248



 


C-terminal
residues 118-130
GSRGPYSIVSPKC


vector residues
of SEQ ID




NO: 248









The amino acid sequence for a J domain fusion protein comprising a J domain of the Erdj3 J protein linked to the FcBP4 peptide used in this experiment included a Flag epitope tag and 13 additional C-terminal amino acid residues from the expression vector used to express the protein as shown in the table below.







TABLE 54







Amino Acid Sequence of a Flag-Tagged Erdj3 J domain-FcBP4


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 249
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


FcBP4 fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAAYYWLHHLEGDYKDDDDKGSR




GPYSIVSPKC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 249
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DIGGGSGGSGGSGGAAA



of SEQ ID




NO: 249



 


FcBP4
residues 101-106
YYWLHH



of SEQ ID




NO: 249



 


Linker
residues 107-109
LEG



of SEQ ID




NO: 249



 


Flag epitope
residues 110-117
DYKDDDDK


domain
of SEQ ID




NO: 249



 


C-terminal
residues 118-130
GSRGPYSIVSPKC


vector residues
of SEQ ID




NO: 249









The amino acid sequence for a J domain fusion protein comprising a J domain of the Erdj3 J protein linked to the FcBP5 peptide used in this experiment included a Flag epitope tag and 13 additional C-terminal amino acid residues from the expression vector used to express the protein as shown in the table below.







TABLE 55







Amino Acid Sequence of a Flag-Tagged Erdj3 J domain-FcBP5


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 250
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


FcBP5 fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAAHVHYYLEGDYKDDDDKGSRG




PYSIVSPKC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 250
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DI GGGSGGSGGSGG AAA



of SEQ ID




NO: 250



 


FcBP5
residues 101-105
HVHYY



of SEQ ID




NO: 250



 


Linker
residues 106-108
LEG



of SEQ ID




NO: 250



 


Flag epitope
residues 109-116
DYKDDDDK


domain
of SEQ ID




NO: 250



 


C-terminal
residues 117-129
GSRGPYSIVSPKC


vector residues
of SEQ ID




NO: 250









The amino acid sequence for a J domain fusion protein comprising a J domain of the Erdj3 J protein linked to the FcBP6 peptide used in this experiment included a Flag epitope tag and 13 additional C-terminal amino acid residues from the expression vector used to express the protein as shown in the table below.







TABLE 56







Amino Acid Sequence of a Flag-Tagged Erdj3 J domain-FcBP6


Fusion Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Flag-tagged
SEQ ID NO: 251
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


Erdj3 J domain-

GVPRSASIKDIKKAYRKLALQLHPDRNPDD


FcBP6 fusion

PQAQEKFQDLGAAYEVLSDSEKRDIGGGSG


protein

GSGGSGGAAAYYWLLEGDYKDDDDKGSRGP




YSIVSPKC


 


J domain
residues 1-83
MAPQNLSTFCLLLLYLIGAVIAGRDFYKIL


(from Erdj3)
of SEQ ID
GVPRSASIKDIKKAYRKLALQLHPDRNPDD



NO: 251
PQAQEKFQDLGAAYEVLSDSEKR


 


Linker
residues 84-100
DIGGGSGGSGGSGGAAA



of SEQ ID




NO: 251



 


FcBP6
residues 101-104
YYWL



of SEQ ID




NO: 251



 


Linker
residues 105-107
LEG



of SEQ ID




NO: 251



 


Flag epitope
residues 108-115
DYKDDDDK


domain
of SEQ ID




NO: 251



 


C-terminal
residues 116-128
GSRGPYSIVSPKC


vector residues
of SEQ ID




NO: 251









Transfected cells were cultured for two days, and samples of cell media were harvested and analyzed by Western blot assay using an anti-V5 antibody to detect secreted V5-tagged IL13Rα2TF-Fc fusion protein. FIG. 17A shows X-ray film images of chemiluminescent signals of the Western blot analysis of culture media. As shown in FIG. 17A, co-expression of the IL13Rα2TF-Fc fusion protein with each of the six J domain-peptide fusion proteins in HEK293 transfectants significantly enhanced the level of expression of secreted IL13Rα2TF-Fc fusion protein (lanes 4-9) as compared to the level of expression of IL13Rα2TF-Fc fusion protein alone (lanes 1 and 3). The experiment also included for comparison the effect of co-expression of IL13Rα2TF-Fc fusion protein with a J domain-Protein A fusion protein (lane 2) or with a J domain-Protein G fusion protein (lane 10) on the expression of secreted IL13Rα2TF-Fc fusion protein. As shown in FIG. 17A, co-expression of IL13Rα2TF-Fc fusion protein with either J domain-Protein A fusion protein (lane 2) or the J domain-Protein G fusion protein (lane 10) significantly enhanced the level of expression of secreted the IL13Rα2TF-Fc fusion protein.
The results of a densitometry analysis of the chemiluminescent signals in the Western blot in FIG. 17A using the NIH ImageJ image processing program are shown in the respective bar graphs in FIG. 17B.
Conclusion of Results of Experiments
The results of the experiments described above indicate that co-expression of a target protein of interest and a fusion protein comprising a protein expression enhancing polypeptide domain linked to a target protein binding domain that binds the target protein significantly enhances the level of expression of the target protein in its proper cellular or extracellular location as compared to the level of expression of the target protein in the absence of the fusion protein.
Example 10. Minimal Sequence Requirements for Protein Expression Enhancing Polypeptides
Further analysis was undertaken to determine the minimal amino acid sequence that is effective for enhancing the level of expression of a target protein of interest when employed in an unmodified or a modified arrangement.
Sequence homology analysis using BLAST was conducted on the existing library of J domain sequences to determine whether J domains shared a similar minimal “core” sequence that could enhance the level of protein expression. The analysis indicated that the J domain of the Erdj3 protein was typical of J domains of other J proteins. Since the J domain of Erdj3 was already known to be effective at enhancing protein expression in both the modified and unmodified arrangements (see, examples above), it was chosen for further deletion and substitution mutation analysis to determine whether a minimal polypeptide sequence could be identified that retained protein expression enhancing activity.
In this study, various deletion and substitution mutations of the J domain of Erdj3 were assessed for enhancing expression of an engineered IL13Rα2TF-V5-Fc protein as the target protein of interest. This engineered protein possesses a V5 epitope tag between the IL13Rα2TF polypeptide and the Fc domain, permitting easy detection with an anti-V5 antibody. Fusion proteins were constructed comprising either the full length J domain of Erdj3 or the various mutated polypeptides linked to Protein A, which binds the Fc domain of the engineered IL13Rα2-Fc target protein (thus acting as a target protein binding domain) Thus, for each of the mutated polypeptides, the general formula of the corresponding fusion proteins used in the study was:
signal sequence-linker 1-(J domain, fragment or J domain analog polypeptide sequence-linker 2-Protein A-linker 3-Flag epitope tag.
The amino acid sequences of the domains of these fusion proteins, excluding the inserted J domain, J domain fragment, or J domain analog sequences, is shown in the table below.







TABLE 57







Amino Acid Structure of Test Flag-Tagged Protein A Fusions.










Sequence
Amino Acid Sequence


Protein Region
Identifier
123456789012345678901234567890





signal sequence
SEQ ID
MGVKVLFALICIAVAEA



NO: 251



 


linker 1
SEQ ID
GTGSGEF



NO: 252



 


J domain,

(various polypeptide


fragment or

sequences)


analog




sequence




 


linker 2
SEQ ID
DIGGGSGGSGGSGGAAA



NO: 122



 


Protein A
SEQ ID
ADNKFNKEQQNAFYEILNMPNLNEEQRNGF



NO: 254
IQSLKDDPSQSANVLGEAKKLNDSQAPK


 


linker 3
SEQ ID
LEG



NO: 255



 


Flag epitope tag
SEQ ID
DYKDDDDK



NO: 111









The protein expression enhancing activity of each fusion protein was determined by dot blot assay using detectable anti-V5 antibody. The IL13Rα2-V5-Fc target protein was expressed with or without the fusion proteins containing each mutated polypeptide sequence, and the cell culture medium was harvested and briefly spun to remove debris. The sample was blotted onto nitrocellulose membrane, and the dried membrane was processed for immunoblot assay. The deletion and substitution polypeptides tested for protein expression enhancement activity are shown in the table below along with the protein expression enhancing activity determined by immunoblotting.







TABLE 58







Amino Acid Sequences of Polypeptides Tested for Protein Expression


Enhancing Activity.










Polypeptide
Sequence
Polypeptide Amino Acid Sequence



No.
Identifier
123456789012345678901234567890
Activity*





3
SEQ ID NO: 256
GRDFYKILGVPRSASIKDIKKAYRKLALQL
HA




HPDRNPDDPQAQEKFQDLGAAYEVLSDSEK





R



 


3-1
SEQ ID NO: 257
ILGVPRSASIKDIKKAYRKLALQLHPDRNP
HA




DDPQAQEKFQDLGAAYEVLSDSEKR



 


3-2
SEQ ID NO: 258
SASIKDIKKAYRKLALQLHPDRNPDDPQAQ
HA




EKFQDLGAAYEVLSDSEKR



 


3-3
SEQ ID NO: 259
GRDFYKILGVPRSASIKDIKKAYRKLALQL
HA




HPDRNPDDPQAQEKFQDLG



 


3-4
SEQ ID NO: 260
ILGVPRSASIKDIKKAYRKLALQLHPDRNP
HA




DDPQAQEKFQDLG



 


3-5
SEQ ID NO: 261
SASIKDIKKAYRKLALQLHPDRNPDDPQAQ
HA




EKFQDLG



 


3-6
SEQ ID NO: 262
KAYRKLALQLHPDRNPDDPQAQEKFQDLG
NA


 


3-7
SEQ ID NO: 263
KAYRKLALQLHPDRNPDDPQAQEKFQDLGA
NA




AYEVLSDSEKR



 


3-8
SEQ ID NO: 264
LQLHPDRNPDDPQAQEKFQDLG
NA


 


3-9
SEQ ID NO: 265
LQLHPDRNPDDPQAQEKFQDLGAAYEVLSD
NA




SEKR



 


3-10
SEQ ID NO: 266
IKDIKKAYRKLALQLKPDRNPDDPQAQEKF
HA




QDLG



 


3-11
SEQ ID NO: 267
SASIKDIKKAYRKLALQLHPDRNPDDPQAQ
HA




E



 


3-12
SEQ ID NO: 268
SASIKDIKKAYRKLALQLHP
HA


 


3-13
SEQ ID NO: 269
IKDIKKAYRKLALQLHPDRNPDDPQAQE
HA


 


3-14
SEQ ID NO: 270
IKDIKKAYRKLALQLHPDRN
HA


 


3-15
SEQ ID NO: 271
DIKKAYRKLALQLHPDRNPDDPQAQE
HA


 


3-16
SEQ ID NO: 272
IKDIKKAYRKLALQLHPD
HA


 


3-17
SEQ ID NO: 273
IKDIKKAYRKLALQL
HA


 


3-18
SEQ ID NO: 274
DIKKAYRKLALQL
HA


 


3-19
SEQ ID NO: 275
DIKKAYRKLALQ
HA


 


3-20
SEQ ID NO: 276
DIKKAYRKLAL
HA


 


3-21
SEQ ID NO: 277
DIKKAYRKLA
HA


 


3-22
SEQ ID NO: 278
DIKKAYRKL
NA


 


3-23
SEQ ID NO: 279
DIKKAYRK
NA


 


3-24
SEQ ID NO: 280
DIKKAYR
NA


 


3-25
SEQ ID NO: 281
IKKAYRKLALQL
HA


 


3-26
SEQ ID NO: 282
KKAYRKLALQL
NA


 


3-27
SEQ ID NO: 283
IKKAYRKLALQ
HA


 


3-28
SEQ ID NO: 284
IKKAYRKLAL
HA


 


3-29
SEQ ID NO: 48
IKKAYRKLA
HA


 


3-30
SEQ ID NO: 285
IKKAYRKL
A


 


3-31
SEQ ID NO: 286
KKAYRKLALQ
NA


 


3-32
SEQ ID NO: 287
KKAYRKLAL
NA


 


3-33
SEQ ID NO: 288
KKAYRKLA
NA


 


3-34
SEQ ID NO: 289
KAYRKLALQ
NA


 


3-35
SEQ ID NO: 290
IKKAYRK
NA


 


3-36
SEQ ID NO: 291
IKKAYR
NA


 


3-37
SEQ ID NO: 292
IKAYRKLALQ
NA


 


3-38
SEQ ID NO: 293
IKKYRKLALQ
A


 


3-39
SEQ ID NO: 294
IKKARKLALQ
NA


 


3-40
SEQ ID NO: 49
IKKAYKLALQ
HA


 


3-41
SEQ ID NO: 50
IKKAYRLALQ
HA


 


3-42
SEQ ID NO: 51
IKKAYRKALQ
HA


 


3-43
SEQ ID NO: 52
IKKAYRKLLQ
HA


 


3-44
SEQ ID NO: 295
IKAYRKLA
NA


 


3-45
SEQ ID NO: 53
IKKYRKLA
A


 


3-46
SEQ ID NO: 54
IKKAYKLA
A


 


3-47
SEQ ID NO: 55
IKKAYRLA
A


 


3-48
SEQ ID NO: 56
IKKAYRKA
A


 


3-49
SEQ ID NO: 57
LKKAYRKLA
HA


 


3-50
SEQ ID NO: 58
VKKAYRKLA
HA


 


3-51
SEQ ID NO: 59
MKKAYRKLA
HA


 


3-52
SEQ ID NO: 60
AKKAYRKLA
HA


 


3-53
SEQ ID NO: 296
SKKAYRKLA
NA


 


3-54
SEQ ID NO: 297
FKKAYRKLA
NA


 


3-55
SEQ ID NO: 298
IAQAYRKLA
NA


 


3-56
SEQ ID NO: 299
ILAAYRKLA
NA


 


3-57
SEQ ID NO: 61
IAKAYRKLA
A


 


3-58
SEQ ID NO: 62
IKAAYRKLA
A


 


3-59
SEQ ID NO: 63
IKKRYRKLA
HA


 


3-60
SEQ ID NO: 64
IKKSYRKLA
A


 


3-61
SEQ ID NO: 65
IKKQYRKLA
A


 


3-62
SEQ ID NO: 66
IKKEYRKLA
A


 


3-63
SEQ ID NO: 67
IKKFYRKLA
A


 


3-64
SEQ ID NO: 68
IKKCYRKLA
A


 


3-65
SEQ ID NO: 69
IKKAFRKLA
HA


 


3-66
SEQ ID NO: 300
IKKAHRKLA
NA


 


3-67
SEQ ID NO: 301
IKKAIRKLA
NA


 


3-68
SEQ ID NO: 70
IKKAWRKLA
HA


 


3-69
SEQ ID NO: 302
IKKAARKLA
NA


 


3-70
SEQ ID NO: 303
IKKASRKLA
NA


 


3-71
SEQ ID NO: 304
IKKAYHQLA
NA


 


3-72
SEQ ID NO: 305
IKKAYYQLA
NA


 


3-73
SEQ ID NO: 306
IKKAYFSLA
NA


 


3-74
SEQ ID NO: 307
IKKAYRKQS
NA


 


3-75
SEQ ID NO: 308
IKKAYRKQC
NA


 


3-76
SEQ ID NO: 309
IKKAYRKDI
NA


 


3-77
SEQ ID NO: 71
IKKAYRKQA
HA


 


3-78
SEQ ID NO: 72
IKKAYRKMA
HA


 


3-79
SEQ ID NO: 73
IKKAYRKIA
A


 


3-80
SEQ ID NO: 74
IKKAYRKAA
A


 


3-81
SEQ ID NO: 75
IKKAYRKVA
A


 


3-82
SEQ ID NO: 76
IKKAYRKRA
A


 


3-83
SEQ ID NO: 77
IKKAYRKLM
HA


 


3-84
SEQ ID NO: 78
IKKAYRKLI
HA


 


3-85
SEQ ID NO: 79
IKKAYRKLV
HA


 


3-86
SEQ ID NO: 80
IKKAYRKLC
A


 


3-87
SEQ ID NO: 81
IKKAYRKLS
HA


 


3-88
SEQ ID NO: 82
IKKAYRKLY
A


 


3-89
SEQ ID NO: 83
IRKAYRKLSLTL
A


 


3-90
SEQ ID NO: 84
IKKQYRLLSLKY
A


 


3-91
SEQ ID NO: 85
IKKAFHKLAMKY
HA


 


3-92
SEQ ID NO: 86
IRQAFKKLALKL
A


 


3-93
SEQ ID NO: 87
IIKAYRKLALQW
A


 


3-94
SEQ ID NO: 88
IARAYRQLARRY
HA


 


3-95
SEQ ID NO: 89
IKRAYRRQALRY
HA


 


3-96
SEQ ID NO: 90
IKKSYRKLALKY
HA


 


3-97
SEQ ID NO: 91
IKKAYKRLAMKY
HA


 


3-98
SEQ ID NO: 310
MRKAYLKKC
NA


 


3-99
SEQ ID NO: 311
ILAEFKVRAL
NA


 





*“HA” = high activity, i.e., protein expression enhancement activity is significantly enhanced, e.g. similar to that provided by the full-length J domain of the Erdj3 protein, as compared to negative control (no fusion protein used);


“A” = improved protein expression enhancement activity in comparison to negative control (no fusion protein used); level of protein production typically less than provided by the full-length J domain of Erdj3;


“NA” = no activity compared to negative control.






As indicated in the above table, each mutated polypeptide was assessed for expression enhancing activity when co-expressed with the IL13Rα2-V5-Fc target protein. The levels of expression were classified as high activity (“HA”), activity (“A”), or no activity (“NA”). Examples of these levels of expression are shown in the immunoblot in FIG. 18. The level of expression of the IL13Rα2-V5-Fc target protein in the absence of a fusion protein was taken as “no activity”. See, lane 2 (from the left) in FIG. 18). Co-expression of a fusion protein comprising the complete J domain of Erdj3, designated polypeptide 3 in Table 58 above, linked to Protein A dramatically enhanced the level of expression of the secreted IL13Rα2-V5-Fc target protein. See, lane 3, from the left, in FIG. 18. This level of expression enhancement is designated “High Activity”. As shown in lane 4 of FIG. 18, co-expression of a fusion protein comprising an internal deletion mutated polypeptide, designated 3-45, linked to Protein A clearly provided a significantly enhanced level of expression of the secreted IL13Rα2-V5-Fc target protein as compared to the control (no fusion protein, lane 2 of FIG. 18), but the expression level was somewhat less than the high activity shown in lane 3 of FIG. 18. This level of expression enhancement is designated “Activity.” In contrast, as shown in lane 5 of FIG. 18, co-expression of a fusion protein comprising a substitution mutation within the minimal polypeptide sequence, designated 3-72, linked to Protein A provided no more than the level of expression detected for the control in lane 2 of FIG. 18. This was designated “No Activity”.
The results of this analysis indicated that an internal polypeptide fragment of the J domain of Erdj3, designated 3-29, has the minimal polypeptide sequence (IKKAYRKLA; SEQ ID NO:48) that provides a high activity for enhancing protein expression. The polypeptide 3-29 sequence is located within a helix II of the J domain, but does not include any residues of the adjacent (C-proximal) loop domain.
Various mutations of the J domain fragment 3-29 sequence were made and assessed for protein expression enhancing activity. The mutated sequences are shown in the table above, see polypeptide nos. 3-44 to 3-88.
The J domains of other J proteins were also assessed for internal polypeptide sequences located in positions similar to that of the 3-29 polypeptide within the J domain of Erdj3. Such sequences are designated 3-89 to 3-99 in the table above. Most of these polypeptides provided complete or partial activity in the assay for enhanced expression of the secreted IL13Rα2-V5-Fc target protein. However, two of the polypeptides, designated 3-98 and 3-99, possessed amino acid sequences that diverged considerably from that of polypeptide 3-29, and these polypeptides also lacked protein expression enhancing activity.
Example 11. Structural Formula Defining a New Family of Protein Expression Enhancing Polypeptides
Below is an overview of the analysis of the polypeptide sequence mutation data that led not only to the discovery of the minimal sequence of a polypeptide fragment of the J domain of Erdj3 that provides protein expression enhancing activity (polypeptide 3-29, SEQ ID NO:48), but also to a structural formula that defines a new family of protein expression enhancing polypeptides as shown below.
FIG. 19 shows an alignment of the amino acid sequence for the J domain of Erdj3 with a series of deletion mutated polypeptides along with their protein expression enhancing activity determined using the unmodified arrangement in which each polypeptide was used to construct a Flag-tagged Protein A fusion protein as described above. The level of expression of secreted IL13Rα2-V5-Fc target protein in the media of cultures of cells co-expressing each Flag-tagged Protein A fusion and the IL13Rα2-V5-Fc target protein was determined by immunoblot using an anti-V5 antibody as described above.
Deletion mutated polypeptides designated 3-6, 3-7, 3-8, and 3-9 in FIG. 19 all lacked protein expression enhancing activity (no activity), indicating that αhelix II amino acid sequences are essential for activity. Deletion mutated polypeptides designated 3-15 and 3-17 in FIG. 19 retained high activity, indicating that the sequence DIKKAYRKLALQL (SEQ ID NO:274) was sufficient for providing high protein expression enhancing activity. This polypeptide was then subjected to further mutation analysis as shown in the table below.







TABLE 59







Amino Acid Sequence and Protein Expression Enhancing


Activity of Mutated Polypeptides.











PP No.
aa
sequence
SEQ ID NO:
Act















3-18
13
DIKKAYRKLALQL
274
HA



3-19
12
DIKKAYRKLALQ
275
HA



3-20
11
DIKKAYRKLAL
276
HA



 3-21
 10
 DIKKAYRKLA
 277
 HA








 {close oversize brace} The last amino acid is essential


 3-22
 9
 DIKKAYRKL
 278
 NA



3-23
8
DIKKAYRK
279
NA



3-24
7
DIKKAYR
280
NA



 3-25
 12
 IKKAYRKLALQL
 281
 HA








 {close oversize brace} The first amino acid is essential


 3-26
 11
 KKAYRKLALQL
 282
 NA



3-27
11
IKKAYRKLALQ
283
HA



3-28
10
IKKAYRKLAL
284
HA



3-29
9
IKKAYRKLA
 48
HA
← Identified Minimum Sequence


3-30
8
IKKAYRKL
285
A



3-31
10
KKAYRKLALQ
286
NA



3-32
9
KKAYRKLAL
287
NA



3-33
8
KKAYRKLA
288
NA



3-34
9
KAYRKLALQ
289
NA



3-35
7
IKKAYRK
290
NA



3-36
6
IKKAYR
291
NA









As noted above, the difference in activity between that of the polypeptide designated 3-21 (high activity, HA) and that of the polypeptide designated 3-22 (no activity, NA) indicated that the C-terminal leucine (L) residue is essential for protein expression enhancing activity. Similarly, the difference in activity between that of polypeptide 3-25 and that of polypeptide 3-26 indicated that the N-terminal isoleucine (I) is essential for activity. As noted previously, polypeptide 3-29 defines the minimal polypeptide sequence of the J domain of Erdj3 for providing complete protein expression enhancing activity.
In addition to the results described above, additional analyses as outlined below led to the identification of an essential amino acid consensus sequence for a protein expression enhancing polypeptide of the invention.
To identify the essential amino acid sequence for providing protein expression enhancing activity, each amino acid of the 3-29 sequence was deleted and the polypeptide tested for protein expression enhancing activity using the IL13Rα2-V5-Fc target protein in the unmodified arrangement described above.
Starting with the minimum sequence of the polypeptide fragment of the J domain of Erdj3, the polypeptide 3-29 sequence (IKKAYRKLA; SEQ ID NO:48) was subjected to the following mutation analysis at each of the nine amino acid positions:

    
    
        (a) 3-29: IKKAYRKLA (SEQ ID NO:48), regarding position 1, see summary analysis (1) below,
        (b) 3-44: IK_AYRKLA (SEQ ID NO:295), no activity, regarding position 3, see summary analysis (2) below,
        (c) 3-45: IKK YRKLA (SEQ ID NO:53), some activity, regarding position 4, see summary analysis (3) below,
        (d) 3-39: IKKA_RKLA (SEQ ID NO:294), no activity, regarding position 5, see summary analysis (4), below,
        (e) 3-46: IKKAY_KLA (SEQ ID NO:54), some activity, regarding position 6, see summary analysis (5) below,
        (f) 3-47: IKKAYR_LA (SEQ ID NO:55), some activity, regarding position 7, see summary analysis (5) below,
        (g) 3-48: IKKAYRK_A (SEQ ID NO:56), some activity, regarding position 8, see summary analysis (6) below,
        (h) IKKAYRKLA (SEQ ID NO:48), high activity, regarding position 9, see summary analysis (6) below.

Summary Analyses

    
    












(1) IKKAYRKLA
(SEQ ID NO: 48)






First amino acid is essential for the activity.
The result for the comparison of the first amino acid among J members (47 J proteins) indicated the following incidences of amino acids at position 1:
I (34), L (6), V (4), M (1), A (1), R (1)
All of these amino acids have a nonpolar side chain group, except Arg (R).
The following constructions derived from other J members were made and tested:









3-49:







(SEQ ID NO: 57)









LKKAYRKLA,






high activity










3-50:







(SEQ ID NO: 58)









VKKAYRKLA,






high activity










3-51:







(SEQ ID NO: 59)









MKKAYRKLA,






high activity










3-52:







(SEQ ID NO: 60)









AKKAYRKLA,






high activity










3-53:







(SEQ ID NO: 296)









SKKAYRKLA,






no activity










3-54:







(SEQ ID NO: 297)









FKKAYRKLA,






no activity.

Therefore, it the first position is preferably an amino acid with a nonpolar amino acid side group that is I, L, V, A, and M.










(2) IK_AYRKLA;
(SEQ ID NO: 295)






no activity

This implies two possibilities:
a) two amino acids are required at this position









3-55:







(SEQ ID NO: 298)









IAQAYRKLA,






no activity










3-56:







(SEQ ID NO: 299)









ILAAYRKLA,






no activity

indicating some specific amino acid is required,
b) two lysines are required or only one is enough.
Through the comparison of these two positions among J members (47 J proteins), these two positions are well conserved as indicated by the following incidences:

    
    
        KK (26), KR (5), RK (3), AR (3), KA (2), KQ (2), KL (1), IK (1), NK (1), RQ (1), RD (1), LA (1)
    
    


All of these harbor at least one amino acid with a basic amino acid side chain with one exception.
Therefore, the following substitution mutations were made and tested:









3-57:







(SEQ ID NO: 61)









IAKAYRKLA,






some activity










3-58:







(SEQ ID NO: 62)









IKAAYRKLA,






some activity.

Therefore, it is concluded that at least one amino acid at positions 2 and 3 is a basic amino acid K or R.










(3) IKK_YRKLA,
(SEQ ID NO: 53)






some activity

This result indicates that it is better to have some amino acid in this position but not absolutely necessary.
Through a comparison of this position among J members (47 J proteins), this position is also well conserved as indicated by the following incidences:

    
    
        A (36), K (2), R (2), S (2), Q (2), T (1), I (1), E (1)
    
    


The following polypeptides were constructed and tested:









Basic amino acid



3-59







(SEQ ID NO: 63)









IKKRYRKLA;






high activity










Polar uncharged amino acid



3-60







(SEQ ID NO: 64)









IKKSYRKLA;






some activity










Polar uncharged amino acid



3-61







(SEQ ID NO: 65)









IKKQYRKLA;






some activity










Acidic amino acid



3-62







(SEQ ID NO: 66)









IKKEYRKLA;






some activity










Aromatic amino acid



3-63







(SEQ ID NO: 67)









IKKFYRKLA;






some activity










Polar uncharged amino acid



3-64







(SEQ ID NO: 68)









IKKCYRKLA;






some activity.

From the above substitution mutations, it is concluded that any of the 20 naturally occurring amino acids may occupy position 4 since deletion at this position still retains activity.










(4) IKKA_RKLA;
(SEQ ID NO: 312)






This result implies that some amino acid in position 5 is essential.
Through the comparison of this position among J members (47 J proteins), the amino acid distribution is given below.

    
    
        Y (34), F (10), H (2), I (1)
    
    


Therefore the following polypeptides were made and tested:









Aromatic amino acid



3-65







(SEQ ID NO: 69)









IKKAFRKLA,






high activity










Positive charged amino acid



3-66







(SEQ ID NO: 300)









IKKAHRKLA,






no activity










Nonpolar amino acid



3-67







(SEQ ID NO: 301)









IKKAIRKLA,






no activity










Aromatic amino acid



3-68







(SEQ ID NO: 70)









IKKAWRKLA,






high activity










Nonpolar amino acid



3-69







(SEQ ID NO: 302)









IKKAARKLA,






no activity










Nonpolar amino acid



3-70







(SEQ ID NO: 303)









IKKASRKLA,






no activity.

Therefore, the amino acid at position 5 is an aromatic amino acid that is Y, F, or W.










(5) IKKAY_KLA,
(SEQ ID NO: 313)






some activity








(SEQ ID NO: 314)









IKKAYR_LA






some activity

Through the comparison of this position among J members (47 J proteins), the case that at least one amino acid is a basic amino acid is 43 out of 47 (both 23, and either one 20).
The following mutated polypeptides have two amino acids replaced at positions 6 and 7:









3-71







(SEQ ID NO: 304)









IKKAYHQLA,






no activity








(SEQ ID NO: 305)









3-72 IKKAYYQLA,






no activity








(SEQ ID NO: 306)









3-73 IKKAYFSLA,






no activity.

Therefore, at least one of the amino acids at positions 6 and 7 is a basic amino acid K or R.









(SEQ ID NO: 56)



(6) IKKAYRK_A,






some activity










(SEQ ID NO: 315)



IKKAYRKL,






some activity

Through the comparison of these positions among J members (47 J proteins), the case that two positions are occupied with L and A is 25 out of 47, in which all of them are L-A. The case that at least one amino acid at these positions is L or A is 14, and 8 cases indicates neither L nor A.
The following mutated polypeptides were made with two amino acids replaced and tested for activity:







(SEQ ID NO: 307)









3-74 IKKAYRKQS,






no activity








(SEQ ID NO: 308)









3-75 IKKAYRKQC,






no activity








(SEQ ID NO: 309)









3-76 IKKAYRKDI,






no activity.

The following mutated polypeptides have position 8 replaced as indicated:









(SEQ ID NO: 71)



Polar amino acid 3-77 IKKAYRKQA,






high activity










(SEQ ID NO: 72)



Nonpolar amino acid 3-78 IKKAYRKMA,






high activity










(SEQ ID NO: 73)



Nonpolar amino acid 3-79 IKKAYRKIA,






some activity










(SEQ ID NO: 74)



Nonpolar amino acid 3-80 IKKAYRKAA,






some activity










(SEQ ID NO: 75)



Nonpolar amino acid 3-81 IKKAYRKVA,






some activity










(SEQ ID NO: 76)



Basic amino acid 3-82 IKKAYRKRA,






some activity.

The following mutated polypeptides have position 9 replaced as indicated:









(SEQ ID NO: 77)



Nonpolar amino acid 3-83 IKKAYRKLM,






high activity










(SEQ ID NO: 78)



Nonpolar amino acid 3-84 IKKAYRKLI,






high activity










Nonpolar amino acid



3-85







(SEQ ID NO: 79)









IKKAYRKLV,






high activity










Polar uncharged amino acid



3-86







(SEQ ID NO: 80)









IKKAYRKLC,






some activity










Polar uncharged amino acid



3-87







(SEQ ID NO: 81)









IKKAYRKLS,






high activity










Aromatic amino acid



3-88







(SEQ ID NO: 82)









IKKAYRKLY,






some activity.

Results of other mutated polypeptides:









Replacement L and A



3-42







(SEQ ID NO: 51)









IKKAYRKALQ,






high activity










Double L



3-43







(SEQ ID NO: 52)









IKKAYRKLLQ,






high activity.

Therefore, at least one of the amino acids at X8 and X9 is L or A.
Through these studies, it is concluded that an isolated protein expression enhancing J domain analog polypeptide comprises the formula:







(SEQ ID NO: 47)









X1-X2-X3-X4-X5-X6-X7-X8-X9,






wherein:

    
    
        X1 is isoleucine (I), leucine (L), valine (V), alanine (A), or methionine (M);
        X2 and X3 are each independently any amino acid with the proviso that one or both are lysine (K) or arginine (R);
        X4 is any amino acid or X4 may be absent when X1 through X3 are present and X5 through X9 are present;
        X5 is tyrosine (Y), tryptophan (W), or phenylalanine (F);
        X6 and X7 are each independently any amino acid with the proviso that one or both are lysine (K) or arginine (R); or either one of X6 and X7 may be absent when the other is K or R and when X1 through X5 are present and X8 and X9 are present; and
        X8 and X9 are any amino acid with the proviso that one or both are leucine (L) or alanine (A); or one of X8 and X9 may be absent when the other is L or A and when X1 through X7 are present.
    
    


The above formula is applicable to the sequence of the following polypeptide fragments from other J proteins, and all of these polypeptides have activity:









Erdj1



3-89







(SEQ ID NO: 83)









IRKAYRKLSLTL,






some activity










Erdj2



3-90







(SEQ ID NO: 84)









IKKQYRLLSLKY,






some activity










Erdj4



3-91







(SEQ ID NO: 85)









IKKAFHKLAMKY,






high activity










Erdj5



3-92







(SEQ ID NO: 86)









IRQAFKKLALKL,






some activity










Erdj6



3-93







(SEQ ID NO: 87)









IIKAYRKLALQW,






high activity










Erdj7



3-94







(SEQ ID NO: 88)









IARAYRQLARRY,






high activity










Hsp40



3-95







(SEQ ID NO: 89)









IKRAYRRQALRY,






high activity










CSP



3-96







(SEQ ID NO: 90)









IKKSYRKLALKY,






high activity










DnaJ



3-97







(SEQ ID NO: 91)









IKKAYKRLAMKY,






The sequences below from other J proteins do not match the above formula and these polypeptides do not have protein expression enhancing activity:









From SV40 J protein



3-98







(SEQ ID NO: 310)









MRKAYLKKC,






no activity










From Dnaj homolog subfamily C member 12



3-99







(SEQ ID NO: 311)









ILAEFKVRAL, 






no activity.

The analyses and results summarized above indicate that the above formula defines a new family of polypeptides that provide protein expression enhancing activity.
Example 12. Minimal Polypeptide of J Domain Enhances Target Protein Expression in a Modified Arrangement
As explained above, the results of the mutation analysis of the J domain of Erdj3 indicated that an internal polypeptide sequence, designated 3-29, is the minimal sequence with the J domain for a polypeptide (IKKAYRKLA; SEQ ID NO:48) to provides high activity for enhancing protein expression using the above assay in an unmodified arrangement. The protein expression enhancing activity of the 3-29 polypeptide was also examined in a modified arrangement.
In this experiment, a first fusion protein comprised IL13Rα2TF as the target protein of interest linked to the BSC1 polypeptide (SEQ ID NO:48), which in turn was linked to an V5 epitope tag. This fusion protein was designated IL13Rα2TF-BSC1 shown in the table below.







TABLE 60







Amino Acid Sequence of a V5-Tagged IL13Rα2TF-BSC1 Fusion


Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2TF-BSC1
SEQ ID NO: 316
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


protein

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD




HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKGTGSEFIKKAYRKLADIGGGS




GGSGGSGGAAALEGKPIPNPLLGLDST


 


IL13Rα2TF
residues 1-339
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI



of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 316
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKK


 


Linker
residues 340-345
GTGSEF



of SEQ ID




NO: 316



 


BSC1
residues 346-354
IKKAYRKLA



of SEQ ID




NO: 316



 


Linker
residues 355-373
DIGGGSGGSGGSGGAAALE



of SEQ ID




NO: 316



 


V5 epitope
residues 374-387
GKPIPNPLLGLDST


domain
of SEQ ID




NO: 316









A second fusion protein comprised IL13Rα2TF as the target protein of interest linked to a mutated version of the BSC1 polypeptide, designated “IL13Rα2TF-BSC1MT” in which the second and third positions of the BSC1 polypeptide were mutated from K-K to A-Q as shown in the table below. The BSC1MT polypeptide is designated 3-55.








TABLE 61







Amino Acid Sequence of a V5-Tagged IL13Rα2TF-BSC1MT Fusion


Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





IL13Rα2TF-BSC1MT
SEQ ID NO: 317
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI


protein

KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD




HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKKGTGSEFIAQAYRKLADIGGGS




GGSGGSGGAAALEGKPIPNPLLGLDST


 


IL13Rα2TF
residues 1-339
MAFVCLAIGCLYTFLISTTFGCTSSSDTEI



of SEQ ID
KVNPPQDFEIVDPGYLGYLYLQWQPPLSLD



NO: 317
HFKECTVEYELKYRNIGSETWKTIITKNLH




YKDGFDLNKGIEAKIHTLLPWQCTNGSEVQ




SSWAETTYWISPQGIPETKVQDMDCVYYNW




QYLLCSWKPGIGVLLDTNYNLFYWYEGLDH




ALQCVDYIKADGQNIGCRFPYLEASDYKDF




YICVNGSSENKPIRSSYFTFQLQNIVKPLP




PVYLTFTRESSCEIKLKWSIPLGPIPARCF




DYEIEIREDDTTLVTATVENETYTLKTTNE




TRQLCFVVRSKVNIYCSDDGIWSEWSDKQC




WEGEDLSKK


 


Linker
residues 340-345
GTGSEF



of SEQ ID




NO: 317



 


BSC1MT
residues 346-354
IAQAYRKLA



of SEQ ID




NO: 317



 


Linker
residues 355-373
DIGGGSGGSGGSGGAAALE



of SEQ ID




NO: 317



 


V5 epitope
residues 374-387
GKPIPNPLLGLDST


domain
of SEQ ID




NO: 317









Schematic diagrams of IL13Rα2TF (target protein alone), IL13Rα2TF-BSC1, and IL13Rα2TF-BSC1MT proteins are shown in FIG. 20A. Cells were transfected with vector comprising a recombinant gene encoding IL13Rα2TF (control), IL13Rα2TF-BSC1, or IL13Rα2TF-BSC1MT and grown in separate cultures as described above. Culture media from each culture was assayed for the presence of the proteins by immunoblot using an anti-V5 antibody as described above.
As shown in FIG. 20B, relatively little IL13Rα2TF protein was detected in culture medium of the control cell culture. See, lane 2 of FIG. 20B. In contrast, a significantly higher level of the IL13Rα2TF-BSC1 fusion protein was detected in culture medium of cells transfected with a vector comprising a gene encoding the IL13Rα2TF-BSC1 fusion protein. See, lane 3 of FIG. 20B. The amount of IL13Rα2TF-BSC1 fusion protein detected in the culture medium was also significantly higher than the level of protein detected in culture medium of cells transfected with a vector encoding the IL13Rα2TF-BSC1MT fusion protein. This latter protein was expressed at approximately the same low level as detected for the IL13Rα2TF protein in control cells. See, lane 4 of FIG. 20B. The results show the BSC1 polypeptide (IKKAYRKLA; SEQ ID NO:48) is effective as a protein expression enhancing polypeptide in a modified arrangement of the invention and that alteration of the internal K-K dipeptide can destroy such activity.
Example 13. BSC1-Protein A Fusion Protein Enhances Expression of IL13Rα2TF-V5-Fc Target Protein in an Unmodified Arrangement
The BSC1 polypeptide (IKKAYRKLA, SEQ ID NO:48), the minimal polypeptide fragment of the J domain of Erdj3 described above, was used to construct a BSC1-Protein A fusion protein shown in the table below to determine whether the BSC1-Protein A fusion protein could be used in an unmodified arrangement for enhancing expression of an IL13Rα2TF-V5-Fc target protein described above.







TABLE 62







Amino acid Sequence of a Flag-Tagged BSC1-Protein A Fusion


Protein










Sequence
Amino Acid Sequence


Protein Domain
Identifier
123456789012345678901234567890





Flag-tagged BSC1-
SEQ ID NO: 318
MGVKVLFALICIAVAEAGTGSGEFIKKAYR


Protein A Fusion

KLADIGGGSGGSGGSGGAAAADNKFNKEQQ




NAFYEILNMPNLNEEQRNGFIQSLKDDPSQ




SANVLGEAKKLNDSQAPKLEGDYKDDDDK


 


signal sequence
residues 1-17
MGVKVLFALICIAVAEA



of SEQ ID




NO: 318



 


linker 1
residues 18-24
GTGSGEF



of SEQ ID




NO: 318



 


BSC1 polypeptide
residues 25-33
IKKAYRKLA



of SEQ ID




NO: 318



 


linker 2
residues 34-50
DIGGGSGGSGGSGGAAA



of SEQ ID




NO: 318



 


Protein A
residues 51-108
ADNKFNKEQQNAFYEILNMPNLNEEQRNGF



of SEQ ID
IQSLKDDPSQSANVLGEAKKLNDSQAPK



NO: 318



 


linker 3
residues 109-111
LEG



of SEQ ID




NO: 318



 


Flag epitope tag
residues 112-119
DYKDDDDK



of SEQ ID




NO: 318









The IL13Rα2TF-V5-Fc target protein was expressed with or without BSC1-Protein A fusion protein in HEK293 cells. Cultures were grown for two days, and the media were harvested and centrifuged to remove the debris. Expression of the IL13Rα2TF-V5-Fc target protein was significantly enhanced in the medium of cells co-expressing the target protein and the BSC1-Protein A fusion compared to level of expression of the target protein in the absence of the BSC1-Protein A fusion protein (data not shown).
To determine whether the IL13Rα2TF-V5-Fc target protein expressed in culture medium retained IL13 binding activity, the following binding assay was performed. Recombinant human IL13 was added to samples of the media from cultures of cells that did not express either of the proteins (control), that expressed only the IL13Rα2TF-V5-Fc target protein, and that co-expressed the IL13Rα2TF-V5-Fc target protein and the BSC1-Protein A fusion protein. The samples were incubated with the IL13 for 2 hours. The samples were used in an IL13 detection assay (RayBio® Human IL13 ELISA Kit; ELH-IL13-001). In this assay, the detection of human IL13 decreases when human IL13 is trapped by IL13Rα2TF-V5-Fc target protein. As shown in FIG. 21B, the medium from a culture of cells expressing neither protein clearly did not bind IL13 as indicated by the high level absorbance (lane 1 of FIG. 21). Medium from a culture of cells expressing only the IL13Rα2TF-V5-Fc target protein bound some IL13 (lane 2), but a significantly greater amount of IL13 was bound the medium from a culture of cells co-expressing the IL13Rα2TF-V5-Fc target protein and the BSC1-Protein A fusion protein (lane 3). The results clearly show that more human IL13 was bound in medium containing the enhanced level of expression of the IL13Rα2TF-V5-Fc target protein. Accordingly, the IL13Rα2TF-V5-Fc target protein expressed in culture medium at an enhanced level retained its IL13 binding activity.
Example 14. BSC1-Protein G Fusion Protein Enhances Expression of a Factor VII-V5-Fc Target Protein in an Unmodified Arrangement
Factor VII (FVII) is the serine esterase of the extrinsic coagulation pathway and widely used to treat a variety of bleeding complications. See, Hedner, Semin. Hematol., 43(suppl 1): S105-S107 (2006). A complex of FVII and tissue factor (TF) in the presence of phospholipids and calcium activates Factor X to Factor Xa.
A BSC1 polypeptide was used to construct a BSC1-Protein G fusion protein to determine whether the fusion protein was effective in enhancing an FVII-V5-Fc target protein in an unmodified arrangement.
The amino acid sequence of the V5-tagged FVII-Fc target protein is shown in the table below.







TABLE 63







Amino Acid Sequence of a V5-Tagged FVII-Fc Target Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged FVII-
SEQ ID NO: 319
MVSQALRLLCLLLGLQGCLAAGGVAKASGG


Fc target

ETRDMPWKPGPHRVFVTQEEAHGVLHRRRR


protein

ANAFLEELRPGSLERECKEEQCSFEEAREI




FKDAERTKLFWISYSDGDQCASSPCQNGGS




CKDQLQSYICFCLPAFEGRNCETHKDDQLI




CVNENGGCEQYCSDHTGTKRSCRCHEGYSL




LADGVSCTPTVEYPCGKIPILEKRNASKPQ




GRIVGGKVCPKGECPWQVLLLVNGAQLCGG




TLINTIWVVSAAHCFDKIKNWRNLIAVLGE




HDLSEHDGDEQSRRVAQVIIPSTYVPGTTN




HDIALLRLHQPVVLTDHVVPLCLPERTFSE




RTLAFVRFSLVSGWGQLLDRGATALELMVL




NVPRLMTQDCLQQSRKVGDSPNITEYMFCA




GYSDGSKDSCKGDSGGPHATHYRGTWYLTG




IVSWGQGCATVGHFGVYTRVSQYIEWLQKL




MRSEPRPGVLLRAPFPLEGKPIPNPLLGLD




STSRPKSCDKTHTCPPCPAPELLGGPSVFL




FPPKPKDTLMISRTPEVTCVVVDVSHEDPE




VKFNWYVDGVEVHNAKTKPREEQYNSTYRV




VSVLTVLHQDWLNGKEYKCKVSNKALPAPI




EKTISKAKGQPREPQVYTLPPSRDELTKNQ




VSLTCLVKGFYPSDIAVEWESNGQPENNYK




TTPPVLDSDGSFFLYSKLTVDKSRWQQGNV




FSCSVMHEALHNHYTQKSLSLSPGK


 


FVII
residues 1-466
MVSQALRLLCLLLGLQGCLAAGGVAKASGG



of SEQ ID
ETRDMPWKPGPHRVFVTQEEAHGVLHRRRR



NO: 319
ANAFLEELRPGSLERECKEEQCSFEEAREI




FKDAERTKLFWISYSDGDQCASSPCQNGGS




CKDQLQSYICFCLPAFEGRNCETHKDDQLI




CVNENGGCEQYCSDHTGTKRSCRCHEGYSL




LADGVSCTPTVEYPCGKIPILEKRNASKPQ




GRIVGGKVCPKGECPWQVLLLVNGAQLCGG




TLINTIWVVSAAHCFDKIKNWRNLIAVLGE




HDLSEHDGDEQSRRVAQVIIPSTYVPGTTN




HDIALLRLHQPVVLTDHVVPLCLPERTFSE




RTLAFVRFSLVSGWGQLLDRGATALELMVL




NVPRLMTQDCLQQSRKVGDSPNITEYMFCA




GYSDGSKDSCKGDSGGPHATHYRGTWYLTG




IVSWGQGCATVGHFGVYTRVSQYIEWLQKL




MRSEPRPGVLLRAPFP


 


Linker 1
residues 467-468
LE



of SEQ ID




NO: 319



 


V5 epitope
residues 469-482
GKPIPNPLLGLDST


domain
of SEQ ID




NO: 319



 


Linker 2
residues 483-484
SR



of SEQ ID




NO: 319



 


Fc domain
residues 485-715
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 319
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









The amino acid sequence of the Flag-tagged BSC1-Protein G fusion protein is shown in the table below.







TABLE 64







Amino Acid Sequence of a Flag-Tagged BSC1-Protein G Fusion


Protein










Sequence
Amino Acid Sequence


Protein Domain
Identifier
123456789012345678901234567890





Flag-tagged BSC1-
SEQ ID NO: 320
MGVKVLFALICIAVAEAGTGSGEFIKKAYR


Protein G Fusion

KLADIGGGSGGSGGSGGAAAATYKLVINGK




TLKGETTTEAVDAATAEKVFKQYANDNGVD




GEWTYDDATKTFTVTEKPEVIDASELTPAV




TLEGDYKDDDDK


 


signal sequence
residues 1-17
MGVKVLFALICIAVAEA



of SEQ ID




NO: 320



 


linker 1
residues 18-24
GTGSGEF



of SEQ ID




NO: 320



 


BSC1 polypeptide
residues 25-33
IKKAYRKLA



of SEQ ID




NO: 320



 


linker 2
residues 34-50
DIGGGSGGSGGSGGAAA



of SEQ ID




NO: 320



 


Protein G
residues 51-121
TYKLVINGKTLKGETTTEAVDAATAEKVFK



of SEQ ID
QYANDNGVDGEWTYDDATKTFTVTEKPEVI



NO: 320
DASELTPAVT


 


linker 3
residues 122-124
LEG



of SEQ ID




NO: 320



 


Flag epitope tag
residues 126-132
DYKDDDDK



of SEQ ID




NO: 320









The level of expression of the FVII-Fc target protein was determined by immunoblot assay using anti-Flag antibody in both culture media and lysates of cells expressing neither protein, of cells expressing only the FVII-Fc target protein, and of cells co-expressing the FVII-Fc target protein and the BSC1-Protein G fusion proteins. The results are shown in FIG. 22A. As shown in the top panel of FIG. 22A, the level of expression of the FVII-Fc target protein secreted into the culture medium was significantly greater in a culture of cells co-expressing the FVII-Fc target protein and the BSC1-Protein G fusion protein (lane 2) than in a culture of cells expressing the FVII-Fc target protein alone (lane 3). The middle panel of FIG. 22A is an immunoblot of cell lysates using an anti-Flag antibody. The immunoblot shows that the BSC1-Protein G fusion protein was expressed in cells expressing both the FVII-Fc target protein and the BSC1-Protein G fusion protein. As shown in the bottom panel of FIG. 22A, no significant amount of the BSC1-Protein G fusion protein was secreted into the medium with the FVII-Fc target protein (see, lane 3).
FIG. 22B shows bar graphs of a densitometry analysis of the signal of the for FVII-Fc target protein expression in culture media shown in the top immunoblot in FIG. 22A. Bar graphs 1, 2, and 3 of FIG. 22B correspond to the signals of lanes 1, 2, and 3 in the top immunoblot in FIG. 22A.
The results show that the co-expression of the BSC1-Protein G fusion protein and the FVII-Fc target protein significantly enhanced the level of expression of the target protein secreted into culture medium as compared to the level in that absence of the BSC1-Protein G fusion protein.
Example 15. BSC1-Protein a Fusion Protein Enhances Expression of a Factor IX-V5-Fc Target Protein in an Unmodified Arrangement
Factor IX has been widely used for the treatment of hemophilia B, and its Fc fusion protein (FIX-Fc) is currently in a clinical trial (phase III) with positive result (prolonged effect).
In this experiment, the effect of the BSC1-Protein A fusion protein described above on the level of expression of an FIX-Fc target protein in an unmodified arrangement was determined
The amino acid sequence of the V5-tagged FIX-Fc target protein is shown in the table below.







TABLE 65







Amino Acid Sequence of a V5-Tagged FIX-Fc Target Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged FIX-Fc
SEQ ID NO: 321
MQRVNMIMAESPGLITICLLGYLLSAECTV


fusion molecule

FLDHENANKILNRPKRYNSGKLEEFVQGNL




ERECMEEKCSFEEAREVFENTERTTEFWKQ




YVDGDQCESNPCLNGGSCKDDINSYECWCP




FGFEGKNCELDVTCNIKNGRCEQFCKNSAD




NKVVCSCTEGYRLAENQKSCEPAVPFPCGR




VSVSQTSKLTRAETVFPDVDYVNSTEAETI




LDNITQSTQSFNDFTRVVGGEDAKPGQFPW




QVVLNGKVDAFCGGSIVNEKWIVTAAHCVE




TGVKITVVAGEHNIEETEHTEQKRNVIRII




PHHNYNAAINKYNHDIALLELDEPLVLNSY




VTPICIADKEYTNIFLKFGSGYVSGWGRVF




HKGRSALVLQYLRVPLVDRATCLRSTKFTI




YNNMFCAGFHEGGRDSCQGDSGGPHVTEVE




GTSFLTGIISWGEECAMKGKYGIYTKVSRY




VNWIKEKTKLTLEGKPIPNPLLGLDSTSRP




KSCDKTHTCPPCPAPELLGGPSVFLFPPKP




KDTLMISRTPEVTCVVVDVSHEDPEVKFNW




YVDGVEVHNAKTKPREEQYNSTYRVVSVLT




VLHQDWLNGKEYKCKVSNKALPAPIEKTIS




KAKGQPREPQVYTLPPSRDELTKNQVSLTC




LVKGFYPSDIAVEWESNGQPENNYKTTPPV




LDSDGSFFLYSKLTVDKSRWQQGNVFSCSV




MHEALHNHYTQKSLSLSPGK


 


FIX
residues 1-461
MQRVNMIMAESPGLITICLLGYLLSAECTV



of SEQ ID
FLDHENANKILNRPKRYNSGKLEEFVQGNL



NO: 321
ERECMEEKCSFEEAREVFENTERTTEFWKQ




YVDGDQCESNPCLNGGSCKDDINSYECWCP




FGFEGKNCELDVTCNIKNGRCEQFCKNSAD




NKVVCSCTEGYRLAENQKSCEPAVPFPCGR




VSVSQTSKLTRAETVFPDVDYVNSTEAETI




LDNITQSTQSFNDFTRVVGGEDAKPGQFPW




QVVLNGKVDAFCGGSIVNEKWIVTAAHCVE




TGVKITVVAGEHNIEETEHTEQKRNVIRII




PHHNYNAAINKYNHDIALLELDEPLVLNSY




VTPICIADKEYTNIFLKFGSGYVSGWGRVF




HKGRSALVLQYLRVPLVDRATCLRSTKFTI




YNNMFCAGFHEGGRDSCQGDSGGPHVTEVE




GTSFLTGIISWGEECAMKGKYGIYTKVSRY




VNWIKEKTKLT


 


Linker 1
residues 462-463
LE



of SEQ ID




NO: 321



 


V5 epitope
residues 464-477
GKPIPNPLLGLDST


domain
of SEQ ID




NO: 321



 


Linker 2
residues 478-479
SR



of SEQ ID




NO: 321



 


Fc domain
residues 480-710
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 321
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









FIG. 23A shows the expression of the FIX-Fc target protein secreted into the media of cultures of transfected cells expressing the FIX-Fc target protein alone (lane 2) and of transfected cells co-expressing the FIX-Fc fusion protein and the BSC1-Protein A fusion protein (lane 3). Lane 1 of FIG. 23A shows medium from a culture of non-expressing cells as a control. As shown in lane 2 of FIG. 23A, some FIX-Fc target protein is secreted by cells expressing the FIX-Fc target protein alone. However, as clearly shown in lane 3 of FIG. 23A, the level of expression of the target protein secreted into medium is significantly enhanced in cells expressing the FIX-Fc target protein and the BSC1-Protein A fusion protein. FIG. 23B shows bar graphs of a densitometry analysis of the signals in the immunoblot of FIG. 23A. Bar graphs 1, 2, and 3 of FIG. 23B correspond to the signals of lanes 1, 2, and 3 in FIG. 23A.

The results clearly show that the co-expression of the BSC1-Protein A fusion protein and the FIX-Fc target protein significantly enhanced the level of expression of the target protein secreted into culture medium as compared to the level in that absence of the BSC1-Protein A fusion protein.
Example 16. BSC1-Protein G Fusion Protein Enhances Expression of a Factor VIII-V5-Fc Target Protein in an Unmodified Arrangement
The biological importance of Factor FVIII is demonstrated in hemophilia A, a congenital bleeding disorder occurring primarily in males that results from an X-chromosome-linked deficiency of FVIII. Standard treatment involves replacing the missing FVIII to stop the bleeding. A FVIII-Fc fusion protein was developed to provide a prolonged half-life of FVIII activity in hemophilia A patients (Powell et al., Blood, 119(13): 3031-3037 (2012)). The fusion protein was approved by the United States Food and Drug Administration in 2013 (ELOCTATETM; Biogen Idec).
This experiment examined the effect of the BSC1-Protein G fusion protein described above on the level of expression of a V5-tagged FVIII-Fc target protein in an unmodified arrangement. The amino acid sequence of the V5-tagged FVIII-Fc target protein is shown in the table below.







TABLE 66







Amino Acid Sequence of a V5-Tagged FVIII-Fc Target Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged FVIII-
SEQ ID NO: 322
MQIELSTCFFLCLLRFCFSATRRYYLGAVE


Fc fusion

LSWDYMQSDLGELPVDARFPPRVPKSFPFN


molecule

TSVVYKKTLFVEFTDHLFNIAKPRPPWMGL




LGPTIQAEVYDTVVITLKNMASHPVSLHAV




GVSYWKASEGAEYDDQTSQREKEDDKVFPG




GSHTYVWQVLKENGPMASDPLCLTYSYLSH




VDLVKDLNSGLIGALLVCREGSLAKEKTQT




LHKFILLFAVFDEGKSWHSETKNSLMQDRD




AASARAWPKMHTVNGYVNRSLPGLIGCHRK




SVYWHVIGMGTTPEVHSIFLEGHTFLVRNH




RQASLEISPITFLTAQTLLMDLGQFLLFCH




ISSHQHDGMEAYVKVDSCPEEPQLRMKNNE




EAEDYDDDLTDSEMDVVRFDDDNSPSFIQI




RSVAKKHPKTWVHYIAAEEEDWDYAPLVLA




PDDRSYKSQYLNNGPQRIGRKYKKVRFMAY




TDETFKTREAIQHESGILGPLLYGEVGDTL




LIIFKNQASRPYNIYPHGITDVRPLYSRRL




PKGVKHLKDFPILPGEIFKYKWTVTVEDGP




TKSDPRCLTRYYSSFVNMERDLASGLIGPL




LICYKESVDQRGNQIMSDKRNVILFSVFDE




NRSWYLTENIQRFLPNPAGVQLEDPEFQAS




NIMHSINGYVFDSLQLSVCLHEVAYWYILS




IGAQTDFLSVFFSGYTFKHKMVYEDTLTLF




PFSGETVFMSMENPGLWILGCHNSDFRNRG




MTALLKVSSCDKNTGDYYEDSYEDISAYLL




SKNNAIEPRSFSQNSRHPSTRQKQFNATTI




PENDIEKTDPWFAHRTPMPKIQNVSSSDLL




MLLRQSPTPHGLSLSDLQEAKYETFSDDPS




PGAIDSNNSLSEMTHFRPQLHHSGDMVFTP




ESGLQLRLNEKLGTTAATELKKLDFKVSST




SNNLISTIPSDNLAAGTDNTSSLGPPSMPV




HYDSQLDTTLFGKKSSPLTESGGPLSLSEE




NNDSKLLESGLMNSQESSWGKNVSSTESGR




LFKGKRAHGPALLTKDNALFKVSISLLKTN




KTSNNSATNRKTHIDGPSLLIENSPSVWQN




ILESDTEFKKVTPLIHDRMLMDKNATALRL




NHMSNKTTSSKNMEMVQQKKEGPIPPDAQN




PDMSFFKMLFLPESARWIQRTHGKNSLNSG




QGPSPKQLVSLGPEKSVEGQNFLSEKNKVV




VGKGEFTKDVGLKEMVFPSSRNLFLTNLDN




LHENNTHNQEKKIQEEIEKKETLIQENVVL




PQIHTVTGTKNFMKNLFLLSTRQNVEGSYD




GAYAPVLQDFRSLNDSTNRTKKHTAHFSKK




GEEENLEGLGNQTKQIVEKYACTTRISPNT




SQQNFVTQRSKRALKQFRLPLEETELEKRI




IVDDTSTQWSKNMKHLTPSTLTQIDYNEKE




KGAITQSPLSDCLTRSHSIPQANRSPLPIA




KVSSFPSIRPIYLTRVLFQDNSSHLPAASY




RKKDSGVQESSHFLQGAKKNNLSLAILTLE




MTGDQREVGSLGTSATNSVTYKKVENTVLP




KPDLPKTSGKVELLPKVHIYQKDLFPTETS




NGSPGHLDLVEGSLLQGTEGAIKWNEANRP




GKVPFLRVATESSAKTPSKLLDPLAWDNHY




GTQIPKEEWKSQEKSPEKTAFKKKDTILSL




NACESNHAIAAINEGQNKPEIEVTWAKQGR




TERLCSQNPPVLKRHQREITRTTLQSDQEE




IDYDDTISVEMKKEDFDIYDEDENQSPRSF




QKKTRHYFIAAVERLWDYGMSSSPHVLRNR




AQSGSVPQFKKVVFQEFTDGSFTQPLYRGE




LNEHLGLLGPYIRAEVEDNIMVTFRNQASR




PYSFYSSLISYEEDQRQGAEPRKNFVKPNE




TKTYFWKVQHHMAPTKDEFDCKAWAYFSDV




DLEKDVHSGLIGPLLVCHTNTLNPAHGRQV




TVQEFALFFTIFDETKSWYFTENMERNCRA




PCNIQMEDPTFKENYRFHAINGYIMDTLPG




LVMAQDQRIRWYLLSMGSNENIHSIHFSGH




VFTVRKKEEYKMALYNLYPGVFETVEMLPS




KAGIWRVECLIGEHLHAGMSTLFLVYSNKC




QTPLGMASGHIRDFQITASGQYGQWAPKLA




RLHYSGSINAWSTKEPFSWIKVDLLAPMII




HGIKTQGARQKFSSLYISQFIIMYSLDGKK




WQTYRGNSTGTLMVFFGNVDSSGIKHNIFN




PPIIARYIRLHPTHYSIRSTLRMELMGCDL




NSCSMPLGMESKAISDAQITASSYFTNMFA




TWSPSKARLHLQGRSNAWRPQVNNPKEWLQ




VDFQKTMKVTGVTTQGVKSLLTSMYVKEFL




ISSSQDGHQWTLFFQNGKVKVFQGNQDSFT




PVVNSLDPPLLTRYLRIHPQSWVHQIALRM




EVLGCEAQDLYLEGKPIPNPLLGLDSTSRP




KSCDKTHTCPPCPAPELLGGPSVFLFPPKP




KDTLMISRTPEVTCVVVDVSHEDPEVKFNW




YVDGVEVHNAKTKPREEQYNSTYRVVSVLT




VLHQDWLNGKEYKCKVSNKALPAPIEKTIS




KAKGQPREPQVYTLPPSRDELTKNQVSLTC




LVKGFYPSDIAVEWESNGQPENNYKTTPPV




LDSDGSFFLYSKLTVDKSRWQQGNVFSCSV




MHEALHNHYTQKSLSLSPGK


 


FVIII
residues 1-2351
MQIELSTCFFLCLLRFCFSATRRYYLGAVE



of SEQ ID
LSWDYMQSDLGELPVDARFPPRVPKSFPFN



NO: 322
TSVVYKKTLFVEFTDHLFNIAKPRPPWMGL




LGPTIQAEVYDTVVITLKNMASHPVSLHAV




GVSYWKASEGAEYDDQTSQREKEDDKVFPG




GSHTYVWQVLKENGPMASDPLCLTYSYLSH




VDLVKDLNSGLIGALLVCREGSLAKEKTQT




LHKFILLFAVFDEGKSWHSETKNSLMQDRD




AASARAWPKMHTVNGYVNRSLPGLIGCHRK




SVYWHVIGMGTTPEVHSIFLEGHTFLVRNH




RQASLEISPITFLTAQTLLMDLGQFLLFCH




ISSHQHDGMEAYVKVDSCPEEPQLRMKNNE




EAEDYDDDLTDSEMDVVRFDDDNSPSFIQI




RSVAKKHPKTWVHYIAAEEEDWDYAPLVLA




PDDRSYKSQYLNNGPQRIGRKYKKVRFMAY




TDETFKTREAIQHESGILGPLLYGEVGDTL




LIIFKNQASRPYNIYPHGITDVRPLYSRRL




PKGVKHLKDFPILPGEIFKYKWTVTVEDGP




TKSDPRCLTRYYSSFVNMERDLASGLIGPL




LICYKESVDQRGNQIMSDKRNVILFSVFDE




NRSWYLTENIQRFLPNPAGVQLEDPEFQAS




NIMHSINGYVFDSLQLSVCLHEVAYWYILS




IGAQTDFLSVFFSGYTFKHKMVYEDTLTLF




PFSGETVFMSMENPGLWILGCHNSDFRNRG




MTALLKVSSCDKNTGDYYEDSYEDISAYLL




SKNNAIEPRSFSQNSRHPSTRQKQFNATTI




PENDIEKTDPWFAHRTPMPKIQNVSSSDLL




MLLRQSPTPHGLSLSDLQEAKYETFSDDPS




PGAIDSNNSLSEMTHFRPQLHHSGDMVFTP




ESGLQLRLNEKLGTTAATELKKLDFKVSST




SNNLISTIPSDNLAAGTDNTSSLGPPSMPV




HYDSQLDTTLFGKKSSPLTESGGPLSLSEE




NNDSKLLESGLMNSQESSWGKNVSSTESGR




LFKGKRAHGPALLTKDNALFKVSISLLKTN




KTSNNSATNRKTHIDGPSLLIENSPSVWQN




ILESDTEFKKVTPLIHDRMLMDKNATALRL




NHMSNKTTSSKNMEMVQQKKEGPIPPDAQN




PDMSFFKMLFLPESARWIQRTHGKNSLNSG




QGPSPKQLVSLGPEKSVEGQNFLSEKNKVV




VGKGEFTKDVGLKEMVFPSSRNLFLTNLDN




LHENNTHNQEKKIQEEIEKKETLIQENVVL




PQIHTVTGTKNFMKNLFLLSTRQNVEGSYD




GAYAPVLQDFRSLNDSTNRTKKHTAHFSKK




GEEENLEGLGNQTKQIVEKYACTTRISPNT




SQQNFVTQRSKRALKQFRLPLEETELEKRI




IVDDTSTQWSKNMKHLTPSTLTQIDYNEKE




KGAITQSPLSDCLTRSHSIPQANRSPLPIA




KVSSFPSIRPIYLTRVLFQDNSSHLPAASY




RKKDSGVQESSHFLQGAKKNNLSLAILTLE




MTGDQREVGSLGTSATNSVTYKKVENTVLP




KPDLPKTSGKVELLPKVHIYQKDLFPTETS




NGSPGHLDLVEGSLLQGTEGAIKWNEANRP




GKVPFLRVATESSAKTPSKLLDPLAWDNHY




GTQIPKEEWKSQEKSPEKTAFKKKDTILSL




NACESNHAIAAINEGQNKPEIEVTWAKQGR




TERLCSQNPPVLKRHQREITRTTLQSDQEE




IDYDDTISVEMKKEDFDIYDEDENQSPRSF




QKKTRHYFIAAVERLWDYGMSSSPHVLRNR




AQSGSVPQFKKVVFQEFTDGSFTQPLYRGE




LNEHLGLLGPYIRAEVEDNIMVTFRNQASR




PYSFYSSLISYEEDQRQGAEPRKNFVKPNE




TKTYFWKVQHHMAPTKDEFDCKAWAYFSDV




DLEKDVHSGLIGPLLVCHTNTLNPAHGRQV




TVQEFALFFTIFDETKSWYFTENMERNCRA




PCNIQMEDPTFKENYRFHAINGYIMDTLPG




LVMAQDQRIRWYLLSMGSNENIHSIHFSGH




VFTVRKKEEYKMALYNLYPGVFETVEMLPS




KAGIWRVECLIGEHLHAGMSTLFLVYSNKC




QTPLGMASGHIRDFQITASGQYGQWAPKLA




RLHYSGSINAWSTKEPFSWIKVDLLAPMII




HGIKTQGARQKFSSLYISQFIIMYSLDGKK




WQTYRGNSTGTLMVFFGNVDSSGIKHNIFN




PPIIARYIRLHPTHYSIRSTLRMELMGCDL




NSCSMPLGMESKAISDAQITASSYFTNMFA




TWSPSKARLHLQGRSNAWRPQVNNPKEWLQ




VDFQKTMKVTGVTTQGVKSLLTSMYVKEFL




ISSSQDGHQWTLFFQNGKVKVFQGNQDSFT




PVVNSLDPPLLTRYLRIHPQSWVHQIALRM




EVLGCEAQDLY


 


Linker
residues 2352-2353
LE



of SEQ ID




NO: 322



 


V5 epitope
residues 2354-2367
GKPIPNPLLGLDST


domain
of SEQ ID




NO: 322



 


Linker
residues 2368-2369
SR



of SEQ ID




NO: 322



 


Fc domain
residues 2370-2600
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 322
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









In this experiment, the level of expression of the FVIII-Fc target protein in the presence and absence of the BSC1-Protein G fusion protein. Media from cultures of cells (HEK293) expressing neither protein, of cells expressing only the FVIII-Fc target protein, and of cells co-expressing the BSC1-Protein G fusion protein and the FVIII-Fc target protein was assayed for FVIII using a commercially available, enzyme-linked immunosorbent assay (ELISA) (VisulizeTM FVIII Antigen Kit, Affinity Biologics Inc.). The results are shown as bar graphs of Absorbance at 450 nm in FIG. 24. Culture medium from cells transfected with an empty vector and expressing neither protein was used for a negative control (first bar graph from left in FIG. 24), and human serum was used as a positive control (last bar graph on right of FIG. 24). The results show that co-expression of the BSC1-Protein G fusion protein with the FVIII-Fc target protein significantly enhanced the level of expression of the FVIII-Fc target protein secreted into the culture medium (third bar graph from left in FIG. 24) as compared to the level of expression of the target protein in the absence of the BSC1-Protein G fusion protein (second bar graph from left in FIG. 24).
Example 17. BSC1-Protein a Fusion Protein Enhances Expression of an Anti-IL-8 Antibody Target Protein in an Unmodified Arrangement
This experiment examined whether a BSC1-Protein A fusion protein as described above could be used in an unmodified arrangement to improve the level of expression of an anti-IL-8 antibody target protein expressed in transfected HEK293 cells.
Expression of anti-IL-8 antibody in culture media was determined by immunodot blot using an anti-IgG antibody. As shown in the immunodot blots in FIG. 25A, co-expression of the anti-IL8 antibody target protein with the BSC1-Protein A fusion protein significantly enhanced the level of expression of the antibody secreted into the culture medium (bottom row 3 of FIG. 25A) as compared to the level of the antibody expressed in cells expressing the antibody alone (middle row 2 of FIG. 25A). The top row of FIG. 25A shows no antibody was secreted into medium from a mock culture of control cells that expressed neither protein.
The results of a densitometry analysis of the chemiluminescent signals in the dot blots in the rows in FIG. 25A using the NIH ImageJ image processing program are shown in the respective bar graphs in FIG. 25B. The bars of FIG. 25B are numbered to correspond to the row numbers of FIG. 25A. The results of this series of experiments clearly show that co-expression of the anti-IL8 antibody target protein with a fusion protein of the invention comprising the BSC1 polypeptide linked to a Protein A (target protein binding domain) significantly enhanced the expression of secreted anti-IL8 antibody.
FIG. 25C shows the results of an ELISA assay. A 96-well plate was coated with recombinant purified human IL8, and incubated with the anti-IL-8 antibody (target protein) secreted into the media of cultures of transfected cells expressing the anti-IL8 antibody alone (lane 2) and of cells co-expressing anti-IL8 antibody target protein and the BSC1-Protein A fusion protein (lane 3, BSC1-Protein A). Mock cultures contained cells transfected with expression vector lacking a structural gene for expressing any protein (no anti-IL8 antibody, first lane). The results clearly show that the secreted anti-IL8 antibody that was expressed at enhanced levels when co-expressed with BSC1-Protein A fusion protein retained its binding activity for human IL8.
Example 18. BSC1-Protein A Fusion Protein Enhances Expression of a Therapeutic Anti-VEGF Antibody (Bevacizumab) Target Protein in an Unmodified Arrangement
This experiment examined whether a BSC1-Protein A fusion protein as described above could be used in an unmodified arrangement to improve the level of expression of a therapeutic antibody.
Bevacizumab (Avastin®, Genentech/Roche) is a humanized monoclonal antibody that inhibits angiogenesis by inhibiting vascular endothelial growth factor A (VEGF-A). Sales of bevacizumab in 2010 were close to $7 billion and exceeded all other antibody drugs. The addition of bevacizumab to standard treatment can prolong the lives of breast and lung cancer patients by several months at a current cost of approximately $100,000 a year in the United States.
The amino acid sequences for the light and heavy chains of bevacizumab are shown in the table below.







TABLE 67







Amino Acid Sequences Light and Heavy Chains of Bevacizumab.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Light chain
SEQ ID NO: 323
MGWSCIILFLVATATGVHSDIQMTQSPSSL




SASVGDRVTITCSASQDISNYLNWYQQKPG




KAPKVLIYFTSSLHSGVPSRFSGSGSGTDF




TLTISSLQPEDFATYYCQQYSTVPWTFGQG




TKVEIKRTVAAPSVFIFPPSDEQLKSGTAS




VVCLLNNFYPREAKVQWKVDNALQSGNSQE




SVTEQDSKDSTYSLSSTLTLSKADYEKHKV




YACEVTHQGLSSPVTKSFNRGEC


 


Heavy chain
SEQ ID NO: 327
MGWSLIILFLVATATGVHSEVQLVESGGGL




VQPGGSLRLSCAASGYTFTNYGMNWVRQAP




GKGLEWVGWINTYTGEPTYAADFKRRFTFS




LDTSKSTAYLQMNSLRAEDTAVYYCAKYPH




YYGSSHWYFDVWGQGTLVTVSSASTKGPSV




FPLAPSSKSTSGGTAALGCLVKDYFPEPVT




VSWNSGALTSGVHTFPAVLQSSGLYSLSSV




VTVPSSSLGTQTYICNVNHKPSNTKVDKKV




EPKSCDKTHTCPPCPAPELLGGPSVFLFPP




KPKDTLMISRTPEVTCVVVDVSHEDPEVKF




NWYVDGVEVHNAKTKPREEQYNSTYRVVSV




LTVLHQDWLNGKEYKCKVSNKALPAPIEKT




ISKAKGQPREPQVYTLPPSRDELTKNQVSL




TCLVKGFYPSDIAVEWESNGQPENNYKTTP




PVLDSDGSFFLYSKLTVDKSRWQQGNVFSC




SVMHEALHNHYTQKSLSLSPGK









The anti-VEGF antibody bevacizumab (target protein) was expressed in human cells in the presence and absence of the BSC1-Protein A fusion protein. A mock culture contained cells that expressed neither protein. Samples of the media from cell cultures were assayed for antibody by immunodot blot assay using an anti-human IgG antibody.
FIG. 26A shows a dot blot assay for expression of the bevacizumab (anti-VEGF antibody) secreted into the media of cultures of transfected cells expressing bevacizumab alone (middle row) and co-expressing bevacizumab and the BSC1-Protein A fusion protein (bottom row). The top row of FIG. 26A shows that no antibody was secreted into medium from a mock culture of control cells that lacked a structural gene for either protein. The results show that co-expression in transfected cells of the bevacizumab target protein and the BSC1-Protein A fusion protein significantly enhanced the level of expression of bevacizumab secreted into the culture medium as compared to the level of the antibody secreted into medium of a culture of cells expressing bevacizumab alone.
FIG. 26B shows the results of a densitometry analysis of the chemiluminescent signals in each of the rows of the dot blot in FIG. 26A using the NIH ImageJ image processing program. The bar graphs of FIG. 26B are numbered to correspond to the row numbers of FIG. 26A. The results of this series of experiments clearly show that co-expression of the anti-VEGF antibody target protein with a BSC1-Protein A fusion protein significantly enhanced the level of expression of the anti-VEGF antibody secreted into the culture medium.
FIG. 26C shows the results of an ELISA to detect VEGF binding activity in culture media. A 96-well plate was coated with recombinant purified human VEGF-A and incubated with the bevacizumab (anti-VEGF antibody target protein) secreted into the media of cultures of transfected cells that expressed the anti-VEGF antibody alone (bar graph 2) or of transfected cells that co-expressed the anti-VEGF antibody and the BSC1-Protein A fusion protein (bar graph 3). Bar graph 1 of FIG. 26C shows that no significant VEGF binding activity was present in medium from a mock culture of cells transfected with expression vector lacking a structural gene for expressing either protein. The results clearly show that the secreted anti-VEGF antibody that was expressed at enhanced levels when co-expressed with the BSC1-Protein A fusion protein retained its binding activity for human VEGF-A.
Example 19. BSC1-Protein A Fusion Protein Enhances Expression of a Therapeutic Anti-TNFα Antibody (Adalimumab) Target Protein in an Unmodified Arrangement
This experiment examined whether a BSC1-Protein A fusion protein as described above could be used in an unmodified arrangement to improve the level of expression of a therapeutic anti-TNFα antibody (adalimumab; Humira®, AbbVie).







TABLE 68







Amino Acid Sequences of Light and Heavy Chains of


Adalimumab.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





Light chain
SEQ ID NO: 324
MGWSCIILFLVATATGVHSDIQMTQSPSSL




SASVGDRVTITCRSSQGIRNYLHWYQQKPG




KAPKLLIYAASTLQSGVPSRFSGSGSGTDF




TLTISSLQPEDVATYYCQRYNRAPYTFGQG




TKVEIKRTVAAPSVFIFPPSDEQLKSGTAS




VVCLLNNFYPREAKVQWKVDNALQSGNSQE




SVTEQDSKDSTYSLSSTLTLSKADYEKHKV




YACEVTHQGLSSPVTKSFNRGEC


 


Heavy chain
SEQ ID NO: 328
MGWSLIILFLVATATGVHSEVQLVESGGGL




VQPGRSLRLSCAASGFTFDDYAMHWVRQAP




GKGLEWVSAITWNSGHIDYADSVEGRFTIS




RDNAKNSLYLQMNSLRAEDTAVYYCAKVSY




LSTASSLDVWGQGTLVTVSSASTKGPSVFP




LAPSSKSTSGGTAALGCLVKDYFPEPVTVS




WNSGALTSGVHTFPAVLQSSGLYSLSSVVT




VPSSSLGTQTYICNVNHKPSNTKVDKKVEP




KSCDKTHTCPPCPAPELLGGPSVFLFPPKP




KDTLMISRTPEVTCVVVDVSHEDPEVKFNW




YVDGVEVHNAKTKPREEQYNSTYRVVSVLT




VLHQDWLNGKEYKCKVSNKALPAPIEKTIS




KAKGQPREPQVYTLPPSRDELTKNQVSLTC




LVKGFYPSDIAVEWESNGQPENNYKTTPPV




LDSDGSFFLYSKLTVDKSRWQQGNVFSCSV




MHEALHNHYTQKSLSLSPGK









FIG. 27A shows a dot blot assay for expression of the anti-TNFα antibody (target protein) secreted into the media of cultures of transfected cells expressing the anti-TNFα antibody alone (middle row) and of transfected cells co-expressing the anti-TNFα antibody and the BSC1-Protein A fusion protein (bottom row of FIG. 27A). No anti-TNFα antibody was detected in medium of mock cultures containing cells transfected with expression vector lacking a structural gene for expressing either protein (top row of FIG. 27A). Expression of the anti-TNFα antibody in culture media was analyzed in the dot blot assay using an anti-human IgG antibody. It can be seen that co-expression in transfected cells of the anti-TNFα antibody and the BSC1-Protein A fusion protein (bottom row) significantly enhanced the level of expression of anti-TNFα antibody secreted into the culture medium as compared to the level of the antibody expressed in transfected cells expressing the anti-TNFα antibody alone (middle row).
FIG. 27B shows the results of a densitometry analysis of the chemiluminescent signals in dot blots in each of the rows in FIG. 27A using the NIH ImageJ image processing program. The bar graphs of FIG. 27B are numbered to correspond to the row numbers of FIG. 27A. The results of this series of experiments clearly show that co-expression of the anti-TNFα antibody target protein with a fusion protein comprising a BSC1 polypeptide linked to a target binding domain (Protein A) significantly enhanced the level of expression of secreted anti-TNFα antibody.
FIG. 27C shows the results of an ELISA for TNFα binding activity by the expressed anti-TNFα antibody. A 96-well plate was coated with recombinant purified human TNFα and incubated with the anti-TNFα antibody (target protein) secreted into the media of cultures of transfected cells expressing the anti-TNFα antibody alone (bar graph 2) or co-expressing anti-TNFα antibody and the BSC1-Protein A fusion protein (bar graph 3). No TNFα binding activity was detected in medium from mock cultures containing cells transfected with an expression vector lacking a structural gene for expressing either protein (bar graph 1). The results of this series of experiments clearly show that the secreted anti-TNFα antibody that was expressed at enhanced levels when co-expressed with the BSC1-Protein A fusion protein retained its binding activity for human TNFα.
Example 20. BSC1-Protein A Fusion Protein Enhances Established Expression of an Anti-IL8 Antibody in CHO-D12 Cell Line in an Unmodified Arrangement
Similar in design to Example 8, above, this experiment examined whether a BSC1-Protein A fusion protein could enhance the level of expression of an anti-IL8 antibody already being produced in an established commercially relevant production CHO-DP12 cell line (American Type Culture Collection Accession No. CRL-124444, American Type Culture Collection, Manassas, Va.).
FIG. 28A shows results of an immune dot blot assay for expression of the anti-IL8 antibody (target protein) secreted into the media of cultures of cells of a CHO-DP12 cell line expressing the anti-IL8 antibody alone (middle row 2) and of cells co-expressing the anti-IL8 antibody and the BSC1-Protein A fusion protein (bottom row 3). It can be seen that co-expression of the antibody with the BSC1-Protein A fusion molecule significantly enhanced the level of expression of the antibody secreted into the culture medium (bottom row 3) as compared to the level of the antibody expressed in the absence of the BSC1-Protein A fusion molecule (row 2). No antibody was detected in medium alone (top row of FIG. 28A).
FIG. 28B shows the results of a densitometry analysis of the chemiluminescent signals in the dot blots in the rows of FIG. 28A using the NIH ImageJ image processing program. The bar graphs in FIG. 28B are numbered to correspond to the rows in FIG. 28A. The results indicate that co-expression of the antibody with the BSC1-Protein A fusion molecule (bar graph 3) significantly enhanced expression of the secreted antibody, providing an approximately four to five-fold greater enhancement in the level of expression as compared to that obtained when the antibody was expressed in the absence of the BSC1-Protein A fusion protein (bar graph 2).
FIG. 28C shows the results of an ELISA for IL8 binding. A 96-well plate was coated with recombinant purified human IL8 and incubated with the anti-IL8 antibody (target protein) secreted into the media of cultures stably expressing the anti-IL8 antibody alone (bar graph 2) or co-expressing the anti-IL8 antibody and the BSC1-Protein A fusion protein (bar graph 3). Cell culture medium was used as a negative control (bar graph 1, no anti-IL8 antibody). The results of this series of experiments clearly show that the secreted anti-IL8 antibody that was expressed at enhanced levels when co-expressed with the BSC1-Protein A fusion protein retained its binding activity for IL8.
The results indicate that a BSC1-Protein A fusion protein can be employed in an unmodified arrangement to significantly enhance the level of production of a target protein that is already stably expressed in an established production cell line.
Example 21. Enhancement of Expression of Secreted Alpha-1 Antitrvpsin Z Protein
This experiment indicates that enhancement of protein expression according to the invention has the potential to treat a disease resulting from an improper conformation of a critical protein.
Alpha1 antitrypsin (AAT) deficiency is an autosomal genetic disorder that affects both genders. AAT is a 52-kDa serine protease inhibitor produced mainly in the liver. Over 90 genetic variants have been identified in the protease inhibitor 1 (PI) gene on chromosome 14 that are associated with AAT deficiency. The most common basis of AAT deficiency is the Z mutation, a single base pair substitution that changes a Glu to Lys at codon 342 (Glu342Lys). The mutant AAT protein with the Z mutation (AATZ protein) retains approximately 80% of the serine protease activity of the wild type AAT protein. The AATZ protein also cannot fold to establish a normal conformation and consequently accumulates in aggregates within the endoplasmic reticulum (ER). Accumulation of aggregated AATZ in liver cells leads to liver toxicity and liver cirrhosis.
For this experiment, the target proteins were an engineered AAT-Fc fusion protein and an engineered V5-tagged α1ATZ-Fc fusion protein. The amino acid sequence of the AAT-Fc fusion protein is the same as described in Example 4.3 above. The amino acid sequence for the AATZ-Fc fusion protein is shown in the table below.







TABLE 69







Amino Acid Sequence of a V5-Tagged α1AATZ-Fc Target Protein.









Protein Region




(N- to C-
Sequence
Amino Acid Sequence


terminal)
Identifier
123456789012345678901234567890





V5-tagged
SEQ ID NO: 325
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD


α1AATZ-Fc fusion

AAQKTDTSHHDQDHPTFNKITPNLAEFAFS


molecule

LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDKKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQKGT




GSEFDIAAALEGKPIPNPLLGLDSTSRPKS




CDKTHTCPPCPAPELLGGPSVFLFPPKPKD




TLMISRTPEVTCVVVDVSHEDPEVKFNWYV




DGVEVHNAKTKPREEQYNSTYRVVSVLTVL




HQDWLNGKEYKCKVSNKALPAPIEKTISKA




KGQPREPQVYTLPPSRDELTKNQVSLTCLV




KGFYPSDIAVEWESNGQPENNYKTTPPVLD




SDGSFFLYSKLTVDKSRWQQGNVFSCSVMH




EALHNHYTQKSLSLSPGK


 


α1AATZ
residues 1-418
MPSSVSWGILLLAGLCCLVPVSLAEDPQGD



of SEQ ID
AAQKTDTSHHDQDHPTFNKITPNLAEFAFS



NO: 325
LYRQLAHQSNSTNIFFSPVSIATAFAMLSL




GTKADTHDEILEGLNFNLTEIPEAQIHEGF




QELLRTLNQPDSQLQLTTGNGLFLSEGLKL




VDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ




INDYVEKGTQGKIVDLVKELDRDTVFALVN




YIFFKGKWERPFEVKDTEEEDFHVDQVTTV




KVPMMKRLGMFNIQHCKKLSSWVLLMKYLG




NATAIFFLPDEGKLQHLENELTHDIITKFL




ENEDRRSASLHLPKLSITGTYDLKSVLGQL




GITKVFSNGADLSGVTEEAPLKLSKAVHKA




VLTIDKKGTEAAGAMFLEAIPMSIPPEVKF




NKPFVFLMIEQNTKSPLFMGKVVNPTQK


 


Linker 1
residues 419-431
GTGSEFDIAAALE



of SEQ ID




NO: 325



 


V5 epitope
residues 432-445
GKPIPNPLLGLDST


domain
of SEQ ID




NO: 325



 


Linker 2
residues 446-447
SR



of SEQ ID




NO: 325



 


Fc domain
residues 448-678
PKSCDKTHTCPPCPAPELLGGPSVFLFPPK



of SEQ ID
PKDTLMISRTPEVTCVVVDVSHEDPEVKFN



NO: 325
WYVDGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIEKTI




SKAKGQPREPQVYTLPPSRDELTKNQVSLT




CLVKGFYPSDIAVEWESNGQPENNYKTTPP




VLDSDGSFFLYSKLTVDKSRWQQGNVFSCS




VMHEALHNHYTQKSLSLSPGK









FIG. 29A shows images of chemiluminescent signals of a Western blot assay using anti-V5 antibody to detect expression of the V5-tagged AAT- and AATZ-Fc fusion proteins. Lane 1 in the top panel of FIG. 29A shows non-expressing cell culture medium as a control. Lane 2 of the top panel shows culture medium of cells expressing AAT-Fc alone. As expected for the wild type AAT protein, the AAT-Fc fusion was secreted into the culture medium. Lane 3 of the top panel of FIG. 29A shows that little if any of AATZ-Fc protein was secreted into the medium of a culture of transfected cells expressing the AATZ-Fc fusion protein alone. As expected for the AATZ protein, which is known to be retained in the endoplasmic reticulum, AATZ-Fc fusion protein was detected in cell lysates of the cells expressing AATZ-Fc protein alone. See, lane 3 of the middle panel (cell lysates). Surprisingly, as shown in lane 4 of the top panel of FIG. 29A, co-expression of the AATZ-Fc protein and the BSC1-Protein A fusion protein resulted in a dramatic increase in the level of expression of AATZ-Fc protein secreted into the cultures medium. Moreover, little if any of AATZ-Fc fusion protein was detected in cell lysate (lane 4, middle panel of FIG. 29A). The same membrane was blotted with anti-tubulin antibody for a loading control.
The results clearly show that co-expression of the BSC1-Protein A fusion protein significantly elevated the level of expression of the AATZ-Fc target protein secreted into the culture medium as compared to the level of expression of the target protein in the absence of the BSC1-Protein A fusion protein. Moreover, little if any of the AATZ-Fc proteins was detected in cell lysates, indicating that the AATZ-Fc protein was not retained in the endoplasmic reticulum. Accordingly, these data suggest for the first time that a gene therapy that would provide a fusion protein comprising an AATZ-binding domain and a protein expression enhancing polypeptide of this invention would be effective in treating an individual for AAT deficiency due to the Z mutation by enhancing expression of secreted AATZ protein from cells of the individual, eliminating or reducing liver toxicity due to retention of AATZ in the endoplasmic reticulum, and restoring required levels of extracellular AAT serine protease activity to individual.
All patents, applications, and publications cited in the above text are incorporated herein by reference.
Other variations and embodiments of the invention described herein will now be apparent to those of skill in the art without departing from the disclosure of the invention or the claims below.

## Claims

1. A fusion protein comprising:
(1) a protein expression enhancing polypeptide (PEEP) domain linked to (2) a target protein binding domain,

wherein said protein expression enhancing polypeptide (1) is selected from the group consisting of:
(a) an isolated J domain of a J protein;
(b) a J domain analog polypeptide comprising the amino acid sequence of formula I:


X1-X2-X3-X4-X5-X6-X7-X8-X9 (SEQ ID NO:47), wherein:  (I)

X1 is isoleucine (I), leucine (L), valine (V), alanine (A), or methionine (M);
X2 and X3 are each independently any amino acid with the proviso that one or both are K or R;
X4 is any amino acid or X4 may be absent when X1 through X3 are present and
X5 through X9 are present;
X5 is tyrosine (Y), tryptophan (W), or phenylalanine (F);
X6 and X7 are each independently any amino acid with the proviso that one or both are lysine (K) or arginine (R); or either one of X6 and X7 may be absent when the other is K or R and when X1 through X5 are present and X8 and X9 are present; and
X8 and X9 are any amino acid with the proviso that one or both are leucine (L) or alanine (A); or one of X8 and X9 may be absent when the other is L or A and when X1 through X7 are present; and

(c) a decapeptide selected from the group consisting of:
IKKAYKLALQ (SEQ ID NO:49),
IKKAYRLALQ (SEQ ID NO:50),
IKKAYRKALQ (SEQ ID NO:51), and
IKKAYRKLLQ (SEQ ID NO:52);


wherein said target protein binding domain (2) is a protein or binding domain thereof that specifically binds a target protein of interest; and
wherein co-expression of said fusion protein with said target protein of interest that is bound by said target protein binding domain of said fusion protein results in an enhanced level of expression of said target protein of interest compared to the level of expression in the absence of said fusion protein.

2. The fusion protein according to claim 1, wherein the protein expression enhancing polypeptide (1) consists of an isolated J domain of a J protein.

3. The fusion protein according to claim 2, wherein the isolated J domain is an isolated J domain of an ERdj protein, a large T antigen of SV40, or a mammalian cysteine string protein alpha (CSP-α).

4. The fusion protein according to claim 2, wherein the isolated J domain is an isolated J domain of an Erdj protein selected from Erdj1, Erdj2, Erdj3, Erdj4, Erdj5, Erdj6 and Erdj7.

5. The fusion protein according to claim 4, wherein the isolated J domain is an isolated J domain of Erdj3.

6. The fusion protein according to claim 1, wherein the protein expression enhancing polypeptide is selected from the group consisting of:
I-K-K-A-Y-R-K-L-A (SEQ ID NO:48),
I-R-K-A-Y-R-K-L-S-L-T-L (SEQ ID NO:83),
I-K-K-Q-Y-R-L-L-S-L-K-Y (SEQ ID NO:84),
I-K-K-A-F-H-K-L-A-M-K-Y (SEQ ID NO:85),
I-R-Q-A-F-K-K-L-A-L-K-L (SEQ ID NO:86),
I-I-K-A-Y-R-K-L-A-L-Q-W (SEQ ID NO:87),
I-A-R-A-Y-R-Q-L-A-R-R-Y (SEQ ID NO:88),
I-K-R-A-Y-R-R-Q-A-L-R-Y (SEQ ID NO:89),
I-K-K-S-Y-R-K-L-A-L-K-Y (SEQ ID NO:90), and
I-K-K-A-Y-K-R-L-A-M-K-Y (SEQ ID NO:91).

7. The fusion protein according to claim 1, wherein the protein expression enhancing polypeptide is a J domain analog polypeptide, wherein said J domain analog polypeptide comprises the amino acid sequence of formula I.

8. The fusion protein according to claim 7, wherein said J domain analog polypeptide comprises the amino acid sequence (SEQ ID NO:326) wherein:
X1 is I, L, V, A, or M;
the dipeptide X2-X3 is selected from the group consisting of: KR, KK, RK, RR, AK, AR, KA, IK, NK, KQ, RQ, and RD;
X4 is A, S, T, R, Q, E, F, C, or I;
X5 is Y or F;
the dipeptide X6-X7 is selected from the group consisting of: KR, KK, RK, RR, RQ, FR, RL, KL, HK, LK, QK, and KV; and
the dipeptide X8-X9 is selected from the group consisting of: LA, LL, AL, AA, LC, LV, QA, KA, LS, LI, LY, and RA.

9. The fusion protein according to claim 1, wherein said protein expression enhancing polypeptide (1) comprises one of the following amino acid sequences:














Amino Acid Sequence



Sequence Identifier
123456789012345








SEQ ID NO: 48
IKKAYRKLA


 



SEQ ID NO: 49
IKKAYKLALQ


 



SEQ ID NO: 50
IKKAYRLALQ


 



SEQ ID NO: 51
IKKAYRKALQ


 



SEQ ID NO: 52
IKKAYRKLLQ


 



SEQ ID NO: 53
IKKYRKLA


 



SEQ ID NO: 54
IKKAYKLA


 



SEQ ID NO: 55
IKKAYRLA


 



SEQ ID NO: 56
IKKAYRKA


 



SEQ ID NO: 57
LKKAYRKLA


 



SEQ ID NO: 58
VKKAYRKLA


 



SEQ ID NO: 59
MKKAYRKLA


 



SEQ ID NO: 60
AKKAYRKLA


 



SEQ ID NO: 61
IAKAYRKLA


 



SEQ ID NO: 62
IKAAYRKLA


 



SEQ ID NO: 63
IKKRYRKLA


 



SEQ ID NO: 64
IKKSYRKLA


 



SEQ ID NO: 65
IKKQYRKLA


 



SEQ ID NO: 66
IKKEYRKLA


 



SEQ ID NO: 67
IKKFYRKLA


 



SEQ ID NO: 68
IKKCYRKLA


 



SEQ ID NO: 69
IKKAFRKLA


 



SEQ ID NO: 70
IKKAWRKLA


 



SEQ ID NO: 71
IKKAYRKQA


 



SEQ ID NO: 72
IKKAYRKMA


 



SEQ ID NO: 73
IKKAYRKIA


 



SEQ ID NO: 74
IKKAYRKAA


 



SEQ ID NO: 75
IKKAYRKVA


 



SEQ ID NO: 76
IKKAYRKRA


 



SEQ ID NO: 77
IKKAYRKLM


 



SEQ ID NO: 78
IKKAYRKLI


 



SEQ ID NO: 79
IKKAYRKLV


 



SEQ ID NO: 80
IKKAYRKLC


 



SEQ ID NO: 81
IKKAYRKLS


 



SEQ ID NO: 82
IKKAYRKLY


 



SEQ ID NO: 83
IRKAYRKLSLTL


 



SEQ ID NO: 84
IKKQYRLLSLKY


 



SEQ ID NO: 85
IKKAFHKLAMKY


 



SEQ ID NO: 86
IRQAFKKLALKL


 



SEQ ID NO: 87
IIKAYRKLALQW


 



SEQ ID NO: 88
IARAYRQLARRY


 



SEQ ID NO: 89
IKRAYRRQALRY


 



SEQ ID NO: 90
IKKSYRKLALKY


 



SEQ ID NO: 91
IKKAYKRLAMKY.

10. The fusion protein according to claim 1, wherein the target protein binding domain (2) is an antibody or an antigen-binding fragment thereof, an antibody binding protein, a ligand binding domain of a receptor protein, a protein ligand of a receptor protein, a protein antigen that is bound by an antibody or an antigen-binding fragment thereof, or a PDZ domain.

11. The fusion protein according to claim 10, wherein the target protein binding domain (2) is an antibody binding protein.

12. The fusion protein according to claim 11, wherein the antibody binding protein is an Fc binding protein.

13. The fusion protein according to claim 12, wherein the Fc binding protein is Protein A, Protein G, or a viral gE protein.

14. The fusion protein according to claim 11, wherein the antibody binding protein is Protein L.

15. The fusion protein according to claim 10, wherein said target protein binding domain (2) is a ligand binding domain of a receptor protein, wherein the receptor protein is a cytokine receptor.

16. The fusion protein according to claim 10, wherein said target protein binding domain (2) is a protein ligand of a receptor protein, wherein the protein ligand is a cytokine.

17. An isolated nucleic acid molecule comprising a nucleic acid sequence encoding a fusion protein according to claim 1 or claim 9.

18. A nucleic acid vector molecule comprising the isolated nucleic acid molecule according to claim 17.

19. A host cell comprising the nucleic acid vector molecule according to claim 18.

20. A method of expressing a fusion protein comprising culturing a host cell according to claim 19 under conditions sufficient to produce the fusion protein.

21. A method of enhancing the expression of a target protein of interest expressed by a host cell comprising transfecting the host cell with an expression vector comprising a structural gene encoding a fusion protein according to claim 1, and culturing said transfected host cell under conditions causing the co-expression of said fusion protein encoded by said structural gene and of said target protein of interest.

22. A method of enhancing the expression of a target protein of interest comprising the steps of:
1) constructing a recombinant gene encoding a fusion protein according to claim 1 wherein the target protein binding domain (2) of the fusion protein binds said target protein of interest;
2) inserting the recombinant gene into an expression vector to form a recombinant expression vector wherein said recombinant gene sequence is operably linked to a transcriptional promoter sequence;
3) transfecting said recombinant expression vector into host cells that are compatible with said promoter sequence; and
4) culturing said transfected host cells under conditions that permit co-expression of said fusion protein encoded by said recombinant gene and of said target protein of interest.

23. A method of restoring a secreted protein function in cells of a mammalian subject that are deficient in the secretion of a native secreted protein that provides said secreted protein function comprising inserting into cells of the subject an exogenous nucleic acid molecule encoding a fusion protein according to claim 1 wherein the target protein binding domain (2) of the fusion protein binds the native secreted protein, wherein expression of the fusion protein and the native secreted protein in the cells enhances secretion of said native protein to provide said protein function to the cells of the subject.

24. The method according to claim 23, wherein the subject has a disease associated with the deficient secretion of the native protein in the subject.

25. The method according to claim 24, wherein said disease is selected from the group consisting of a prion-associated disease, Alzheimer's disease, Parkinson's disease, Huntington's disease, cystic fibrosis (CF), and α1-antitrypsin (AAT) deficiency.

26. The method according to claim 25, wherein the subject is a human subject deficient in the secretion of cystic fibrosis transmembrane conductance regulator protein and the disease is cystic fibrosis.

27. The method according to claim 25, wherein the subject is a human subject deficient in secretion of AAT and the disease is AAT deficiency.