# Patent

## Title
Methods and compositions for diagnosing disease

## Abstract

The present invention relates to methods and compositions for diagnosing a disease or disorder in a subject by introducing into cells of the subject a diagnostic gene switch construct and monitoring expression of a reporter gene. The invention further relates to methods and compositions for monitoring the progression of a disease or disorder or the effectiveness of a treatment for a disease or disorder.

## Background
REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY
The content of the sequence listing text file (File Name: Sequence Listing.ST25.txt; Size: 107 KB bytes; and Date of Creation: Aug. 22, 2008) filed herewith with the application is incorporated herein by reference in its entirety.
BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to methods and compositions for diagnosing a disease or disorder in a subject by introducing into cells of the subject a diagnostic gene switch construct and monitoring expression of a reporter gene. The invention further relates to methods and compositions for monitoring the progression of a disease or disorder or monitoring the effectiveness or toxicity of a treatment for a disease or disorder.
2. Background Art
Diagnostic tests for the presence of a disease in a subject have long been in existence, but researchers are constantly searching for improved tests exhibiting increased sensitivity (allowing earlier detection) and specificity (eliminating false positives and false negatives). Other desired characteristics for diagnostic tests include ease of use, rapid results, and the ability to constantly monitor progression of a disease or the effectiveness of ongoing treatment.
Thus, there is a need in the art for new diagnostic methods and compositions that provide these desired characteristics.
SUMMARY OF THE INVENTION
The present invention is based on a combination of the specificity and sensitivity provided by the use of disease specific promoters to detect a disease coupled with the regulatory control of a ligand-dependent gene switch system to provide diagnostic and monitoring methods. The present invention relates to methods and compositions for diagnosing a disease or disorder in a subject. The invention further relates to methods and compositions for monitoring the progression of a disease or disorder in a subject or monitoring the effectiveness or toxicity of an administered treatment for a disease or disorder in a subject.
One embodiment of the invention comprises methods of diagnosing a disease or disorder in a subject, comprising:

    (a) introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (2) administering ligand to said modified cells; and
    (3) detecting reporter gene expression;


wherein expression of the reporter gene indicates that said subject has said disease or disorder.
In one embodiment, the diagnostic methods are carried out ex vivo in cells that have been isolated from said subject.
In one embodiment, the diagnostic methods are carried out by introducing the compositions of the invention into cells that have been isolated from said subject to produce modified cells, and the modified cells are re-introduced into said subject.
In one embodiment, the diagnostic methods are carried out in vivo.
In a further embodiment, the diagnostic methods are carried out using non-autologous cells, e.g., cells that are allogeneic or xenogeneic to the subject, and the modified non-autologous cells are introduced into the subject. In one embodiment, the non-autologous cells are surrounded by a barrier (e.g., encapsulated) prior to being introduced into the subject.
In one aspect of the invention, the gene switch is an ecdysone receptor (EcR)-based gene switch.
In one embodiment, the gene switch comprises a first transcription factor sequence under the control of a first diagnostic switch promoter and a second transcription factor sequence under the control of a second diagnostic switch promoter, wherein the proteins encoded by said first transcription factor sequence and said second transcription factor sequence interact to form a protein complex which functions as a ligand-dependent transcription factor.
In another aspect of the invention, said first transcription factor sequence encodes a protein comprising a heterodimer partner and a transactivation domain and said second transcription factor sequence encodes a protein comprising a DNA binding domain and a ligand-binding domain.
An additional embodiment of the invention relates to methods of monitoring the progression of a disease or disorder in a subject, comprising:

    (a) introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) administering ligand to said modified cells; and
    (c) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates progression of said disease or disorder in said subject.
A further embodiment of the invention relates to methods of monitoring the effectiveness of a treatment for a disease or disorder in a subject, comprising:

    (a) administering said treatment to said subject;
    (b) introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (c) administering ligand to said modified cells; and
    (d) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates the effectiveness of said treatment.
Another embodiment of the invention relates to methods of monitoring the potential toxicity of an administered treatment for a disease or disorder in a subject, comprising:

    (a) administering said treatment to said subject;
    (b) introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by factors found in cells that are being exposed to toxic conditions, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (c) administering ligand to said modified cells; and
    (d) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates the toxicity of said treatment.
Another embodiment of the invention relates to methods of monitoring the level of a factor that is being administered to a subject for treatment for a disease or disorder, comprising:

    (a) administering said treatment to said subject;
    (b) introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by said factor that is being administered for treatment, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (c) administering ligand to said modified cells; and
    (d) detecting reporter gene expression;


wherein the level of expression of said reporter gene indicates the level of the factor being administered for treatment.
In a further embodiment, each of the methods may be carried out using non-autologous cells, e.g., cells that are allogeneic or xenogeneic to the subject, and the modified non-autologous cells are administered to the subject. In one embodiment, the modified non-autologous cells are surrounded by a barrier (e.g., encapsulated) prior to being introduced into the subject.
One embodiment of the invention comprises methods of detecting transplant rejection in a subject that has received an organ or tissue transplant, comprising:

    (a) introducing into cells of said organ or tissue transplant (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during transplant rejection, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) administering ligand to said modified cells; and
    (c) detecting reporter gene expression;


wherein expression of the reporter gene indicates that transplant rejection has been detected.
An additional embodiment of the invention relates to methods of monitoring the progression of transplant rejection in a subject that has received an organ or tissue transplant, comprising:

    (a) introducing into cells of said organ or tissue transplant (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during transplant rejection, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) administering ligand to said modified cells; and
    (c) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates progression of said transplant rejection in said subject.
In a further embodiment, the methods of detecting or monitoring transplant rejection may be carried out by introducing the polynucleotides of the invention into non-autologous cells, e.g., cells that are allogeneic or xenogeneic to the organ or tissue being transplanted, and the modified non-autologous cells are introduced to the organ or tissue prior to transplantation. In one embodiment, the modified non-autologous cells are surrounded by a barrier (e.g., encapsulated) prior to being introduced into the organ or tissue.
In the methods described above, in one embodiment, the polynucleotide encoding the gene switch and the polynucleotide encoding the reporter gene linked to a promoter are part of one larger polynucleotide, e.g., a vector. In another embodiment, the polynucleotide encoding the gene switch and the polynucleotide encoding the reporter gene linked to a promoter are separate polynucleotides.
The invention further relates to diagnostic gene switch constructs that are useful in the disclosed methods.
The invention additionally relates to vectors comprising the diagnostic gene switch constructs of the invention.
The invention also relates to kits for carrying out the methods of the invention, comprising, e.g., gene switch constructs, vectors, ligands, etc. In one embodiment, the kits may comprise cells (e.g., autologous or non-autologous cells) that may comprise the polynucleotides of the invention. The non-autologous cells may be surrounded by a barrier (e.g., encapsulated).



BRIEF DESCRIPTION OF THE DRAWINGS/FIGURES
FIG. 1 shows an embodiment of the diagnostic gene switch of the invention in which two transcription factor sequences encoding two separate portions of a ligand-dependent transcription factor are under the control of different promoters. “Dx-Switch Components” represents a gene switch; “AD” represents a transactivation domain; “DBD” represents a DNA binding domain; “LBD” represents a ligand binding domain; “StandardDx-Reporter” represents a reporter gene; and “P1” and “P2” represent two different disease- or disorder-responsive promoters. In an alternative embodiment of FIG. 1, “P1” is a constitutive promoter, and “P2” and “P3” are different disease- or disorder-responsive promoters.
FIG. 2 shows an embodiment of the diagnostic gene switch of the invention in which two transcription factor sequences encoding two separate portions of a ligand-dependent transcription factor are under the control of different promoters. “Dx-Switch Components” represents a gene switch; “AD” represents a transactivation domain; “DBD-A” represents a first DNA binding domain; “DBD-B” represents a second DNA binding domain; “LBD” represents a ligand binding domain; “StandardDx-Reporter-A” represents a first reporter gene; “StandardDx-Reporter-B” represents a second reporter gene; and “P1,” “P2,” and “P3” represent three different disease- or disorder-responsive promoters. In an alternative embodiment of FIG. 2, “P1” is a constitutive promoter; and “P2” and “P3” are different disease- or disorder-responsive promoters.
FIG. 3 shows an embodiment of the diagnostic gene switch of the invention in which two transcription factor sequences encoding two separate portions of a ligand-dependent transcription factor are under the control of different diagnostic switch promoters. “Dx-Switch Components” represents a gene switch; “AD” represents a transactivation domain; “DBD” represents a DNA binding domain; “LBD” represents a ligand binding domain; “StandardDx-Reporter” represents a reporter gene; and “P1,” “P2,” “P3,” and “P4” represent four different disease- or disorder-responsive promoters.
FIG. 4 shows an embodiment of the diagnostic gene switch of the invention in which two transcription factor sequences encoding two separate portions of a ligand-dependent transcription factor are under the control of different promoters and a control reporter gene is present. “Dx-Switch Components” represents a gene switch; “AD” represents a transactivation domain; “DBD-A” represents a first DNA binding domain; “DBD-B” represents a second DNA binding domain; “LBD” represents a ligand binding domain; “StandardDx-Reporter-A” represents a first reporter gene; “Control-Reporter-B” represents a second reporter gene; and “P1” and “P2” represent two different disease- or disorder-responsive promoters; and “P3” and “P4” represent two different control promoters. In an alternative embodiment of FIG. 4, “P3” and “P4” are constitutive promoters.
FIG. 5 shows an embodiment of a single promoter shuttle vector (SEQ ID No.: 5), which includes the IL-24/mda-7 promoter. Adenovirus produced using this vector is used to transduce cells isolated from lymphatic samples.
FIG. 6 shows an embodiment of a dual promoter vector (SEQ ID NO.: 6), which includes TRPM4 and TRGC1/TARP promoters. This DNA vector is used to transduce a prostate biopsy using non-viral transduction systems.
FIG. 7 shows an embodiment of a single promoter vector (SEQ ID NO.: 7), which includes the ADAM-17 promoter and the CD95-ADAM8 dual reporter (SEQ ID NO.: 10).
FIG. 8 shows an embodiment of a dual promoter vector (SEQ ID NO.: 8), which includes the CXCL9 and SEMA7A promoters and the CD40-CD3 dual reporter (SEQ ID NO.: 12).
FIG. 9 shows an embodiment of a single promoter vector (SEQ ID NO.: 9), which includes the ADAM-17 promoter and the alkaline phosphatase—c terminal CD40 reporter (SEQ ID NO.: 14).
FIG. 10 shows embodiments of the serum-based reporters that are designed to exhibit no immunogenic profile when expressed within the human body. These reporters are made up of human based amino acid sequences that are present either on the cell surface or within the serum naturally. Hence, these reporters are not immunogenic nor are they subject to immune attack when expressed in the human body. In one embodiment, serum-based reporters are dual epitope reporter, for e.g., CD95-ADAM8 reporter (SEQ ID NOs.: 10-11), CD40-CD3 reporter (SEQ ID NOs.: 12-13), CD28-CD3 reporter (SEQ ID. NOs.: 16-17) and CD28-CD40 reporter (SEQ ID NOs.: 18-19) that allows ELISA based capture and detection. The designs utilize a signal peptide (Signal P) for transport into the secretory pathway, followed by epitopes from cell surface antigens with linkers (L). In alternative embodiments, different combinations of linkers and epitopes are used for each design. In another embodiment, the serum-based reporter is an alkaline phosphatase reporter, for e.g., alkaline phosphatase—c terminal CD40 reporter (SEQ ID NOs.: 14-15), that allows immunocapture followed by enzymatic detection of reporter activity. Alkaline phosphatase reporters utilize the tissue non-specific alkaline phosphatase for an enzymatic reporter that can be secreted. An epitope from a cell surface antigen is included at the carboxy terminus for immunocapture prior to measurement of alkaline phosphatase activity. In additional embodiments of FIG. 10, additional alkaline phosphatase reporters are: alkaline phosphatase—amiono terminal CD40 reporter (SEQ ID NOs.: 20-21) and alkaline phosphatase—c terminal CD28 reporter (SEQ ID. NOs.: 22-23).



DETAILED DESCRIPTION OF THE INVENTION
The invention relates to methods and compositions for using a gene switch for the diagnosis of diseases or disorders in a subject. The invention further relates to methods and compositions for monitoring the progression of diseases or disorders or the treatment thereof in a subject. The methods of the invention can be carried out either ex vive (by introducing the gene switch into isolated cells of a subject) or in vive (by introducing the gene switch into isolated cells of a subject and reintroducing the cells to the subject or by introducing the gene switch directly into cells of the subject). In another embodiment, the cells harboring the gene switch may be non-autologous cells (e.g., allogeneic or xenogeneic cells). The non-autologous cells may be surrounded by a barrier that prevents the non-autologous cells from raising an immune response after introduction and/or prevents the non-autologous cells from escaping from the site of introduction. The methods of the invention involve the use of a gene switch in which expression of a ligand-dependent transcription factor is under the control of one or more diagnostic switch promoters. The methods and compositions described herein provide a highly sensitive and highly specific diagnostic technique in which the timing of the diagnostic step is controlled by administration of ligand to cells comprising the gene switch, permitting optimal detection of the presence of a disease or disorder as well as continuous or intermittent monitoring of the progression of a disease or disorder or the effectiveness or toxicity of a treatment.
The following definitions are provided and should be helpful in understanding the scope and practice of the present invention.
The term “isolated” for the purposes of the present invention designates a biological material (cell, nucleic acid or protein) that has been removed from its original environment (the environment in which it is naturally present). For example, a polynucleotide present in the natural state in a plant or an animal is not isolated, however the same polynucleotide separated from the adjacent nucleic acids in which it is naturally present, is considered “isolated.”
The term “purified,” as applied to biological materials does not require the material to be present in a form exhibiting absolute purity, exclusive of the presence of other compounds. It is rather a relative definition.
“Nucleic acid,” “nucleic acid molecule,” “oligonucleotide,” and “polynucleotide” are used interchangeably and refer to the phosphate ester polymeric form of ribonucleosides (adenosine, guanosine, uridine or cytidine; “RNA molecules”) or deoxyribonucleosides (deoxyadenosine, deoxyguanosine, deoxythymidine, or deoxycytidine; “DNA molecules”), or any phosphoester analogs thereof, such as phosphorothioates and thioesters, in either single stranded form, or a double-stranded helix. Double stranded DNA-DNA, DNA-RNA and RNA-RNA helices are possible. The term nucleic acid molecule, and in particular DNA or RNA molecule, refers only to the primary and secondary structure of the molecule, and does not limit it to any particular tertiary forms. Thus, this term includes double-stranded DNA found, inter alia, in linear or circular DNA molecules (e.g., restriction fragments), plasmids, supercoiled DNA and chromosomes. In discussing the structure of particular double-stranded DNA molecules, sequences may be described herein according to the normal convention of giving only the sequence in the 5′ to 3′ direction along the non-transcribed strand of DNA (i.e., the strand having a sequence homologous to the mRNA). A “recombinant DNA molecule” is a DNA molecule that has undergone a molecular biological manipulation. DNA includes, but is not limited to, cDNA, genomic DNA, plasmid DNA, synthetic DNA, and semi-synthetic DNA.
The term “fragment,” as applied to polynucleotide sequences, refers to a nucleotide sequence of reduced length relative to the reference nucleic acid and comprising, over the common portion, a nucleotide sequence identical to the reference nucleic acid. Such a nucleic acid fragment according to the invention may be, where appropriate, included in a larger polynucleotide of which it is a constituent. Such fragments comprise, or alternatively consist of; oligonucleotides ranging in length from at least 6, 8, 9, 10, 12, 15, 18, 20, 21, 22, 23, 24, 25, 30, 39, 40, 42, 45, 48, 50, 51, 54, 57, 60, 63, 66, 70, 75, 78, 80, 90, 100, 105, 120, 135, 150, 200, 300, 500, 720, 900, 1000, 1500, 2000, 3000, 4000, 5000, or more consecutive nucleotides of a nucleic acid according to the invention.
As used herein, an “isolated nucleic acid fragment” refers to a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. An isolated nucleic acid fragment in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA or synthetic DNA.
A “gene” refers to a polynucleotide comprising nucleotides that encode a functional molecule, including functional molecules produced by transcription only (e.g., a bioactive RNA species) or by transcription and translation (e.g., a polypeptide). The term “gene” encompasses cDNA and genomic DNA nucleic acids. “Gene” also refers to a nucleic acid fragment that expresses a specific RNA, protein or polypeptide, including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers to any gene that is not a native gene, comprising regulatory and/or coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. A chimeric gene may comprise coding sequences derived from different sources and/or regulatory sequences derived from different sources. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign” gene or “heterologous” gene refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A “transgene” is a gene that has been introduced into the genome by a transformation procedure.
“Heterologous DNA” refers to DNA not naturally located in the cell, or in a chromosomal site of the cell. The heterologous DNA may include a gene foreign to the cell.
The term “genome” includes chromosomal as well as mitochondrial, chloroplast and viral DNA or RNA.
A nucleic acid molecule is “hybridizable” to another nucleic acid molecule, such as a cDNA, genomic DNA, or RNA, when a single stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule under the appropriate conditions of temperature and solution ionic strength. Hybridization and washing conditions are well known and exemplified in Sambrook et al. in Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989), particularly Chapter 11 and Table 11.1 therein (entirely incorporated herein by reference). The conditions of temperature and ionic strength determine the “stringency” of the hybridization.
Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms. For preliminary screening for homologous nucleic acids, low stringency hybridization conditions, corresponding to a Tm of 55°, can be used, e.g., 5×SSC, 0.1% SDS, 0.25% milk, and no formamide; or 30% formamide, 5×SSC, 0.5% SDS. Moderate stringency hybridization conditions correspond to a higher Tm, e.g., 40% formamide, with 5× or 6×SSC. High stringency hybridization conditions correspond to the highest Tm, e.g., 50% formamide, 5× or 6×SSC.
Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The term “complementary” is used to describe the relationship between nucleotide bases that are capable of hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine. Accordingly, the present invention also includes isolated nucleic acid fragments that are complementary to the complete sequences as disclosed or used herein as well as those substantially similar nucleic acid sequences.
In one embodiment of the invention, polynucleotides are detected by employing hybridization conditions comprising a hybridization step at Tm of 55° C., and utilizing conditions as set forth above. In other embodiments, the Tm is 60° C., 63° C., or 65° C.
Post-hybridization washes also determine stringency conditions. One set of conditions uses a series of washes starting with 6×SSC, 0.5% SDS at room temperature for 15 minutes (min), then repeated with 2×SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with 0.2×SSC, 0.5% SDS at 50° C. for 30 min. A preferred set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2×SSC, 0.5% SDS is increased to 60° C. Another preferred set of highly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDS at 65° C.
The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook et al., supra, 9.50-0.51). For hybridization with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra, 11.7-11.8).
In one embodiment of the invention, polynucleotides are detected by employing hybridization conditions comprising a hybridization step in less than 500 mM salt and at least 37° C., and a washing step in 2×SSPE at a temperature of at least 63° C. In another embodiment, the hybridization conditions comprise less than 200 mM salt and at least 37° C. for the hybridization step. In a further embodiment, the hybridization conditions comprise 2×SSPE and 63° C. for both the hybridization and washing steps.
In another embodiment, the length for a hybridizable nucleic acid is at least about 10 nucleotides. Preferably a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; e.g., at least about 20 nucleotides; e.g., at least 30 nucleotides. Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration may be adjusted as necessary according to factors such as length of the probe.
The term “probe” refers to a single-stranded nucleic acid molecule that can base pair with a complementary single stranded target nucleic acid to form a double-stranded molecule.
As used herein, the term “oligonucleotide” refers to a short nucleic acid that is hybridizable to a genomic DNA molecule, a cDNA molecule, a plasmid DNA or an mRNA molecule. Oligonucleotides can be labeled, e.g., with 32P-nucleotides or nucleotides to which a label, such as biotin, has been covalently conjugated. A labeled oligonucleotide can be used as a probe to detect the presence of a nucleic acid. Oligonucleotides (one or both of which may be labeled) can be used as PCR primers, either for cloning full length or a fragment of a nucleic acid, for DNA sequencing, or to detect the presence of a nucleic acid. An oligonucleotide can also be used to form a triple helix with a DNA molecule. Generally, oligonucleotides are prepared synthetically, preferably on a nucleic acid synthesizer. Accordingly, oligonucleotides can be prepared with non-naturally occurring phosphoester analog bonds, such as thioester bonds, etc.
A “primer” refers to an oligonucleotide that hybridizes to a target nucleic acid sequence to create a double stranded nucleic acid region that can serve as an initiation point for DNA synthesis under suitable conditions. Such primers may be used in a polymerase chain reaction or for DNA sequencing.
“Polymerase chain reaction” is abbreviated PCR and refers to an in vitro method for enzymatically amplifying specific nucleic acid sequences. PCR involves a repetitive series of temperature cycles with each cycle comprising three stages: denaturation of the template nucleic acid to separate the strands of the target molecule, annealing a single stranded PCR oligonucleotide primer to the template nucleic acid, and extension of the annealed primer(s) by DNA polymerase. PCR provides a means to detect the presence of the target molecule and, under quantitative or semi-quantitative conditions, to determine the relative amount of that target molecule within the starting pool of nucleic acids.
“Reverse transcription-polymerase chain reaction” is abbreviated RT-PCR and refers to an in vitro method for enzymatically producing a target cDNA molecule or molecules from an RNA molecule or molecules, followed by enzymatic amplification of a specific nucleic acid sequence or sequences within the target cDNA molecule or molecules as described above. RT-PCR also provides a means to detect the presence of the target molecule and, under quantitative or semi-quantitative conditions, to determine the relative amount of that target molecule within the starting pool of nucleic acids.
A DNA “coding sequence” refers to a double-stranded DNA sequence that encodes a polypeptide and can be transcribed and translated into a polypeptide in a cell in vitro or in vive when placed under the control of suitable regulatory sequences. “Suitable regulatory sequences” refers to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing sites, effector binding sites and stem-loop structures. The boundaries of the coding sequence are determined by a start codon at the 5′ (amino) terminus and a translation stop codon at the 3′ (carboxyl) terminus. A coding sequence can include, but is not limited to, prokaryotic sequences, cDNA from mRNA, genomic DNA sequences, and even synthetic DNA sequences. If the coding sequence is intended for expression in a eukaryotic cell, a polyadenylation signal and transcription termination sequence will usually be located 3′ to the coding sequence.
“Open reading frame” is abbreviated ORF and refers to a length of nucleic acid sequence, either DNA, cDNA or RNA, that comprises a translation start signal or initiation codon, such as an ATG or AUG, and a termination codon and can be potentially translated into a polypeptide sequence.
The term “head-to-head” is used herein to describe the orientation of two polynucleotide sequences in relation to each other. Two polynucleotides are positioned in a head-to-head orientation when the 5′ end of the coding strand of one polynucleotide is adjacent to the 5′ end of the coding strand of the other polynucleotide, whereby the direction of transcription of each polynucleotide proceeds away from the 5′ end of the other polynucleotide. The term “head-to-head” may be abbreviated (5′)-to-(5′) and may also be indicated by the symbols (← →) or (3′←5′5′→3′).
The term “tail-to-tail” is used herein to describe the orientation of two polynucleotide sequences in relation to each other. Two polynucleotides are positioned in a tail-to-tail orientation when the 3′ end of the coding strand of one polynucleotide is adjacent to the 3′ end of the coding strand of the other polynucleotide, whereby the direction of transcription of each polynucleotide proceeds toward the other polynucleotide. The term “tail-to-tail” may be abbreviated (3′)-to-(3′) and may also be indicated by the symbols (→ ←) or (5′→3′3′←5′).
The term “head-to-tail” is used herein to describe the orientation of two polynucleotide sequences in relation to each other. Two polynucleotides are positioned in a head-to-tail orientation when the 5′ end of the coding strand of one polynucleotide is adjacent to the 3′ end of the coding strand of the other polynucleotide, whereby the direction of transcription of each polynucleotide proceeds in the same direction as that of the other polynucleotide. The term “head-to-tail” may be abbreviated (5′)-to-(3′) and may also be indicated by the symbols (→ →) or (5′→3′5′→3′).
The term “downstream” refers to a nucleotide sequence that is located 3′ to a reference nucleotide sequence. In particular, downstream nucleotide sequences generally relate to sequences that follow the starting point of transcription. For example, the translation initiation codon of a gene is located downstream of the start site of transcription.
The term “upstream” refers to a nucleotide sequence that is located 5′ to a reference nucleotide sequence. In particular, upstream nucleotide sequences generally relate to sequences that are located on the 5′ side of a coding sequence or starting point of transcription. For example, most promoters are located upstream of the start site of transcription.
The terms “restriction endonuclease” and “restriction enzyme” are used interchangeably and refer to an enzyme that binds and cuts within a specific nucleotide sequence within double stranded DNA.
“Homologous recombination” refers to the insertion of a foreign DNA sequence into another DNA molecule, e.g., insertion of a vector in a chromosome. Preferably, the vector targets a specific chromosomal site for homologous recombination. For specific homologous recombination, the vector will contain sufficiently long regions of homology to sequences of the chromosome to allow complementary binding and incorporation of the vector into the chromosome. Longer regions of homology, and greater degrees of sequence similarity, may increase the efficiency of homologous recombination.
Several methods known in the art may be used to propagate a polynucleotide according to the invention. Once a suitable host system and growth conditions are established, recombinant expression vectors can be propagated and prepared in quantity. As described herein, the expression vectors which can be used include, but are not limited to, the following vectors or their derivatives: human or animal viruses such as vaccinia virus or adenovirus; insect viruses such as baculovirus; yeast vectors; bacteriophage vectors (e.g., lambda), and plasmid and cosmid DNA vectors, to name but a few.
A “vector” refers to any vehicle for the cloning of and/or transfer of a nucleic acid into a host cell. A vector may be a replicon to which another DNA segment may be attached so as to bring about the replication of the attached segment. A “replicon” refers to any genetic element (e.g., plasmid, phage, cosmid, chromosome, virus) that functions as an autonomous unit of DNA replication in vivo, i.e., capable of replication under its own control. The term “vector” includes both viral and nonviral vehicles for introducing the nucleic acid into a cell in vitro, ex vivo or in vivo. A large number of vectors known in the art may be used to manipulate nucleic acids, incorporate response elements and promoters into genes, etc. Possible vectors include, for example, plasmids or modified viruses including, for example bacteriophages such as lambda derivatives, or plasmids such as pBR322 or pUC plasmid derivatives, or the Bluescript vector. Another example of vectors that are useful in the present invention is the UltraVectorTM Production System (Intrexon Corp., Blacksburg, Va.) as described in WO 2007/038276, incorporated herein by reference. For example, the insertion of the DNA fragments corresponding to response elements and promoters into a suitable vector can be accomplished by ligating the appropriate DNA fragments into a chosen vector that has complementary cohesive termini. Alternatively, the ends of the DNA molecules may be enzymatically modified or any site may be produced by ligating nucleotide sequences (linkers) into the DNA termini. Such vectors may be engineered to contain selectable marker genes that provide for the selection of cells that have incorporated the marker into the cellular genome. Such markers allow identification and/or selection of host cells that incorporate and express the proteins encoded by the marker.
Viral vectors, and particularly retroviral vectors, have been used in a wide variety of gene delivery applications in cells, as well as living animal subjects. Viral vectors that can be used include, but are not limited to, retrovirus, adeno-associated virus, pox, baculovirus, vaccinia, herpes simplex, Epstein-Barr, adenovirus, geminivirus, and caulimovirus vectors. Non-viral vectors include plasmids, liposomes, electrically charged lipids (cytofectins), DNA-protein complexes, and biopolymers. In addition to a nucleic acid, a vector may also comprise one or more regulatory regions, and/or selectable markers useful in selecting, measuring, and monitoring nucleic acid transfer results (transfer to which tissues, duration of expression, etc.).
The term “plasmid” refers to an extra-chromosomal element often carrying a gene that is not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA molecules. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear, circular, or supercoiled, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3′ untranslated sequence into a cell.
A “cloning vector” refers to a “replicon,” which is a unit length of a nucleic acid, preferably DNA, that replicates sequentially and which comprises an origin of replication, such as a plasmid, phage or cosmid, to which another nucleic acid segment may be attached so as to bring about the replication of the attached segment. Cloning vectors may be capable of replication in one cell type and expression in another (“shuttle vector”). Cloning vectors may comprise one or more sequences that can be used for selection of cells comprising the vector and/or one or more multiple cloning sites for insertion of sequences of interest.
The term “expression vector” refers to a vector, plasmid or vehicle designed to enable the expression of an inserted nucleic acid sequence following transformation into the host. The cloned gene, i.e., the inserted nucleic acid sequence, is usually placed under the control of control elements such as a promoter, a minimal promoter, an enhancer, or the like. Initiation control regions or promoters, which are useful to drive expression of a nucleic acid in the desired host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving expression of these genes can be used in an expression vector, including but not limited to, viral promoters, bacterial promoters, animal promoters, mammalian promoters, synthetic promoters, constitutive promoters, tissue specific promoters, pathogenesis or disease related promoters, developmental specific promoters, inducible promoters, light regulated promoters; CYC1, HIS3, GAL1, GAL4, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI, alkaline phosphatase promoters (useful for expression in Saccharomyces); AOX1 promoter (useful for expression in Pichia); β-lactamase, lac, ara, tet, trp, lPL, lPR, T7, tac, and trc promoters (useful for expression in Escherichia coli); light regulated-, seed specific-, pollen specific-, ovary specific-, cauliflower mosaic virus 35S, CMV 35S minimal, cassava vein mosaic virus (CsVMV), chlorophyll a/b binding protein, ribulose 1,5-bisphosphate carboxylase, shoot-specific, root specific, chitinase, stress inducible, rice tungro bacilliform virus, plant super-promoter, potato leucine aminopeptidase, nitrate reductase, mannopine synthase, nopaline synthase, ubiquitin, zein protein, and anthocyanin promoters (useful for expression in plant cells); animal and mammalian promoters known in the art including, but are not limited to, the SV40 early (SV40e) promoter region, the promoter contained in the 3′ long terminal repeat (LTR) of Rous sarcoma virus (RSV), the promoters of the E1A or major late promoter (MLP) genes of adenoviruses (Ad), the cytomegalovirus (CMV) early promoter, the herpes simplex virus (HSV) thymidine kinase (TK) promoter, a baculovirus IE1 promoter, an elongation factor 1 alpha (EF1) promoter, a phosphoglycerate kinase (PGK) promoter, a ubiquitin (Ubc) promoter, an albumin promoter, the regulatory sequences of the mouse metallothionein-L promoter and transcriptional control regions, the ubiquitous promoters (HPRT, vimentin, α-actin, tubulin and the like), the promoters of the intermediate filaments (desmin, neurofilaments, keratin, GFAP, and the like), the promoters of therapeutic genes (of the MDR, CFTR or factor VIII type, and the like), pathogenesis or disease related-promoters, and promoters that exhibit tissue specificity and have been utilized in transgenic animals, such as the elastase I gene control region which is active in pancreatic acinar cells; insulin gene control region active in pancreatic beta cells, immunoglobulin gene control region active in lymphoid cells, mouse mammary tumor virus control region active in testicular, breast, lymphoid and mast cells; albumin gene, Apo AI and Apo AII control regions active in liver, alpha-fetoprotein gene control region active in liver, alpha 1-antitrypsin gene control region active in the liver, beta-globin gene control region active in myeloid cells, myelin basic protein gene control region active in oligodendrocyte cells in the brain, myosin light chain-2 gene control region active in skeletal muscle, and gonadotropic releasing hormone gene control region active in the hypothalamus, pyruvate kinase promoter, villin promoter, promoter of the fatty acid binding intestinal protein, promoter of the smooth muscle cell α-actin, and the like. In addition, these expression sequences may be modified by addition of enhancer or regulatory sequences and the like.
Vectors may be introduced into the desired host cells by methods known in the art, e.g., transfection, electroporation, microinjection, transduction, cell fusion, DEAE dextran, calcium phosphate precipitation, lipofection (lysosome fusion), use of a gene gun, or a DNA vector transporter (see, e.g., Wu et al., J. Biol. Chem. 267:963 (1992); Wu et al., J. Biol. Chem. 263:14621 (1988); and Hartmut et al., Canadian Patent Application No. 2,012,311).
A polynucleotide according to the invention can also be introduced in vivo by lipofection. For the past decade, there has been increasing use of liposomes for encapsulation and transfection of nucleic acids in vitro. Synthetic cationic lipids designed to limit the difficulties and dangers encountered with liposome-mediated transfection can be used to prepare liposomes for in vivo transfection of a gene encoding a marker (Feigner et al., Proc. Natl. Acad. Sci. USA. 84:7413 (1987); Mackey et al., Proc. Natl. Acad. Sci. USA 85:8027 (1988); and Ulmer et al., Science 259:1745 (1993)). The use of cationic lipids may promote encapsulation of negatively charged nucleic acids, and also promote fusion with negatively charged cell membranes (Feigner et al., Science 337:387 (1989)). Particularly useful lipid compounds and compositions for transfer of nucleic acids are described in WO95/18863, WO096/17823 and U.S. Pat. No. 5,459,127. The use of lipofection to introduce exogenous genes into the specific organs in vivo has certain practical advantages. Molecular targeting of liposomes to specific cells represents one area of benefit. It is clear that directing transfection to particular cell types would be particularly preferred in a tissue with cellular heterogeneity, such as pancreas, liver, kidney, and the brain. Lipids may be chemically coupled to other molecules for the purpose of targeting (Mackey et al. 1988, supra). Targeted peptides, e.g., hormones or neurotransmitters, and proteins such as antibodies, or non-peptide molecules could be coupled to liposomes chemically.
Other molecules are also useful for facilitating transfection of a nucleic acid in vivo, such as a cationic oligopeptide (e.g., WO95/21931), peptides derived from DNA binding proteins (e.g., WO96/25508), or a cationic polymer (e.g., WO95/21931).
It is also possible to introduce a vector in vivo as a naked DNA plasmid (see U.S. Pat. Nos. 5,693,622, 5,589,466 and 5,580,859). Receptor-mediated DNA delivery approaches can also be used (Curiel et al., Hum. Gene Ther. 3:147 (1992); and Wu et al., J. Biol. Chem. 262:4429 (1987)).
The term “transfection” refers to the uptake of exogenous or heterologous RNA or DNA by a cell. A cell has been “transfected” by exogenous or heterologous RNA or DNA when such RNA or DNA has been introduced inside the cell. A cell has been “transformed” by exogenous or heterologous RNA or DNA when the transfected RNA or DNA effects a phenotypic change. The transforming RNA or DNA can be integrated (covalently linked) into chromosomal DNA making up the genome of the cell.
“Transformation” refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” or “recombinant” or “transformed” organisms.
In addition, the recombinant vector comprising a polynucleotide according to the invention may include one or more origins for replication in the cellular hosts in which their amplification or their expression is sought, markers or selectable markers.
The term “selectable marker” refers to an identifying factor, usually an antibiotic or chemical resistance gene, that is able to be selected for based upon the marker gene's effect, i.e., resistance to an antibiotic, resistance to a herbicide, colorimetric markers, enzymes, fluorescent markers, and the like, wherein the effect is used to track the inheritance of a nucleic acid of interest and/or to identify a cell or organism that has inherited the nucleic acid of interest. Examples of selectable marker genes known and used in the art include: genes providing resistance to ampicillin, streptomycin, gentamycin, kanamycin, hygromycin, bialaphos herbicide, sulfonamide, and the like; and genes that are used as phenotypic markers, i.e., anthocyanin regulatory genes, isopentanyl transferase gene, and the like.
The term “reporter gene” refers to a nucleic acid encoding an identifying factor that is able to be identified based upon the reporter gene's effect, wherein the effect is used to track the inheritance of a nucleic acid of interest, to identify a cell or organism that has inherited the nucleic acid of interest, and/or to measure gene expression induction or transcription. Examples of reporter genes known and used in the art include: luciferase (Luc), green fluorescent protein (GFP), chloramphenicol acetyltransferase (CAT), β-galactosidase (LacZ), β-glucuronidase (Gus), and the like. Selectable marker genes may also be considered reporter genes.
“Promoter and “promoter sequence” are used interchangeably and refer to a DNA sequence capable of controlling the transcription of a nucleic acid. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental or physiological conditions. Promoters that cause a gene to be expressed in most cell types at most times are commonly referred to as “constitutive promoters.” Promoters that cause a gene to be expressed in a specific cell type are commonly referred to as “cell-specific promoters” or “tissue-specific promoters.” Promoters that cause a gene to be expressed at a specific stage of development or cell differentiation are commonly referred to as “developmentally-specific promoters” or “cell differentiation-specific promoters.” Promoters that are induced and cause a gene to be expressed following exposure or treatment of the cell with an agent, biological molecule, chemical, ligand, light, or the like that induces the promoter are commonly referred to as “inducible promoters” or “regulatable promoters.” It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity.
The promoter sequence is typically bounded at its 3′ terminus by the transcription initiation site and extends upstream (5′ direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. Within the promoter sequence will be found a transcription initiation site (conveniently defined for example, by mapping with nuclease S1), as well as protein binding domains (consensus sequences) responsible for the binding of transcription factors that recruit RNA polymerase-mediated transcription.
“Diagnostic switch promoter” refers to a promoter the activity of which is modulated by a factor in a manner that can be used as a diagnostic in the present invention. The term encompasses promoters that increase or decrease expression of a coding sequence during a disease or disorder as a change in promoter activity in either direction will be diagnostic. The term includes, without limitation, disease-specific promoters, promoters responsive to particular physiological or pathological conditions, and promoters responsive to specific biological molecules. Diagnostic switch promoters can comprise the sequence of naturally occurring promoters, modified sequences derived from naturally occurring promoters, or synthetic sequences (e.g., insertion of a response element into a promoter sequence to alter the responsiveness of the promoter).
A “coding sequence” is a DNA sequence that encodes a polypeptide or a RNA (e.g., a functional RNA).
A coding sequence is “under the control” of transcriptional and translational control sequences in a cell when RNA polymerase transcribes the coding sequence into RNA. If the coding sequence is a protein coding sequence, the primary RNA transcript is then further processed (e.g., trans-RNA spliced (if the coding sequence contains introns) and polyadenylated), exported to the cytoplasm, and translated into the protein encoded by the coding sequence. Non-protein-coding bioactive RNA species (including, but not limited to RNAi or microRNAs) can be functional in the nucleus as a primary transcript, a spliced transcript (with or without polyadenylation), and/or an excised intron; or can exert bioactivity in extra-nuclear cellular regions as any RNA form that is exported from the nucleus.
“Transcriptional and translational control sequences” refer to DNA regulatory sequences, such as promoters, enhancers, terminators, and the like, that provide for the expression of a coding sequence in a host cell. In eukaryotic cells, polyadenylation signals are control sequences.
The term “response element” refers to one or more cis-acting DNA elements which confer responsiveness on a promoter mediated through interaction with the DNA-binding domains of a transcription factor. This DNA element may be either palindromic (perfect or imperfect) in its sequence or composed of sequence motifs or half sites separated by a variable number of nucleotides. The half sites can be similar or identical and arranged as either direct or inverted repeats or as a single half site or multimers of adjacent half sites in tandem. The response element may comprise a minimal promoter isolated from different organisms depending upon the nature of the cell or organism into which the response element will be incorporated. The DNA binding domain of the transcription factor binds, in the presence or absence of a ligand, to the DNA sequence of a response element to initiate or suppress transcription of downstream gene(s) under the regulation of this response element. Examples of DNA sequences for response elements of the natural ocdysone receptor include: RRGG/TTCANTGAC/ACYY (SEQ ID NO: 1) (see Cherbas et. al., Genes Dev. 5:120 (1991)); AGGTCAN(n)AGGTCA, where N(n) can be one or more spacer nucleotides (SEQ ID NO: 2) (see D'Avino et al., Mol. Cell. Endocrinol. 113:1 (1995)); and GGGTTGAATGAATTT (SEQ ID NO: 3) (see Antoniewski et al., Mol. Cell Biol. 14:4465 (1994)).
The term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.
The term “expression” as used herein refers to the production of RNA (e.g., sense RNA, antisense RNA, microRNA, messenger RNA, heterologous nuclear RNA, ribosomal RNA, small interfering RNA, ribozymes, etc.) by transcription of a nucleic acid or polynucleotide. Expression may also include translation of mRNA into a protein or polypeptide.
The terms “cassette,” “expression cassette” and “gene expression cassette” refer to a segment of DNA that can be inserted into a nucleic acid or polynucleotide at specific restriction sites or by homologous recombination. The segment of DNA comprises a polynucleotide that encodes a polypeptide of interest, and the cassette and restriction sites are designed to ensure insertion of the cassette in the proper reading frame for transcription and translation. “Transformation cassette” refers to a specific vector comprising a polynucleotide that encodes a polypeptide of interest and having elements in addition to the polynucleotide that facilitate transformation of a particular host cell. Cassettes, expression cassettes, gene expression cassettes and transformation cassettes of the invention may also comprise elements that allow for enhanced expression of a polynucleotide encoding a polypeptide of interest in a host cell. These elements may include, but are not limited to: a promoter, a minimal promoter, an enhancer, a response element, a terminator sequence, a polyadenylation sequence, and the like.
For purposes of this invention, the term “gene switch” refers to the combination of a response element associated with a promoter, and a ligand-dependent transcription factor-based system which, in the presence of one or more ligands, modulates the expression of a gene into which the response element and promoter are incorporated.
The term “ecdysone-based,” with respect to a gene switch, refers to a gene switch comprising at least a functional part of a naturally occurring or synthetic ecdysone receptor ligand binding domain and which regulates gene expression in response to a ligand that binds to the ecdysone receptor ligand binding domain.
The terms “modulate” and “modulates” mean to induce, reduce or inhibit nucleic acid or gene expression, resulting in the respective induction, reduction or inhibition of protein or polypeptide production.
The polynucleotides or vectors according to the invention may further comprise at least one promoter suitable for driving expression of a gene in a host cell.
Enhancers that may be used in embodiments of the invention include but are not limited to: an SV40 enhancer, a cytomegalovirus (CMV) enhancer, an elongation factor 1 (EF1) enhancer, yeast enhancers, viral gene enhancers, and the like.
Termination control regions, i.e., terminator or polyadenylation sequences, may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary, however, it is most preferred if included. In a one embodiment of the invention, the termination control region may be comprised or be derived from a synthetic sequence, synthetic polyadenylation signal, an SV40 late polyadenylation signal, an SV40 polyadenylation signal, a bovine growth hormone (BGH) polyadenylation signal, viral terminator sequences, or the like.
The terms “3′ non-coding sequences” or “3′ untranslated region (UTR)” refer to DNA sequences located downstream (3′) of a coding sequence and may comprise polyadenylation [poly(A)] recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor.
“Regulatory region” refers to a nucleic acid sequence that regulates the expression of a second nucleic acid sequence. A regulatory region may include sequences which are naturally responsible for expressing a particular nucleic acid (a homologous region) or may include sequences of a different origin that are responsible for expressing different proteins or even synthetic proteins (a heterologous region). In particular, the sequences can be sequences of prokaryotic, eukaryotic, or viral genes or derived sequences that stimulate or repress transcription of a gene in a specific or non-specific manner and in an inducible or non-inducible manner. Regulatory regions include origins of replication, RNA splice sites, promoters, enhancers, transcriptional termination sequences, and signal sequences which direct the polypeptide into the secretory pathways of the target cell.
A regulatory region from a “heterologous source” refers to a regulatory region that is not naturally associated with the expressed nucleic acid. Included among the heterologous regulatory regions are regulatory regions from a different species, regulatory regions from a different gene, hybrid regulatory sequences, and regulatory sequences which do not occur in nature, but which are designed by one having ordinary skill in the art.
“RNA transcript” refers to the product resulting from RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be a RNA sequence derived from post-transcriptional processing of the primary transcript and is referred to as the mature RNA. “Messenger RNA (mRNA)” refers to the RNA that is without introns and that can be translated into protein by the cell. “cDNA” refers to a double-stranded DNA that is complementary to and derived from mRNA. “Sense” RNA refers to RNA transcript that includes the mRNA and so can be translated into protein by the cell. “Antisense RNA” refers to a RNA transcript that is complementary to all or part of a target primary transcript or mRNA and that blocks the expression of a target gene. The complementarity of an antisense RNA may be with any part of the specific gene transcript, i.e., at the 5′ non-coding sequence, 3′ non-coding sequence, or the coding sequence. “Functional RNA” refers to antisense RNA, ribozyme RNA, or other RNA that is not translated yet has an effect on cellular processes.
“Polypeptide,” “peptide” and “protein” are used interchangeably and refer to a polymeric compound comprised of covalently linked amino acid residues.
An “isolated polypeptide,” “isolated peptide” or “isolated protein” refer to a polypeptide or protein that is substantially free of those compounds that are normally associated therewith in its natural state (e.g., other proteins or polypeptides, nucleic acids, carbohydrates, lipids). “Isolated” is not meant to exclude artificial or synthetic mixtures with other compounds, or the presence of impurities which do not interfere with biological activity, and which may be present, for example, due to incomplete purification, addition of stabilizers, or compounding into a pharmaceutically acceptable preparation.
A “substitution mutant polypeptide” or a “substitution mutant” will be understood to mean a mutant polypeptide comprising a substitution of at least one wild-type or naturally occurring amino acid with a different amino acid relative to the wild-type or naturally occurring polypeptide. A substitution mutant polypeptide may comprise only one wild-type or naturally occurring amino acid substitution and may be referred to as a “point mutant” or a “single point mutant” polypeptide. Alternatively, a substitution mutant polypeptide may comprise a substitution of two or more wild-type or naturally occurring amino acids with two or more amino acids relative to the wild-type or naturally occurring polypeptide. According to the invention, a Group H nuclear receptor ligand binding domain polypeptide comprising a substitution mutation comprises a substitution of at least one wild-type or naturally occurring amino acid with a different amino acid relative to the wild-type or naturally occurring Group H nuclear receptor ligand binding domain polypeptide.
When the substitution mutant polypeptide comprises a substitution of two or more wild-type or naturally occurring amino acids, this substitution may comprise either an equivalent number of wild-type or naturally occurring amino acids deleted for the substitution, i.e., 2 wild-type or naturally occurring amino acids replaced with 2 non-wild-type or non-naturally occurring amino acids, or a non-equivalent number of wild-type amino acids deleted for the substitution, i.e., 2 wild-type amino acids replaced with 1 non-wild-type amino acid (a substitution+deletion mutation), or 2 wild-type amino acids replaced with 3 non-wild-type amino acids (a substitution+insertion mutation).
Substitution mutants may be described using an abbreviated nomenclature system to indicate the amino acid residue and number replaced within the reference polypeptide sequence and the new substituted amino acid residue. For example, a substitution mutant in which the twentieth (20th) amino acid residue of a polypeptide is substituted may be abbreviated as “x20z”, wherein “x” is the amino acid to be replaced, “20” is the amino acid residue position or number within the polypeptide, and “z” is the new substituted amino acid. Therefore, a substitution mutant abbreviated interchangeably as “E20A” or “Glu20Ala” indicates that the mutant comprises an alanine residue (commonly abbreviated in the art as “A” or “Ala”) in place of the glutamic acid (commonly abbreviated in the art as “E” or “Glu”) at position 20 of the polypeptide.
A substitution mutation may be made by any technique for mutagenesis known in the art, including but not limited to, in vitro site-directed mutagenesis (Hutchinson et al., J. Biol. Chem. 253:6551 (1978); Zoller et al., DNA 3:479 (1984); Oliphant et al, Gene 44:177 (1986); Hutchinson et al., Proc. Natl. Acad. Sci. USA 83:710 (1986)), use of TAB® linkers (Pharmacia), restriction endonuclease digestion/fragment deletion and substitution, PCR-mediated/oligonucleotide-directed mutagenesis, and the like. PCR-based techniques are preferred for site-directed mutagenesis (see Higuchi, 1989, “Using PCR to Engineer DNA”, in PCR Technology: Principles and Applications for DNA Amplification, H. Erlich, ed., Stockton Press, Chapter 6, pp. 61-70).
The term “fragment,” as applied to a polypeptide, refers to a polypeptide whose amino acid sequence is shorter than that of the reference polypeptide and which comprises, over the entire portion with these reference polypeptides, an identical amino acid sequence. Such fragments may, where appropriate, be included in a larger polypeptide of which they are a part. Such fragments of a polypeptide according to the invention may have a length of at least 2, 3, 4, 5, 6, 8, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 30, 35, 40, 45, 50, 100, 200, 240, or 300 or more amino acids.
A “variant” of a polypeptide or protein refers to any analogue, fragment, derivative, or mutant which is derived from a polypeptide or protein and which retains at least one biological property of the polypeptide or protein. Different variants of the polypeptide or protein may exist in nature. These variants may be allelic variations characterized by differences in the nucleotide sequences of the structural gene coding for the protein, or may involve differential splicing or post-translational modification. The skilled artisan can produce variants having single or multiple amino acid substitutions, deletions, additions, or replacements. These variants may include, inter alia: (a) variants in which one or more amino acid residues are substituted with conservative or non-conservative amino acids, (b) variants in which one or more amino acids are added to the polypeptide or protein, (c) variants in which one or more of the amino acids includes a substituent group, and (d) variants in which the polypeptide or protein is fused with another polypeptide such as serum albumin. The techniques for obtaining these variants, including genetic (suppressions, deletions, mutations, etc.), chemical, and enzymatic techniques, are known to persons having ordinary skill in the art. In one embodiment, a variant polypeptide comprises at least about 14 amino acids.
The term “homology” refers to the percent of identity between two polynucleotide or two polypeptide moieties. The correspondence between the sequence from one moiety to another can be determined by techniques known to the art. For example, homology can be determined by a direct comparison of the sequence information between two polypeptide molecules by aligning the sequence information and using readily available computer programs. Alternatively, homology can be determined by hybridization of polynucleotides under conditions that form stable duplexes between homologous regions, followed by digestion with single-stranded-specific nuclease(s) and size determination of the digested fragments.
As used herein, the term “homologous” in all its grammatical forms and spelling variations refers to the relationship between proteins that possess a “common evolutionary origin,” including proteins from superfamilies (e.g., the immunoglobulin superfamily) and homologous proteins from different species (e.g., myosin light chain, etc.) (Reeck et al., Cell 50:667 (1987)). Such proteins (and their encoding genes) have sequence homology, as reflected by their high degree of sequence similarity. However, in common usage and in the present application, the term “homologous,” when modified with an adverb such as “highly,” may refer to sequence similarity and not a common evolutionary origin.
Accordingly, the term “sequence similarity” in all its grammatical forms refers to the degree of identity or correspondence between nucleic acid or amino acid sequences of proteins that may or may not share a common evolutionary origin (see Reeck et al, Cell 50:667 (1987)). In one embodiment, two DNA sequences are “substantially homologous” or “substantially similar” when at least about 50% (e.g., at least about 75%, 90%, or 95%) of the nucleotides match over the defined length of the DNA sequences. Sequences that are substantially homologous can be identified by comparing the sequences using standard software available in sequence data banks, or in a Southern hybridization experiment under, for example, stringent conditions as defined for that particular system. Defining appropriate hybridization conditions is within the skill of the art (see e.g., Sambrook et al., 1989, supra).
As used herein, “substantially similar” refers to nucleic acid fragments wherein changes in one or more nucleotide bases results in substitution of one or more amino acids, but do not affect the functional properties of the protein encoded by the DNA sequence. “Substantially similar” also refers to nucleic acid fragments wherein changes in one or more nucleotide bases do not affect the ability of the nucleic acid fragment to mediate alteration of gene expression by antisense or co-suppression technology. “Substantially similar” also refers to modifications of the nucleic acid fragments of the present invention such as deletion or insertion of one or more nucleotide bases that do not substantially affect the functional properties of the resulting transcript. It is therefore understood that the invention encompasses more than the specific exemplary sequences. Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products.
Moreover, the skilled artisan recognizes that substantially similar sequences encompassed by this invention are also defined by their ability to hybridize, under stringent conditions (0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS), with the sequences exemplified herein. Substantially similar nucleic acid fragments of the present invention are those nucleic acid fragments whose DNA sequences are at least about 70%, 80%, 90% or 95% identical to the DNA sequence of the nucleic acid fragments reported herein.
Two amino acid sequences are “substantially homologous” or “substantially similar” when greater than about 40% of the amino acids are identical, or greater than 60% are similar (functionally identical). Preferably, the similar or homologous sequences are identified by alignment using, for example, the GCG (Genetics Computer Group, Program Manual for the GCG Package, Version 7, Madison, Wis.) pileup program.
The term “corresponding to” is used herein to refer to similar or homologous sequences, whether the exact position is identical or different from the molecule to which the similarity or homology is measured. A nucleic acid or amino acid sequence alignment may include spaces. Thus, the term “corresponding to” refers to the sequence similarity, and not the numbering of the amino acid residues or nucleotide bases.
A “substantial portion” of an amino acid or nucleotide sequence comprises enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul et al., J. Mol. Biol. 215:403 (1993)); available at ncbi.nlm.nih.gov/BLAST/). In general, a sequence often or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence.
The term “percent identity,” as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including but not limited to those described in: Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, New York (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, New York (1993); Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press, New Jersey (1994); Sequence Analysis in Molecular Biology (von Heinje, G., ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J., eds.) Stockton Press, New York (1991). Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using sequence analysis software such as the Megalign program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequences may be performed using the Clustal method of alignment (Higgins et al., CABIOS. 5:151 (1989)) with the default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments using the Clustal method may be selected: KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5.
The term “sequence analysis software” refers to any computer algorithm or software program that is useful for the analysis of nucleotide or amino acid sequences. “Sequence analysis software” may be commercially available or independently developed. Typical sequence analysis software includes, but is not limited to, the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.), BLASTP, BLASTN, BLASTX (Altschul et al., J. Mol. Biol. 215:403 (1990)), and DNASTAR (DNASTAR, Inc. 1228 S. Park St. Madison, Wis. 53715 USA). Within the context of this application it will be understood that where sequence analysis software is used for analysis, that the results of the analysis will be based on the “default values” of the program referenced, unless otherwise specified. As used herein “default values” will mean any set of values or parameters which originally load with the software when first initialized.
“Chemically synthesized,” as related to a sequence of DNA, means that the component nucleotides were assembled in vitro. Manual chemical synthesis of DNA may be accomplished using well-established procedures, or automated chemical synthesis can be performed using one of a number of commercially available machines. Accordingly, the genes can be tailored for optimal gene expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene expression if codon usage is biased towards those codons favored by the host. Determination of preferred codons can be based on a survey of genes derived from the host cell where sequence information is available.
As used herein, two or more individually operable gene regulation systems are said to be “orthogonal” when; a) modulation of each of the given systems by its respective ligand, at a chosen concentration, results in a measurable change in the magnitude of expression of the gene of that system, and b) the change is statistically significantly different than the change in expression of all other systems simultaneously operable in the cell, tissue, or organism, regardless of the simultaneity or sequentially of the actual modulation. Preferably, modulation of each individually operable gene regulation system effects a change in gene expression at least 2-fold greater than all other operable systems in the cell, tissue, or organism, e.g., at least 5-fold, 10-fold, 100-fold, or 500-fold greater. Ideally, modulation of each of the given systems by its respective ligand at a chosen concentration results in a measurable change in the magnitude of expression of the gene of that system and no measurable change in expression of all other systems operable in the cell, tissue, or organism. In such cases the multiple inducible gene regulation system is said to be “fully orthogonal.” The present invention is useful to search for orthogonal ligands and orthogonal receptor-based gene expression systems such as those described in US 2002/0110861 A1, which is incorporated herein by reference in its entirety.
The term “exogenous gene” means a gene foreign to the subject, that is, a gene which is introduced into the subject through a transformation process, an unmutated version of an endogenous mutated gene or a mutated version of an endogenous unmutated gene. The method of transformation is not critical to this invention and may be any method suitable for the subject known to those in the art. Exogenous genes can be either natural or synthetic genes and therapeutic genes which are introduced into the subject in the form of DNA or RNA which may function through a DNA intermediate such as by reverse transcriptase. Such genes can be introduced into target cells, directly introduced into the subject, or indirectly introduced by the transfer of transformed cells into the subject. The term “therapeutic gene” means a gene which imparts a beneficial function to the host cell in which such gene is expressed.
The term “ecdysone receptor complex” generally refers to a heterodimeric protein complex having at least two members of the nuclear receptor family, ecdysone receptor (“EcR”) and ultraspiracle (“USP”) proteins (see Yao et al., Nature 366:476 (1993)); Yao et al., Cell 71:63 (1992)). The functional EcR complex may also include additional protein(s) such as immunophilins. Additional members of the nuclear receptor family of proteins, known as transcriptional factors (such as DHR38, betaFZ-1 or other insect homologs), may also be ligand dependent or independent partners for EcR and/or USP. The EcR complex can also be a heterodimer of EcR protein and the vertebrate homolog of ultraspiracle protein, retinoic acid-X-receptor (“RXR”) protein. The term EcR complex also encompasses homodimer complexes of the EcR protein or USP.
An EcR complex can be activated by an active ecdysteroid or non-steroidal ligand bound to one of the proteins of the complex, inclusive of EcR, but not excluding other proteins of the complex. As used herein, the term “ligand,” as applied to EcR-based gene switches, describes small and soluble molecules having the capability of activating a gene switch to stimulate expression of a polypeptide encoded therein. Examples of ligands include, without limitation, an ecdysteroid, such as ecdysone, 20-hydroxyecdysone, ponasterone A, muristerone A, and the like, 9-cis-retinoic acid, synthetic analogs of retinoic acid, N,N′-diacylhydrazines such as those disclosed in U.S. Pat. Nos. 6,013,836; 5,117,057; 5,530,028; and 5,378,726 and U.S. Published Application Nos. 2005/0209283 and 2006/0020146; oxadiazolines as described in U.S. Published Application No. 2004/0171651; dibenzoylalkyl cyanohydrazines such as those disclosed in European Application No. 461,809; N-alkyl-N,N′-diaroylhydrazines such as those disclosed in U.S. Pat. No. 5,225,443; N-acyl-N-alkylcarbonylhydrazines such as those disclosed in European Application No. 234,994; N-aroyl-N-alkyl-N′-aroylhydrazines such as those described in U.S. Pat. No. 4,985,461; amidoketones such as those described in U.S. Published Application No. 2004/0049037; each of which is incorporated herein by reference and other similar materials including 3,5-di-tert-butyl-4-hydroxy-N-isobutyl-benzamide, 8-O-acetylharpagide, oxysterols, 22(R) hydroxycholesterol, 24(S) hydroxycholesterol, 25-epoxycholesterol, T0901317, 5-alpha-6-alpha-epoxycholesterol -3-sulfate (ECHS), 7-ketocholesterol-3-sulfate, famesol, bile acids, 1,1-biphosphonate esters, juvenile hormone III, and the like. Examples of diacylhydrazine ligands useful in the present invention include RG-115819 (3,5-Dimethyl-benzoic acid N-(l-ethyl-2,2-dimethyl-propyl)-N′-(2-methyl-3-methoxy-benzoyl)-hydrazide), RG-115830 (3,5-Dimethyl-benzoic acid N-(l-tert-butyl-butyl)-N′-(2-ethyl-3-methoxy-benzoyl)-hydrazide), and RG-115932 ((R)-3,5-Dimethyl-benzoic acid N-(1-tert-butyl-butyl)-N′-(2-ethyl-3-methoxy-benzoyl)-hydrazide). See U.S. application Ser. No. 12/155,111.
The EcR complex includes proteins which are members of the nuclear receptor superfamily wherein all members are characterized by the presence of an amino-terminal transactivation domain (“TA”), a DNA binding domain (“DBD”), and a ligand binding domain (“LBD”) separated by a hinge region. Some members of the family may also have another transactivation domain on the carboxy-terminal side of the LBD. The DBD is characterized by the presence of two cysteine zinc fingers between which are two amino acid motifs, the P-box and the D-box, which confer specificity for ecdysone response elements. These domains may be either native, modified, or chimeras of different domains of heterologous receptor proteins.
The DNA sequences making up the exogenous gene, the response element, and the EcR complex may be incorporated into archaebacteria, procaryotic cells such as Escherichia coli, Bacillus subtilis, or other enterobacteria, or eucaryotic cells such as plant or animal cells. However, because many of the proteins expressed by the gene are processed incorrectly in bacteria, eucaryotic cells are preferred. The cells may be in the form of single cells or multicellular organisms. The nucleotide sequences for the exogenous gene, the response element, and the receptor complex can also be incorporated as RNA molecules, preferably in the form of functional viral RNAs such as tobacco mosaic virus. Of the eucaryotic cells, vertebrate cells are preferred because they naturally lack the molecules which confer responses to the ligands of this invention for the EcR. As a result, they are “substantially insensitive” to the ligands of this invention. Thus, the ligands useful in this invention will have negligible physiological or other effects on transformed cells, or the whole organism. Therefore, cells can grow and express the desired product, substantially unaffected by the presence of the ligand itself.
The term “subject” means an intact insect, plant or animal. It is also anticipated that the ligands will work equally well when the subject is a fungus or yeast. When the subject is an intact animal, preferably the animal is a vertebrate, most preferably a mammal.
EcR ligands, when used with the EcR complex which in turn is bound to the response element linked to an exogenous gene (e.g., a reporter gene), provide the means for external temporal regulation of expression of the exogenous gene. The order in which the various components bind to each other, that is, ligand to receptor complex and receptor complex to response element, is not critical. Typically, modulation of expression of the exogenous gene is in response to the binding of the EcR complex to a specific control, or regulatory, DNA element. The EcR protein, like other members of the nuclear receptor family, possesses at least three domains, a transactivation domain, a DNA binding domain, and a ligand binding domain. This receptor, like a subset of the nuclear receptor family, also possesses less well-defined regions responsible for heterodimerization properties. Binding of the ligand to the ligand binding domain of EcR protein, after heterodimerization with USP or RXR protein, enables the DNA binding domains of the heterodimeric proteins to bind to the response element in an activated form, thus resulting in expression or suppression of the exogenous gene. This mechanism does not exclude the potential for ligand binding to either EcR or USP, and the resulting formation of active homodimer complexes (e.g. EcR+EcR or USP+USP). In one embodiment, one or more of the receptor domains can be varied producing a chimeric gene switch. Typically, one or more of the three domains may be chosen from a source different than the source of the other domains so that the chimeric receptor is optimized in the chosen host cell or organism for transactivating activity, complementary binding of the ligand, and recognition of a specific response element. In addition, the response element itself can be modified or substituted with response elements for other DNA binding protein domains such as the GAL-4 protein from yeast (see Sadowski et al., Nature 335:563 (1988) or LexA protein from E. coli (see Brent et al., Cell 43:729 (1985)) to accommodate chimeric EcR complexes. Another advantage of chimeric systems is that they allow choice of a promoter used to drive the exogenous gene according to a desired end result. Such double control can be particularly important in areas of gene therapy, especially when cytotoxic proteins are produced, because both the timing of expression as well as the cells wherein expression occurs can be controlled. When exogenous genes, operatively linked to a suitable promoter, are introduced into the cells of the subject, expression of the exogenous genes is controlled by the presence of the ligand of this invention. Promoters may be constitutively or inducibly regulated or may be tissue-specific (that is, expressed only in a particular type of cell) or specific to certain developmental stages of the organism.
Numerous genomic and cDNA nucleic acid sequences coding for a variety of polypeptides, such as transcription factors and reporter genes, are well known in the art. Those skilled in the art have access to nucleic acid sequence information for virtually all known genes and can either obtain the nucleic acid molecule directly from a public depository, the institution that published the sequence, or employ routine methods to prepare the molecule.
For in vivo use, the ligands described herein may be taken up in pharmaceutically acceptable carriers, such as, for example, solutions, suspensions, tablets, capsules, ointments, elixirs, and injectable compositions. Pharmaceutical compositions may contain from 0.01% to 99% by weight of the ligand. Compositions may be either in single or multiple dose forms. The amount of ligand in any particular pharmaceutical composition will depend upon the effective dose, that is, the dose required to elicit the desired gene expression or suppression.
Suitable routes of administering the pharmaceutical preparations include oral, rectal, topical (including dermal, buccal and sublingual), vaginal, parenteral (including subcutaneous, intramuscular, intravenous, intradermal, intrathecal and epidural) and by naso-gastric tube. It will be understood by those skilled in the art that the preferred route of administration will depend upon the condition being diagnosed and may vary with factors such as the condition of the recipient.
One embodiment of the invention comprises methods of diagnosing a disease or disorder in a subject, comprising:

    (a) introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) administering ligand to said modified cells; and
    (c) detecting reporter gene expression;


wherein expression of the reporter gene indicates that said subject has said disease, disorder, or condition.
In one embodiment, the diagnostic methods are carried out ex vivo in cells that have been isolated from said subject.
In one embodiment, the diagnostic methods are carried out by introducing the compositions of the invention into cells that have been isolated from said subject to produce modified cells, and the modified cells are re-introduced into said subject.
In one embodiment, the diagnostic methods are carried out in vivo.
In a different embodiment, the diagnostic methods may be carried out using non-autologous cells, e.g., cells that are allogeneic or xenogeneic to the subject, instead of autologous cells from the subject. The polynucleotides may be introduced into the non-autologous cells ex vivo to produce modified cells and the modified cells may then be introduced into the subject. The non-autologous cells may be any cells that are viable after transplantation into a subject, including, without limitation, stem cells (such as embryonic stem cells or hematopoietic stem cells) and fibroblasts.
One embodiment of the invention relates to methods of diagnosing a disease or disorder in a subject, comprising:

    (a) introducing into non-autologous cells (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) introducing said modified cells into said subject;
    (c) administering ligand to said modified cells; and
    (d) detecting reporter gene expression;


wherein expression of said reporter gene indicates that said subject has said disease or disorder.
In one aspect of this embodiment, the modified cells are surrounded by a barrier (e.g., encapsulated) prior to being introduced into the subject. The encapsulated cells will function as an implantable biosensor. In one embodiment, encapsulation of cells and methods for making them are provided, which provide improved structural characteristics and immune protection. Such encapsulated cells will withstand mechanical, chemical or immune destruction within the host, and will additionally provide for free permeability to nutrients, ions, oxygen, and other materials needed to both maintain the cell and support normal metabolic functions. In one embodiment, the encapsulated cells are impermeable to bacteria, lymphocytes, and large proteins of the type responsible for immunochemical reactions. In one embodiment, the barrier will also function to prevent the non-autologous cells from escaping from the site of introduction, e.g., rogue cells that might cause harm to the subject if allowed to circulate. In one embodiment, the barrier is a selectively permeable barrier, e.g., a barrier that is permeable to small molecules such as hormones and small peptides but impermeable to larger polypeptides such as antibodies. For example, the barrier may be impermeable to molecules with a molecular weight greater than about 100,000, about 50,000, about 25,000, about 10,000, about 5,000 or about 1,000 daltons.
Two encapsulation methods, microencapsulation and macroencapsulation, are known in the art. Typically, microencapsulated cells are sequestered in a small spherical container, whereas macroencapsulated cells are entrapped in a larger non-spherical membrane. For encapsulation, living cells and other sensitive materials are treated under sufficiently mild conditions allowing the cells or biomaterial to remain substantially unaffected by the encapsulation process, yet permitting the formation of a capsule of sufficient strength to exist over long periods of time.
In one embodiment, the cells are encapsulated within a biocompatible semi-permeable membrane. The term “biocompatible” as used herein refers collectively to both the intact capsule and its contents. Specifically, it refers to the capability of the implanted intact encapsulated cell to avoid detrimental effects of the body's various protective systems, such as immune system or foreign body fibrotic response, and remain functional for a significant period of time.
The capsules of the present invention are especially useful for the administration of cells by injection, implantation or transplantation to a subject. Living cells can be encapsulated in a variety of gels, to form implantable devices, e.g., microbeads or microspheres to physically isolate the cells once implanted into a host. To prevent entry of smaller molecular weight substances such as antibodies and complement (with a molecular weight of about 150 kDa) into these mircoparticles, they can be coated with a material such as poly-L-lysine, chitosan, or PAN-PVC, which provides an outer shell with a controlled pore size or they can be treated by e.g., cross-linking, to control their internal porosity. Additional examples of useful materials include conventional biocompatible materials made up of natural or synthetic polymers or co-polymers, such as alginate, poly-L-lysine-alginate, collagen, gelatin, laminin, methyl methacrylate, hydroxyethyl methacrylate, MATRIGEL, VIRTOGEN, polyvinylalcohol, agarose, polyethylene glycol, hydrogels, polylactic acid, polyglycolic acid, poly(lactide-co-glycolide), polyhydroxybutyrate-polyhydroxyvalerate, copolymer, poly(lactide-co-caprolactone), polyesteramides, polyorthoesters, poly 13-hydroxybutyric acid, polyanhydrides, polyethylene terephthalate, polyetrafluoroethylene, polyacrylates (including acrylic copolymers), polyvinylidenes, polyvinyl chloride copolymers, polyurethanes, polystyrenes, polyamides, cellulose acetates, cellulose nitrates, polysulfones (including polyether sulfones), polyphosphazenes, polyacrylonitriles, and poly(acrylonitrile/covinyl chloride).
In one embodiment, the cells are isolated and suspended in liquid medium and then encapsulated by a supporting matrix, e.g., a hydrogel matrix to form a microbead. This microbead may serve as a core of an implantable device. The core will maintain a proper cell distribution, provide strength, and enhance cell viability, longevity, and function. The core will also contribute to immunoisolation. The core will also protect the internal particle from direct cell-cell interactions that can elicit an undesirable host response.
The barrier may contain multiple layers, e.g., where each layer serves a different purpose (e.g., support, control of permeability). Barriers may also comprise contrast agents or other properties that render the barrier imageable (e.g., by x-ray, sonography, etc.) to ensure proper positioning of the implanted cells. Examples of barrier systems useful for cell implantation are described in U.S. Pat. Nos. 7,226,978, RE39,542 (agarose), U.S. Pat. Nos. 6,960,351, 6,916,640, 6,911,227 (polyethylene glycol), U.S. Pat. Nos. 6,818,018, 6,808,705, 6,783,964, 6,762,959, 6,727,322, 6,610,668 (poly-14-N-acetylglucosamine (p-GlcNAc) polysaccharide), U.S. Pat. Nos. 6,558,665, RE38,027, 6,495,161, 6,368,612, 6,365,385, 6,337,008, 6,306,454 (polyalkylene), U.S. Pat. Nos. 6,303,355, 6,287,558 (gel super matrix), U.S. Pat. Nos. 6,281,015, 6,264,941, 6,258,870, 6,180,007, 6,126,936 (polyamine acid), U.S. Pat. Nos. 6,123,700, 6,083,523, 6,020,200, 5,916,790, 5,912,005, 5,908,623, 5,902,745, 5,858,746, 5,846,530 (polysaccaharides), U.S. Pat. Nos. 5,843,743, 5,837,747, 5,837,234, 5,834,274, 5,834,001, 5,801,033, 5,800,829, 5,800,828, 5,798,113, 5,788,988, 5,786,216, 5,773,286, 5,759,578, 5,700,848, 5,656,481, 5,653,975, 5,648,099, 5,550,178, 4,806,355, 4,689,293, 4,680,174, 4,673,566, 4,409,331, 4,352,883, and U.S. Patent Application Publications 2006/0263405 (alginate/polymer) and 2004/0005302 (alignate-poly-L-lysine), each incorporated herein by references in its entirety.
In one embodiment, the polynucleotide encoding the gene switch and the polynucleotide encoding the reporter gene linked to a promoter are part of one larger polynucleotide, e.g., a vector. In another embodiment, the polynucleotide encoding the gene switch and the polynucleotide encoding the reporter gene linked to a promoter are separate polynucleotides.
The subject on which the diagnostic methods are carried out may be any subject for which a diagnosis is desired. For example, the subject may be one that is exhibiting one or more symptoms of a disease or disorder. The subject may also be one that is predisposed to a disease or disorder, e.g., due to genetics, family history, or environmental exposure. The subject may be a member of the general public, e.g., as part of a screening for the prevalence of a disease or disorder in a population.
The disease or disorder to be diagnosed by the methods of the invention may be any disease or disorder for which one or more diagnostic switch promoters are available. Examples of diseases or disorders which may be diagnosed by the methods of the invention include, without limitation, hyperproliferative diseases (e.g., cancer), cardiovascular diseases, neural diseases, autoimmune diseases, graft versus host disease, transplant rejection, bone diseases, gastrointestinal diseases, blood diseases, metabolic diseases, inflammatory diseases, and infections.
One embodiment of the invention relates to methods of preparing modified cells for diagnosing a disease or disorder in a subject, comprising introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells.
Another embodiment of the invention relates to methods of diagnosing a disease or disorder in a subject, comprising:

    (a) administering ligand to modified cells of said subject; and
    (b) detecting reporter gene expression;


wherein expression of said reporter gene indicates that said subject has said disease or disorder, and
wherein said modified cells of said subject comprise (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor.
The diagnostic switch promoters of the invention may be any promoter that is useful for diagnosing a specific disease or disorder, monitoring the progression of a disease, or monitoring the effectiveness or toxicity of a treatment. Examples include, without limitation, promoters of genes that exhibit increased or decreased expression only during a specific disease or disorder and promoters of genes that exhibit increased or decreased expression under specific cell conditions (e.g., proliferation, apoptosis, change in pH, oxidation state, oxygen level). In some embodiments where the gene switch comprises more than one transcription factor sequence, the specificity of the diagnostic methods can be increased by combining a disease- or condition-specific promoter with a tissue- or cell type-specific promoter to limit the tissues in which a diagnostic measurement occurs. Thus, tissue- or cell type-specific promoters are encompassed within the definition of diagnostic switch promoter.
As an example of disease-specific promoters, useful promoters for diagnosing cancer include the promoters of oncogenes. Examples of classes of oncogenes include, but are not limited to, growth factors, growth factor receptors, protein kinases, programmed cell death regulators and transcription factors. Specific examples of oncogenes include, but are not limited to, sis, erb B, erb B-2, ras, abl, myc and bcl-2 and TERT. Examples of other cancer-related genes include tumor associated antigen genes and other genes that are overexpressed in neoplastic cells (e.g., MAGE-1, carcinoembryonic antigen, tyrosinase, prostate specific antigen, prostate specific membrane antigen, p53, MUC-1, MUC-2, MUC-4, HER-2/neu, T/Tn, MART-1, gp100, GM2, Tn, sTn, and Thompson-Friedenreich antigen (TF)).
Examples of promoter sequences and other regulatory elements (e.g., enhancers) that are known in the art and are useful as diagnostic switch promoters in the present invention are disclosed in the references listed in Tables 1 and 2, along with the disease/disorder (Table 1) or tissue specificity (Table 2) associated with each promoter. The promoter sequences disclosed in these references are herein incorporated by reference in their entirety.









TABLE 1







Patent/Published


Promoter Sequence
Disease/Disorder
Application No.







Her-2/neu (ERBB2/c-erbB-2)
cancer
5,518,885


osteocalcin
calcified tumors
5,772,993


stromelysin-1
cancer
5,824,794


prostate specific antigen
prostate cancer
5,919,652


human sodium-iodide symporter
thyroid carcinoma
6,015,376


H19, IF-1, IGF-2
cancer
6,306,833


thymosin β15
breast, pancreatic, prostate
6,489,463



cancer


T cell factor
cancer
6,608,037


cartilage-derived retinoic acid-
chondrosarcoma,
6,610,509


sensitive protein
mammary tumor


insulin
pancreatic cancer
6,716,824


PEG-3
cancer
6,737,523


telomerase reverse transcriptase
cancer
6,777,203


melanoma differentiation associated
cancer
6,841,362


gene-7


prostasin
cancer
6,864,093


telomerase catalytic subunit;
cancer
6,936,595


cyclin-A


midkine; c-erbB-2
cancer
7,030,099


prostate-specific membrane antigen
prostate cancer
7,037,647


p51
cancer
7,038,028


telomerase RNA
cancer
7,084,267


prostatic acid phosphatase
prostate cancer
7,094,533


PCA3dd3
prostate cancer
7,138,235


DF3/MUC1
cancer
7,247,297


hex II
cancer
2001/0011128


cyclooxygenase-2
cancer
2002/0107219


super PSA
prostate cancer
2003/0078224


skp2
cancer
2003/0109481


PRL-3
metastatic colon cancer
2004/0126785


CA125/M17S2
ovarian cancer
2004/0126824


IAI.3B
ovarian cancer
2005/0031591


CRG-L2
liver cancer
2005/0124068


TRPM4
prostate cancer
2006/0188990


RTVP
glioma
2006/0216731


TARP
prostate cancer, breast
2007/0032439



cancer


telomere reverse transcriptase
cancer
2007/0059287


A4 amyloid protein
Alzheimer's disease
5,151,508


amyloid β-protein precursor
Alzheimer's disease
5,643,726


precursor of the Alzheimer's Disease
Alzheimer's disease
5,853,985


A4 amyloid protein


neuropeptide FF
CNS disorders
6,320,038


endoplasmic reticulum stress
stress
7,049,132


elements


urocortin II
psychopathologies
7,087,385


tyrosine hydroxylase
neurological disorders
7,195,910


complement factor 3; serum amyloid
inflammation
5,851,822


A3


tissue inhibitor of metalloproteinase-
rheumatism, cancer,
5,854,019


3 (TIMP-3)
autoimmune disease,



inflammation


p75 tumor necrosis factor receptor
autoimmune disease
5,959,094


tumor necrosis factor-α
inflammation
6,537,784


peroxisome proliferator activated
inflammation
6,870,044


receptor/IIA-1 nonpancreatic


secreted phospholipase A2


SOCS-3
growth disorders,
2002/0174448



autoimmune disease,



inflammation


SR-BI
lipid disorders
5,965,790


Ob
obesity
5,698,389


site-1 protease
obesity, diabetes
7,045,294


TIGR
glaucoma
7,138,511


VL30
anoxia
5,681,706


excitatory amino acid transporter-2
nervous system ischemia
2004/0171108


MDTS9
renal failure
2006/0014931


LIM, pyrroline 5-carboxylate
prostate disorders
2006/0134688


reductase, SIM2


Bax
apoptosis
5,744,310


fas
apoptosis
5,888,764


bbc3
apoptosis
7,202,024


PINK-1
PI-3 kinase/Akt pathway
2006/0228776



disorders


















TABLE 2







Patent/Published


Promoter Sequence
Tissue Specificity
Application No.







troponin T
skeletal muscle
5,266,488


myoD
muscle
5,352,595


actin
muscle
5,374,544


smooth muscle 22α
arterial smooth muscle
5,837,534


utrophin
muscle
5,972,609


myostatin
muscle
6,284,882


smooth muscle myosin heavy chain
smooth muscle
6,780,610


cardiac ankyrin repeat protein
cardiac muscle
7,193,075


MLP
muscle
2002/0042057


smoothelin
smooth muscle
2003/0157494


MYBPC3
cardiomyocytes
2004/0175699


Tα1 α-tubulin
neurons
5,661,032


intercellular adhesion molecule-4
neurons
5,753,502


(ICAM-4)


γ-aminobutyric acid type A receptor
hippocampus
6,066,726


β1 subunit


neuronal nicotinic acetylcholine
neurons
6,177,242


receptor β2-subunit


presenilin-1
neurons
6,255,473


calcium-calmodulin-dependent
forebrain
6,509,190


kinase IIα


CRF2α receptor
brain
7,071,323


nerve growth factor
neurons
2003/159159


GLP-2 receptor
gut, brain
2002/0045173


type I transglutaminase
keratinocytes
5,643,746


K14
keratinocytes
6,596,515


stearoyl-CoA desaturase
skin
2002/0151018


megsin
renal cells
6,790,617


prolactin
pituitary
5,082,779


GDF-9
ovary, testes,
7,227,013



hypothalamus, pituitary,



placenta


PSP94
prostate
2003/0110522


NRL; NGAL
mammary gland
5,773,290


long whey acidic protein
mammary gland
5,831,141


mammary associated amyloid A
mammary ductal epithelial
2005/0107315



cells


endothelin-1
endothelial cells
5,288,846


serglycin
hematopoietic cells
5,340,739


platelet-endothelial cell adhesion
platelets, leukocytes,
5,668,012


molecule-1 (PECAM-1)
endothelial cells


Tie receptor tyrosine kinase
endothelial cells, bone
5,877,020



marrow


KDR/flk-1
endothelial cells
5,888,765


endoglin
endothelial cells
6,103,527


CCR5
myeloid and lymphoid
6,383,746



cells


CD11d
myeloid cells
6,881,834


platelet glycoprotein IIb
hematopoietic cells
6,884,616


preproendothelin-1
endothelial cells
7,067,649


interleukin-18 binding protein
mononuclear cells
2006/0239984


CD34
hematopoietic stem cells
5,556,954


Tec tyrosine kinase
hematopoietic stem cells,
6,225,459



liver


AC133
stem cells
2005/0125849









Other genes that exhibit changes in expression levels during specific diseases or disorders and therefore are useful in the present invention include, without limitation, the genes (along with the associated disease/disorder) listed in Table 3.









TABLE 3







Patent/Published


Gene
Disease/Disorder
Application No.







MLH1, MSH2, MSH6, PMS1, APC
Colorectal cancer
7,148,016


LEF-1
Colon cancer
2002/0169300


F2 receptor
Colon cancer
2002/0187502


TGF-β type II receptor
Colon cancer
2004/0038284


EYA4
Colon cancer
2005/0003463


PCA3
Prostate cancer
7,138,235


K2
Prostate cancer
6,303,361


PROST 03
Prostate cancer metastases
2002/0009455


PCAM-1
Prostate cancer
2002/0042062


PCADM-1
Prostate cancer
2003/0100033


PCA3dd3
Prostate cancer
2003/0165850


PCAV
Prostate cancer
2006/0275747


PAcP
Androgen-insensitive
2006/0294615



prostate cancer


SEQ ID NO: 1 of the patent
Liver cancer
5,866,329


5,866,329, incorporated by reference


herein


SEQ ID NOS: 1, 3 of the U.S. patent
Hepatocellular cancer
2002/0115094


application publication


2002/0115094, incorporated by


reference herein


SEQ ID NO: 1 of the patent U.S.
Hepatocellular carcinoma
2005/0037372


application publication


2005/0037372, incorporated by


reference herein


ATB0
Hepatocellular carcinoma
2006/0280725


SEQ ID NOS: 1, 3 of the U.S. patent
Liver cancer
2007/0042420


application publication


2007/0042420, incorporated by


reference herein


CSA-1
Chondrosarcoma
2001/0016649


SEQ ID NOS: 1-15 of the U.S. patent
Pancreatic cancer
2001/0016651


application publication


2001/0016651, incorporated by


reference herein


SEQ ID NOS: 1-15 of the U.S. patent
Pancreatic cancer
2003/0212264


application publication


2003/0212264, incorporated by


reference herein


SYG972
Breast cancer
2002/0055107


Urb-ctf
Breast cancer
2003/0143546


BCU399
Breast cancer
2003/0180728


TBX2
Breast cancer
2004/0029185


Cyr61
Breast cancer
2004/0086504


DIAPH3
Breast cancer
2005/0054826


SEQ ID NOS: 1-24 of the U.S. patent
Breast cancer
2007/0134669


application publication


2007/0134669, incorporated by


reference herein


Human aspartyl (asparaginyl) beta-
CNS cancer
2002/0102263


hydroxylase


BEHAB
CNS cancer
2003/0068661


IL-8
Kaposi's Sarcoma
2003/0096781


SEQ ID NOS: 1-278 of the U.S.
Hematological cancers
2002/0198362


patent application publication


2002/0198362, incorporated by


reference herein


BLSA
B-cell cancer
2003/0147887


BP1
Leukemia
2003/0171273


DAP-kinase, HOXA9
Non-small cell lung cancer
2003/0224509


ARP
Clear cell renal carcinoma,
2004/0010119



inflammatory disorders


Nbk
Renal cancer
2005/0053931


CD43
Ovarian cancer
2006/0216231


SEQ ID NOS: 1-84 of the U.S. patent
Ovarian cancer
2007/0054268


application publication


2007/0054268, incorporated by


reference herein


β7-hcG, β6-hCG, β6e-hCG,
Uterine tumors
2006/0292567


β5-hCG, β8-hcG, β3-hCG


MTA1s
Hormone insensitive
2006/0204957



cancer


Old-35, Old-64
Tumor proliferation
2003/0099660


LAGE-1
Cancer
6,794,131


CIF150/hTAFII150
Cancer
6,174,679


P65 oncofetal protein
Cancer
5,773,215


Telomerase
Cancer
2002/0025518


CYP1B1
Cancer
2002/0052013


14-3-3σ
Cancer
2002/0102245


NES1
Cancer
2002/0106367


CAR-1
Cancer
2002/0119541


HMGI, MAG
Cancer
2002/0120120


ELL2
Cancer
2002/0132329


Ephrin B2
Cancer
2002/0136726


WAF1
Cancer
2002/0142442


CIF130
Cancer
2002/0143154


C35
Cancer
2002/0155447


BMP2
Cancer
2002/0159986


BUB3
Cancer
2002/0160403


Polymerase kappa
Cancer
2003/0017573


EAG1, EAG2
Cancer
2003/0040476


SEQ ID NOS: 18, 20, 22 of the U.S.
Cancer
2003/0044813


patent application publication


2003/0044813, incorporated by


reference herein


HMG I
Cancer
2003/0051260


HLTF
Cancer
2003/0082526


Barx2
Cancer
2003/0087243


SEQ ID NOS: 18, 20, 22, 32, 34, 36
Cancer
2003/0108920


of the U.S. patent application


publication 2003/0108920,


incorporated by reference herein


Cables
Cancer
2003/0109443


Pp 32r1
Cancer
2003/0129631


BMP4
Cancer
2003/0134790


TS10q23.3
Cancer
2003/0139324


Nuclear spindle-associating protein
Cancer
2003/0157072


PFTAIRE
Cancer
2003/0166217


SEMA3B
Cancer
2003/0166557


MOGp
Cancer, multiple sclerosis,
2003/0166898



inflammatory disease


Fortilin
Cancer
2003/0172388


SEQ ID NO: 1 of the U.S. patent
Cancer
2003/0215833


application publication


2003/0215833, incorporated by


reference herein


IGFBP-3
Cancer
2004/0005294


Polyhomeotic 2
Cancer
2004/0006210


PNQALRE
Cancer
2004/0077009


SEQ ID NOS: 1, 3 of the U.S. patent
Cancer
2004/0086916


application publication


2004/0086916, incorporated by


reference herein


SCN5A
Cancer
2004/0146877


miR15, miR16
Cancer
2004/0152112


Headpin
Cancer
2004/0180371


PAOh1/SMO
Cancer
2004/0229241


Hippo, Mst2
Cancer
2005/0053592


PSMA-like
Cancer, neurological
2005/0064504



disorders


JAB1
Cancer
2005/0069918


NF-AT
Cancer
2005/0079496


P28ING5
Cancer
2005/0097626


MTG16
Cancer
2005/0107313


ErbB-2
Cancer
2005/0123538


HDAC9
Cancer
2005/0130146


GPBP
Cancer
2005/0130227


MG20
Cancer
2005/0153352


KLF6
Cancer
2005/0181374


ARTS1
Cancer
2005/0266443


Dock 3
Cancer
2006/0041111


Annexin 8
Cancer
2006/0052320


MH15
Cancer
2006/0068411


DELTA-N p73
Cancer
2006/0088825


RapR6
Cancer
2006/099676


StarD10
Cancer
2006/0148032


Ciz1
Cancer
2006/0155113


HLJ1
Cancer
2006/0194235


RapR7
Cancer
2006/0240021


A34
Cancer
2006/0292154


Sef
Cancer
2006/0293240


Killin
Cancer
2007/0072218


SGA-1M
Cancer
2007/0128593


TGFβ Type II receptor
Cancer
2002/0064786


GCA-associated genes
Giant cell arteritis
6,743,903


PRV-1
Polycythemia vera
6,686,153


SEQ ID NOS: 2, 4 of the U.S. Pat. No.
Ischemia
5,948,637


5,948,637, incorporated by reference


herein


Vezf1
Vascular disorders
2002/0023277


MLP
Dilatative cardiomyopathy
2002/0042057


VEGI
Pathological angiogenesis
2002/0111325


PRO256
Cardiovascular disorders
2002/0123091


AOP2
Atherosclerosis
2002/0142417


Remodelin
Arterial restenosis, fibrosis
2002/0161211


Phosphodiesterase 4D
Stroke
2003/0054531


Prostaglandin receptor subtype EP3
Peripheral arterial
2003/0157599



occlusive disease


CARP
Heart disorders
2004/0014706


HOP
Congenital heart disease
2004/0029158


SEQ ID NOS: 1-4 of the U.S. patent
Apoplexy
2004/0087784


application publication


2004/0087784, incorporated by


reference herein


PLTP
Atherosclerosis, vascular
2006/0252787



disease,



hypercholesterolemia,



Tangier's disease, familial



HDL deficiency disease


SEQ ID NOS: 1, 3-8, 15, 16 of the
Thrombosis
2007/0160996


U.S. patent application publication


2007/0160996, incorporated by


reference herein


UCP-2
Stroke
2002/0172958


FLJ11011
Fanconi's Anemia
2006/0070134


Codanin-1
Anemia
2006/0154331


SEQ ID NOS: 1, 6, 8 of the U.S.
Insulin-dependent diabetes
5,763,591


Pat. No. 5,763,591, incorporated by
mellitus


reference herein


Resistin
Type II diabetes
2002/0161210


Archipelin
Diabetes
2003/0202976


SEQ ID NOS: 2, 7, 16, 27 of the U.S.
Diabetes, hyperlipidemia
2004/0053397


patent application publication


2004/0053397, incorporated by


reference herein


Neuronatin
Metabolic disorders
2004/0259777


Ncb5or
Diabetes
2005/0031605


7B2
Endocrine disorders
2005/0086709


PTHrP, PEX
Metabolic bone diseases
2005/0113303


KChIPl
Type II diabetes
2005/0196784


SLIT-3
Type II diabetes
2006/0141462


CX3CR1
Type II diabetes
2006/0160076


SMAP-2
Diabetes
2006/0210974


SEQ ID NOS: 2, 8, 12, 16, 22, 26,
Type II diabetes
2006/0228706


28, 32 of the U.S. patent application


publication 2006/0228706,


incorporated by reference herein


IC-RFX
Diabetes
2006/0264611


E2IG4
Diabetes, insulin
2007/0036787



resistance, obesity


SEQ ID NOS: 2, 8, 10, 14, 18, 24,
Diabetes
2007/0122802


26, 30, 34, 38, 44, 50, 54, 60, 62, 68,


74, 80, 86, 92, 98, 104, 110 of the


U.S. patent application publication


2007/0122802, incorporated by


reference herein


UCP2
Body weight disorders
2002/0127600


Ob receptor
Body weight disorders
2002/0182676


Ob
Bodyweight disorders
2004/0214214


Dp1
Neurodegenerative
2001/0021771



disorders


NRG-1
Schizophrenia
2002/0045577


Synapsin III
Schizophrenia
2002/0064811


NRG1AG1
Schizophrenia
2002/0094954


AL-2
Neuronal disorders
2002/0142444


Proline dehydrogenase
Bipolar disorder, major
2002/0193581



depressive disorder,



schizophrenia, obsessive



compulsive disorder


MNR2
Chronic neurodegenerative
2002/0197678



disease


ATM
Ataxia-telangiectasia
2004/0029198


Ho-1
Dementing diseases
2004/0033563


CON202
Schizophrenia
2004/0091928


Ataxin-1
Neurodegenerative
2004/0177388



disorders


NR3B
Motor neuron disorders
2005/0153287


NIPA-1
Hereditary spastic
2005/0164228



paraplegia


DEPP, adrenomedullin, csdA
Schizophrenia
2005/0227233


Inf-20
Neurodegenerative
2006/0079675



diseases


EOPA
Brain development and
2007/0031830



degeneration disorders


SERT
Autism
2007/0037194


FRP-1
Glaucoma
2002/0049177


Serum amyloid A
Glaucoma
2005/0153927


BMP2
Osteoporosis
2002/0072066


BMPR1A
Juvenile polyposis
2003/0072758


ACLP
Gastroschisis
2003/0084464


Resistin-like molecule β
Familial adenomatous
2003/0138826



polyposis, diabetes, insulin



resistance, colon cancer,



inflammatory bowel



disorder


Dlg5
Inflammatory bowel
2006/0100132



disease


SEQ ID NOS: 1-82 of the U.S. patent
Osteoarthritis
2002/0119452


application publication


2002/0119452, incorporated by


reference herein


TRANCE
Immune system disorders
2003/0185820


Matrilin-3
Osteoarthritis
2003/0203380


Synoviolin
Rheumatoid arthritis
2004/0152871


SEQ ID NOS: 9, 35 of the U.S.
Osteoarthritis
2007/0028314


patent application publication


2007/0028314, incorporated by


reference herein


HIV LTR
HIV infection
5,627,023


SHIVA
HIV infection
2004/0197770


EBI 1, EBI 2, EBI 3
Epstein Barr virus infection
2002/0040133


NM23 family
Skin/intestinal disorders
2002/0034741


SEQ ID NO: 1 of the U.S. patent
Psoriasis
2002/0169127


application publication


2002/0169127, incorporated by


reference herein


Eps8
Skin disorders, wound
2003/0180302



healing


Beta-10
Thyroid gland pathology
2002/0015981


SEQ ID NO: 2 of the U.S. patent
Thyroid conditions
2003/0207403


application publication


2003/0207403, incorporated by


reference herein


SEQ ID NO: 3 of the U.S. patent
Thyroid disorders
2007/0020275


application publication


2007/0020275, incorporated by


reference herein


Hair follicle growth factor
Alopecia
2003/0036174


Corneodesmosin
Alopecia
2003/0211065


GCR9
Asthma, lymphoma,
2003/0166150



leukemia


SEQ ID NO: 1-71 of the U.S. patent
Asthma
2004/0002084


application publication


2004/0002084, incorporated by


reference herein


Bg
Chediak-Higashi syndrome
2002/0115144


SEQ ID NOS: 1-16 of the U.S. patent
Endometriosis
2002/0127555


application publication


2002/0127555, incorporated by


reference herein


FGF23
Hypophosphatemic
2005/0156014



disorders


BBSR
Bardet-Biedl syndrome
2003/0152963


MIC-1
Fetal abnormalities, cancer,
2004/0053325



inflammatory disorders,



miscarriage, premature



birth


MIA-2
Liver damage
2004/0076965


IL-17B
Cartilage degenerative
2004/0171109



disorders


Formylglycine generating enzyme
Multiple sulfatase
2004/0229250



deficiency


LPLA2
Pulmonary alveolar
2006/0008455



proteinosis


CXCL1O
Respiratory illnesses
2006/0040329


SEQ ID NOS: 1, 2 of the U.S. patent
Nephropathy
2006/0140945


application publication


2006/0140945, incorporated by


reference herein


HFE2A
Iron metabolism disease
2007/0166711









Once a gene with an expression pattern that is modulated during a disease or disorder is identified, the promoter of the gene may be used in the gene switch of the invention. The sequence of many genes, including the promoter region, is known in the art and available in public databases, e.g., GenBank. Thus, once an appropriate gene is identified, the promoter sequence can be readily identified and obtained. Another aspect of the present invention is directed towards identifying suitable genes whose promoter can be isolated and placed into a gene switch. The identity of the gene, therefore, may not be critical to specific embodiments of the present invention, provided the promoter can be isolated and used in subsequent settings or environments. The current invention thus includes the use of promoters from genes that are yet to be identified. Once suitable genes are identified, it can be a matter of routine skill or experimentation to determine the genetic sequences needed for promoter function. Indeed, several commercial protocols exist to aid in the determination of the promoter region of genes of interest. By way of example, Ding et al. recently elucidated the promoter sequence of the novel Sprouty4 gene (Am. J. Physiol. Lung Cell. Mol. Physiol. 287: L52 (2004), which is incorporated by reference) by progressively deleting the 5′-flanking sequence of the human Sprouty4 gene. Briefly, once the transcription initiation site was determined, PCR fragments were generated using common PCR primers to clone segments of the 5′-flanking segment in a unidirectional manner. The generated segments were cloned into a luciferase reporter vector and luciferase activity was measured to determine the promoter region of the human Sprouty4 gene.
Another example of a protocol for acquiring and validating gene promoters includes the following steps: (1) acquire diseased and non-diseased cell/tissue samples of similar/same tissue type; (2) isolate total RNA or mRNA from the samples; (3) perform differential microarray analysis of diseased and non-diseased RNA; (4) identify candidate disease-specific transcripts; (5) identify genomic sequences associated with the disease-specific transcripts; (6) acquire or synthesize DNA sequence upstream and downstream of the predicted transcription start site of the disease-specific transcript; (7) design and produce promoter reporter vectors using different lengths of DNA from step 6; and (8) test promoter reporter vectors in diseased and non-diseased cells/tissues, as well as in unrelated cells/tissues.
The source of the promoter that is inserted into the gene switch can be natural or synthetic, and the source of the promoter should not limit the scope of the invention described herein. In other words, the promoter may be directly cloned from cells, or the promoter may have been previously cloned from a different source, or the promoter may have been synthesized.
The gene switch may be any gene switch that regulates gene expression by addition or removal of a specific ligand. In one embodiment, the gene switch is one in which the level of gene expression is dependent on the level of ligand that is present. Examples of ligand-dependent transcription factors that may be used in the gene switches of the invention include, without limitation, members of the nuclear receptor superfamily activated by their respective ligands (e.g., glucocorticoid, estrogen, progestin, retinoid, ecdysone, and analogs and mimetics thereof) and rTTA activated by tetracycline. In one aspect of the invention, the gene switch is an EcR-based gene switch. Examples of such systems include, without limitation, the systems described in U.S. Pat. Nos. 6,258,603, 7,045,315, U.S. Published Patent Application Nos. 2006/0014711, 2007/0161086, and International Published Application No. WO 01/70816. Examples of chimeric ecdysone receptor systems are described in U.S. Pat. No. 7,091,038, U.S. Published Patent Application Nos. 2002/0110861, 2004/0033600, 2004/0096942, 2005/0266457, and 2006/0100416, and International Published Application Nos. WO 01/70816, WO 02/066612, WO 02/066613, WO 02/066614, WO 02/066615, WO 02/29075, and WO 2005/108617, each of which is incorporated by reference in its entirety. An example of a non-steroidal ecdysone agonist-regulated system is the RheoSwitch® Mammalian Inducible Expression System (New England Biolabs, Ipswich, Mass.).
In one embodiment, the gene switch comprises a single transcription factor sequence encoding a ligand-dependent transcription factor under the control of a diagnostic switch promoter. The transcription factor sequence may encode a ligand-dependent transcription factor that is a naturally occurring or an artificial transcription factor. An artificial transcription factor is one in which the natural sequence of the transcription factor has been altered, e.g., by mutation of the sequence or by the combining of domains from different transcription factors. In one embodiment, the transcription factor comprises a Group H nuclear receptor LBD. In one embodiment, the Group H nuclear receptor LBD is from an EcR, a ubiquitous receptor, an orphan receptor 1, a NER-1, a steroid hormone nuclear receptor 1, a retinoid X receptor interacting protein-15, a liver X receptor β, a steroid hormone receptor like protein, a liver X receptor, a liver X receptor α, a famesoid X receptor, a receptor interacting protein 14, or a farnesol receptor. In another embodiment, the Group H nuclear receptor LBD is from an ecdysone receptor.
The EcR and the other Group H nuclear receptors are members of the nuclear receptor superfamily wherein all members are generally characterized by the presence of an amino-terminal transactivation domain (TD), a DNA binding domain (DBD), and a LBD separated from the DBD by a hinge region. As used herein, the term “DNA binding domain” comprises a minimal polypeptide sequence of a DNA binding protein, up to the entire length of a DNA binding protein, so long as the DNA binding domain functions to associate with a particular response element. Members of the nuclear receptor superfamily are also characterized by the presence of four or five domains: A/B, C, D, E, and in some members F (see U.S. Pat. No. 4,981,784 and Evans, Science 240:889 (1988)). The “A/B” domain corresponds to the transactivation domain, “C” corresponds to the DNA binding domain, “D” corresponds to the hinge region, and “E” corresponds to the ligand binding domain. Some members of the family may also have another transactivation domain on the carboxy-terminal side of the LBD corresponding to “F”.
The DBD is characterized by the presence of two cysteine zinc fingers between which are two amino acid motifs, the P-box and the D-box, which confer specificity for response elements. These domains may be either native, modified, or chimeras of different domains of heterologous receptor proteins. The EcR, like a subset of the nuclear receptor family, also possesses less well-defined regions responsible for heterodimerization properties. Because the domains of nuclear receptors are modular in nature, the LBD, DBD, and TD may be interchanged.
In another embodiment, the transcription factor comprises a TD, a DBD that recognizes a response element associated with the reporter gene whose expression is to be modulated; and a Group H nuclear receptor LBD. In certain embodiments, the Group H nuclear receptor LBD comprises a substitution mutation.
In another embodiment, the gene switch comprises a first transcription factor sequence under the control of a first diagnostic switch promoter and a second transcription factor sequence under the control of a second diagnostic switch promoter, wherein the proteins encoded by said first transcription factor sequence and said second transcription factor sequence interact to form a protein complex which functions as a ligand-dependent transcription factor, i.e., a “dual switch”- or “two-hybrid”-based gene switch. The first and second diagnostic switch promoters may be the same or different. In this embodiment, the presence of two different diagnostic switch promoters in the gene switch that are required for reporter gene expression enhances the specificity of the diagnostic method (see FIG. 3). FIG. 3 also demonstrates the ability to modify the diagnostic gene switch to detect any disease or disorder simply by inserting the appropriate diagnostic switch promoters.
In a further embodiment, the first transcription factor sequence is under the control of a diagnostic switch promoter (e.g., P2 or P3 in FIG. 1) and the second transcription factor sequence is under the control of a constitutive promoter (e.g., P1 in FIG. 1). In this embodiment, one portion of the ligand-dependent transcription factor will be constitutively present while the second portion will only be synthesized if the subject has the disease or disorder.
In another embodiment, the first transcription factor sequence is under the control of a first diagnostic switch promoter (e.g., P1 in FIG. 2) and two or more different second transcription factor sequences are under the control of different diagnostic switch promoters (e.g., P2 and P3 in FIG. 2). In this embodiment, each of the second transcription factor sequences may have a different DBD that recognizes a different inducible promoter sequence (e.g., DBD-A binds to inducible promoter A and DBD-B binds to inducible promoter B). Each of the inducible promoters may be operably linked to a different reporter gene that produces a unique signal. In this manner, multiple diagnoses may be made simultaneously or a differential diagnosis between two or more possible diseases may be made.
In one embodiment, the first transcription factor sequence encodes a polypeptide comprising a TD, a DBD that recognizes a response element associated with the reporter gene whose expression is to be modulated; and a Group H nuclear receptor LBD, and the second transcription factor sequence encodes a transcription factor comprising a nuclear receptor LBD selected from the group consisting of a vertebrate RXR LBD, an invertebrate RXR LBD, an ultraspiracle protein LBD, and a chimeric LBD comprising two polypeptide fragments, wherein the first polypeptide fragment is from a vertebrate RXR LBD, an invertebrate RXR LBD, or an ultraspiracle protein LBD, and the second polypeptide fragment is from a different vertebrate RXR LBD, invertebrate RXR LBD, or ultraspiracle protein LBD.
In another embodiment, the gene switch comprises a first transcription factor sequence encoding a first polypeptide comprising a nuclear receptor LBD and a DBD that recognizes a response element associated with the reporter gene whose expression is to be modulated, and a second transcription factor sequence encoding a second polypeptide comprising a TD and a nuclear receptor LBD, wherein one of the nuclear receptor LBDs is a Group H nuclear receptor LBD. In a preferred embodiment, the first polypeptide is substantially free of a TD and the second polypeptide is substantially free of a DBD. For purposes of the invention, “substantially free” means that the protein in question does not contain a sufficient sequence of the domain in question to provide activation or binding activity.
In another aspect of the invention, the first transcription factor sequence encodes a protein comprising a heterodimer partner and a TD and the second transcription factor sequence encodes a protein comprising a DBD and a LBD.
When only one nuclear receptor LBD is a Group H LBD, the other nuclear receptor LBD may be from any other nuclear receptor that forms a dimer with the Group H LBD. For example, when the Group H nuclear receptor LBD is an EcR LBD, the other nuclear receptor LBD “partner” may be from an EcR, a vertebrate RXR, an invertebrate RXR, an ultraspiracle protein (USP), or a chimeric nuclear receptor comprising at least two different nuclear receptor LBD polypeptide fragments selected from the group consisting of a vertebrate RXR, an invertebrate RXR, and a USP (see WO 01/70816 A2, International Patent Application No. PCT/US02/05235 and US 2004/0096942 A1, incorporated herein by reference in their entirety). The “partner” nuclear receptor ligand binding domain may further comprise a truncation mutation, a deletion mutation, a substitution mutation, or another modification.
In one embodiment, the vertebrate RXR LBD is from a human Homo sapiens, mouse Mus musculus, rat Rattus norvegicus, chicken Gallus gallus, pig Sus scrofa domestica, frog Xenopus laevis, zebrafish Danio rerio, tunicate Polyandrocarpa misakiensis, or jellyfish Tripedalia cysophora RXR.
In one embodiment, the invertebrate RXR ligand binding domain is from a locust Locusta migratoria ultraspiracle polypeptide (“LmUSP”), an ixodid tick Amblyomma americanum RXR homolog 1 (“AmaRXR1”), an ixodid tick Amblyomma americanum RXR homolog 2 (“AmaRXR2”), a fiddler crab Celuca pugilator RXR homolog (“CpRXR”), a beetle Tenebrio molitor RXR homolog (“TmRXR”), a honeybee Apis mellifera RXR homolog (“AmRXR”), an aphid Myzus persicae RXR homolog (“MpRXR”), or a non-Dipteran/non-Lepidopteran RXR homolog.
In one embodiment, the chimeric RXR LBD comprises at least two polypeptide fragments selected from the group consisting of a vertebrate species RXR polypeptide fragment, an invertebrate species RXR polypeptide fragment, and a non-Dipteran/non-Lepidopteran invertebrate species RXR homolog polypeptide fragment. A chimeric RXR ligand binding domain for use in the present invention may comprise at least two different species RXR polypeptide fragments, or when the species is the same, the two or more polypeptide fragments may be from two or more different isoforms of the species RXR polypeptide fragment.
In one embodiment, the chimeric RXR ligand binding domain comprises at least one vertebrate species RXR polypeptide fragment and one invertebrate species RXR polypeptide fragment.
In another embodiment, the chimeric RXR ligand binding domain comprises at least one vertebrate species RXR polypeptide fragment and one non-Dipteran/non-Lepidopteran invertebrate species RXR homolog polypeptide fragment.
The ligand, when combined with the LBD of the nuclear receptor(s), which in turn are bound to the response element linked to the reporter gene, provides external temporal regulation of expression of the reporter gene. The binding mechanism or the order in which the various components of this invention bind to each other, that is, for example, ligand to LBD, DBD to response element, TD to promoter, etc., is not critical.
In a specific example, binding of the ligand to the LBD of a Group H nuclear receptor and its nuclear receptor LBD partner enables expression of the reporter gene. This mechanism does not exclude the potential for ligand binding to the Group H nuclear receptor (GHNR) or its partner, and the resulting formation of active homodimer complexes (e.g. GHNR+GHNR or partner+partner). Preferably, one or more of the receptor domains is varied producing a hybrid gene switch. Typically, one or more of the three domains, DBD, LBD, and TD, may be chosen from a source different than the source of the other domains so that the hybrid genes and the resulting hybrid proteins are optimized in the chosen host cell or organism for transactivating activity, complementary binding of the ligand, and recognition of a specific response element. In addition, the response element itself can be modified or substituted with response elements for other DNA binding protein domains such as the GAL-4 protein from yeast (see Sadowski et al., Nature 335:563 (1988)) or LexA protein from Escherichia coli (see Brent et al., Cell 43:729 (1985)), or synthetic response elements specific for targeted interactions with proteins designed, modified, and selected for such specific interactions (see, for example, Kim et al., Proc. Natl. Acad. Sci. USA, 94:3616 (1997)) to accommodate hybrid receptors.
The functional EcR complex may also include additional protein(s) such as immunophilins. Additional members of the nuclear receptor family of proteins, known as transcriptional factors (such as DHR38 or betaFTZ-1), may also be ligand dependent or independent partners for EcR, USP, and/or RXR. Additionally, other cofactors may be required such as proteins generally known as coactivators (also termed adapters or mediators). These proteins do not bind sequence-specifically to DNA and are not involved in basal transcription. They may exert their effect on transcription activation through various mechanisms, including stimulation of DNA-binding of activators, by affecting chromatin structure, or by mediating activator-initiation complex interactions. Examples of such coactivators include RIP140, TIF1, RAP46/Bag-1, ARA70, SRC -1/NCoA-1, TIF2/GRIP/NCoA-2, ACTR/AIB1/RAC3/pCIP as well as the promiscuous coactivator C response element B binding protein, CBP/p300 (for review see Glass et al., Curr. Opin. Cell Biol. 9:222 (1997)). Also, protein cofactors generally known as corepressors (also known as repressors, silencers, or silencing mediators) may be required to effectively inhibit transcriptional activation in the absence of ligand. These corepressors may interact with the unliganded EcR to silence the activity at the response element. Current evidence suggests that the binding of ligand changes the conformation of the receptor, which results in release of the corepressor and recruitment of the above described coactivators, thereby abolishing their silencing activity. Examples of corepressors include N-CoR and SMRT (for review, see Horwitz et al., Mol Endocrinol. 10:1167 (1996)). These cofactors may either be endogenous within the cell or organism, or may be added exogenously as transgenes to be expressed in either a regulated or unregulated fashion.
The reporter gene may be any gene that encodes a detectable protein. The protein may be secreted or non-secreted. In one embodiment, the protein is one that can be assayed using various standard assay methods, e.g., immunoassays (such as those immunofluorescent antibodies), colorimetric assays, fluorescent assays, or luminescent assays. Examples of suitable reporter genes include, without limitation, luciferase, green fluorescent protein, β-galactosidase, β-glucuronidase, thymidine kinase, and chloramphenicol acetyltransferase.
The reporter gene is operably linked to a promoter comprising at least one response element that is recognized by the DBD of the ligand-dependent transcription factor encoded by the gene switch. In one embodiment, the promoter comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more copies of the response element. Promoters comprising the desired response elements may be naturally occurring promoters or artificial promoters created using techniques that are well known in the art, e.g., one or more response elements operably linked to a minimal promoter.
To introduce the polynucleotides into the cells, a vector can be used. The vector may be, for example, a plasmid vector or a single- or double-stranded RNA or DNA viral vector. Such vectors may be introduced into cells by well-known techniques for introducing DNA and RNA into cells. Viral vectors may be replication competent or replication defective. In the latter case, viral propagation generally will occur only in complementing host cells. As used herein, the term “host cell” or “host” is used to mean a cell of the present invention that is harboring one or more polynucleotides of the invention.
Thus, at a minimum, the vectors must include the polynucleotides of the invention. Other components of the vector may include, but are not limited to, selectable markers, chromatin modification domains, additional promoters driving expression of other polypeptides that may also be present on the vector (e.g., a lethal polypeptide), genomic integration sites, recombination sites, and molecular insertion pivots. The vectors may comprise any number of these additional elements, either within or not within the polynucleotides, such that the vector can be tailored to the specific goals of the diagnostic methods desired.
In one embodiment of the present invention, the vectors that are introduced into the cells further comprise a “selectable marker gene” which, when expressed, indicates that the diagnostic gene switch construct of the present invention has been integrated into the genome of the host cell. In this manner, the selector gene can be a positive marker for the genome integration. While not critical to the methods of the present invention, the presence of a selectable marker gene allows the practitioner to select for a population of live cells where the vector construct has been integrated into the genome of the cells. Thus, certain embodiments of the present invention comprise selecting cells where the vector has successfully been integrated. As used herein, the term “select” or variations thereof, when used in conjunction with cells, is intended to mean standard, well-known methods for choosing cells with a specific genetic make-up or phenotype. Typical methods include, but are not limited to, culturing cells in the presence of antibiotics, such as G418, neomycin and ampicillin. Other examples of selectable marker genes include, but are not limited to, genes that confer resistance to dihydrofolate reductase, hygromycin, or mycophenolic acid. Other methods of selection include, but are not limited to, a selectable marker gene that allows for the use of thymidine kinase, hypoxanthine-guanine phosphoribosyltransferase or adenine phosphoribosyltransferase as selection agents. Cells comprising a vector construct comprising an antibiotic resistance gene or genes would then be capable of tolerating the antibiotic in culture. Likewise, cells not comprising a vector construct comprising an antibiotic resistance gene or genes would not be capable of tolerating the antibiotic in culture.
As used herein, a “chromatin modification domain” (CMD) refers to nucleotide sequences that interact with a variety of proteins associated with maintaining and/or altering chromatin structure, such as, but not limited to, DNA insulators. See Ciavatta et al., Proc. Nat'l Acad Sci. U.S.A., 103:9958 (2006), which is incorporated by reference herein. Examples of CMDs include, but are not limited to, the chicken β-globulin insulator and the chicken hypersensitive site 4 (cHS4). The use of different CMD sequences between one or more gene programs (i.e., a promoter, coding sequence, and 3′ regulatory region), for example, can facilitate the use of the differential CMD DNA sequences as “mini homology arms” in combination with various microorganism or in vitro recombineering technologies to “swap” gene programs between existing multigenic and monogenic shuttle vectors. Other examples of chromatin modification domains are known in the art or can be readily identified.
Particular vectors for use with the present invention are expression vectors that code for proteins or portions thereof. Generally, such vectors comprise cis-acting control regions effective for expression in a host operatively linked to the polynucleotide to be expressed. Appropriate trans-acting factors are supplied by the host, supplied by a complementing vector or supplied by the vector itself upon introduction into the host.
A great variety of expression vectors can be used to express proteins. Such vectors include chromosomal, episomal and virus-derived vectors, e.g., vectors derived from bacterial plasmids, from bacteriophage, from yeast episomes, from yeast chromosomal elements, from viruses such as adeno-associated viruses, lentiviruses, baculoviruses, papova viruses, such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids. All may be used for expression in accordance with this aspect of the present invention. Generally, any vector suitable to maintain, propagate or express polynucleotides or proteins in a host may be used for expression in this regard.
The DNA sequence in the expression vector is operatively linked to appropriate expression control sequence(s) including, for instance, a promoter to direct mRNA transcription. Representatives of additional promoters include, but are not limited to, constitutive promoters and tissue specific or inducible promoters. Examples of constitutive eukaryotic promoters include, but are not limited to, the promoter of the mouse metallothionein I gene (Hamer et al., J. Mol. Appl. Gen. 1:273 (1982)); the TK promoter of Herpes virus (McKnight, Cell 31:355 (1982)); the SV40 early promoter (Benoist et al., Nature 290:304 (1981)); and the vaccinia virus promoter. All of the above listed references are incorporated by reference herein. Additional examples of the promoters that could be used to drive expression of a protein include, but are not limited to, tissue-specific promoters and other endogenous promoters for specific proteins, such as the albumin promoter (hepatocytes), a proinsulin promoter (pancreatic beta cells) and the like. In general, expression constructs will contain sites for transcription, initiation and termination and, in the transcribed region, a ribosome binding site for translation. The coding portion of the mature transcripts expressed by the constructs may include a translation initiating AUG at the beginning and a termination codon (UAA, UGA or UAG) appropriately positioned at the end of the polypeptide to be translated.
In addition, the constructs may contain control regions that regulate, as well as engender expression. Generally, such regions will operate by controlling transcription, such as repressor binding sites and enhancers, among others.
Examples of eukaryotic vectors include, but are not limited to, pW-LNEO, pSV2CAT, pOG44, pXT1 and pSG available from Stratagene; pSVK3, pBPV, pMSG and pSVL available from Amersham Pharmacia Biotech; and pCMVDsRed2-express, pIRES2-DsRed2, pDsRed2-Mito, pCMV-EGFP available from Clontech. Many other vectors are well-known and commercially available.
Particularly useful vectors, which comprise molecular insertion pivots for rapid insertion and removal of elements of gene programs, are described in United States Published Patent Application No. 2004/0185556, U.S. patent application Ser. No. 11/233,246 and International Published Application Nos. WO 2005/040336 and WO 2005/116231, all of which are incorporated by reference. An example of such vectors is the UltraVectorTM Production System (Intrexon Corp., Blacksburg, Va.), as described in WO 2007/038276, incorporated herein by reference. As used herein, a “gene program” is a combination of genetic elements comprising a promoter (P), an expression sequence (E) and a 3′ regulatory sequence (3), such that “PE3” is a gene program. The elements within the gene program can be easily swapped between molecular pivots that flank each of the elements of the gene program. A molecular pivot, as used herein, is defined as a polynucleotide comprising at least two non-variable rare or uncommon restriction sites arranged in a linear fashion. In one embodiment, the molecular pivot comprises at least three non-variable rare or uncommon restriction sites arranged in a linear fashion. Typically any one molecular pivot would not include a rare or uncommon restriction site of any other molecular pivot within the same gene program. Cognate sequences of greater than 6 nucleotides upon which a given restriction enzyme acts are referred to as “rare” restriction sites. There are, however, restriction sites of 6 bp that occur more infrequently than would be statistically predicted, and these sites and the endonucleases that cleave them are referred to as “uncommon” restriction sites. Examples of either rare or uncommon restriction enzymes include, but are not limited to, AsiS I, Pac I, Sbf I, Fse I, Asc I, Mlu I, SnaB I, Not I, Sal I, Swa I, Rsr II, BSiW I, Sfo I, Sgr AI, AflIII, Pvu I, Ngo MIV, Ase I, Flp I, Pme I, Sda I, Sgf I, Srf I, and Sse8781 I.
The vector may also comprise restriction sites for a second class of restriction enzymes called homing endonuclease (HE) enzymes. HE enzymes have large, asymmetric restriction sites (12-40 base pairs), and their restriction sites are infrequent in nature. For example, the HE known as I-SceI has an 18 bp restriction site (5′TAGGGATAACAGGGTAAT3′ (SEQ ID NO:4)), predicted to occur only once in every 7×1010 base pairs of random sequence. This rate of occurrence is equivalent to only one site in a genome that is 20 times the size of a mammalian genome. The rare nature of HE sites greatly increases the likelihood that a genetic engineer can cut a gene program without disrupting the integrity of the gene program if HE sites were included in appropriate locations in a cloning vector plasmid.
Selection of appropriate vectors and promoters for expression in a host cell is a well-known procedure, and the requisite techniques for vector construction and introduction into the host, as well as its expression in the host are routine skills in the art.
The introduction of the polynucleotides into the cells can be a transient transfection, stable transfection, or can be a locus-specific insertion of the vector. Transient and stable transfection of the vectors into the host cell can be effected by calcium phosphate transfection, DEAE-dextran mediated transfection, cationic lipid-mediated transfection, electroporation, transduction, infection, or other methods. Such methods are described in many standard laboratory manuals, such as Davis el al., Basic Methods in Molecular Biology (1986); Keown et al., 1990, Methods Enzymol. 185: 527-37; Sambrook et al., 2001, Molecular Cloning, A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, N.Y., which are hereby incorporated by reference. These stable transfection methods result in random insertion of the vector into the genome of the cell. Further, the copy number and orientation of the vectors are also, generally speaking, random.
In one embodiment of the invention, the vector is inserted into a bio-neutral site in the genome. A bio-neutral site is a site in the genome where insertion of the polynucleotides interferes very little, if any, with the normal function of the cell. Bio-neutral sites may be analyzed using available bioinformatics. Many bio-neutral sites are known in the art, e.g., the ROSA-equivalent locus. Other bio-neutral sites may be identified using routine techniques well known in the art. Characterization of the genomic insertion site(s) is performed using methods known in the art. To control the location, copy number and/or orientation of the polynucleotides when introducing the vector into the cells, methods of locus-specific insertion may be used. Methods of locus-specific insertion are well-known in the art and include, but are not limited to, homologous recombination and recombinase-mediated genome insertion. Of course, if locus-specific insertion methods are to be used in the methods of the present invention, the vectors may comprise elements that aid in this locus-specific insertion, such as, but not limited to, homologous recombination. For example, the vectors may comprise one, two, three, four or more genomic integration sites (GISs). As used herein, a “genomic integration site” is defined as a portion of the vector sequence which nucleotide sequence is identical or nearly identical to portions of the genome within the cells that allows for insertion of the vector in the genome. In particular, the vector may comprise two genomic insertion sites that flank at least the polynucleotides. Of course, the GISs may flank additional elements, or even all elements present on the vector.
In another embodiment, locus-specific insertion may be carried out by recombinase-site specific gene insertion. Briefly, bacterial recombinase enzymes, such as, but not limited to, PhiC31 integrase can act on “pseudo” recombination sites within the human genome. These pseudo recombination sites can be targets for locus-specific insertion using the recombinases. Recombinase-site specific gene insertion is described in Thyagarajan et al., Mol. Cell Biol. 21:3926 (2001), which is hereby incorporated by reference. Other examples of recombinases and their respective sites that may be used for recombinase-site specific gene insertion include, but are not limited to, serine recombinases such as R4 and TP901-1 and recombinases described in WO 2006/083253, incorporated herein by reference.
In a further embodiment, the vector may comprise a chemo-resistance gene, e.g., the multidrug resistance gene mdr1, dihydrofolate reductase, or O6-alkylguanine-DNA alkyltransferase. The chemo-resistance gene may be under the control of a constitutive (e.g., CMV) or inducible (e.g., RheoSwitch®) promoter. In this embodiment, if it is desired to treat a disease diagnosed in a subject while maintaining the modified cells within the subject, a clinician may apply a chemotherapeutic agent to destroy diseased cells while the modified cells would be protected from the agent due to expression of a suitable chemo-resistance gene and may continue to be used for monitoring of the progression of the disease or effectiveness of the treatment. By placing the chemo-resistance gene under an inducible promoter, the unnecessary expression of the chemo-resistance gene can be avoided, yet it will still be available in case continued diagnosis is desired during treatment. If the modified cells themselves become diseased, they could still be destroyed by inducing expression of a lethal polypeptide as described below.
The methods of the invention are carried out by introducing the polynucleotides encoding the gene switch and the reporter gene into cells of a subject. Any method known for introducing a polynucleotide into a cell known in the art, such as those described above, can be used.
In an alternative embodiment, the polynucleotides encoding the gene switch and the reporter gene are introduced into non-autologous cells, e.g., cells that are allogeneic or xenogeneic to the subject.
When the polynucleotides are to be introduced into cells ex vivo, the cells may be obtained from a subject by any technique known in the art, including, but not limited to, biopsies, scrapings, and surgical tissue removal. The isolated cells may be cultured for a sufficient amount of time to allow the polynucleotides to be introduced into the cells, e.g., 2, 4, 6, 8, 10, 12, 18, 24, 36, 48, hours or more. Methods for culturing primary cells for short periods of time are well known in the art. For example, cells may be cultured in plates (e.g., in microwell plates) either attached or in suspension.
For ex vivo diagnosis methods, cells are isolated from a subject and cultured under conditions suitable for introducing the polynucleotides into the cells. Once the polynucleotides have been introduced into the cells, the cells are incubated for a sufficient period of time to allow the ligand-dependent transcription factor to be expressed, e.g., 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, or 24 hours or more. If expression of the ligand-dependent transcription factor is increased or decreased compared to control levels (i.e., if the subject has the disease or disorder and the promoters controlling expression of the transcription factor are activated or deactivated), the presence and/or level of the ligand-dependent transcription factor is detected by the addition of ligand, leading to expression of the reporter gene at a level corresponding to the level of the ligand-dependent transcription factor. The ligand may be added to the cells at any time before, during or after introduction of the polynucleotides into the cells. The optimal timing of ligand administration can be determined for each type of cell and disease or disorder using only routine techniques. In one embodiment, the ligand may be added, reporter gene expression determined, the ligand removed, and the process repeated one or more times to obtain multiple diagnostic measurements of the cells. In another embodiment, ligand is continuously present and reporter gene expression is measured periodically.
The first in vivo diagnostic embodiment of the invention (modification of isolated cells followed by reintroduction of the cells to the subject) may be used where the ex vive method using isolated cells is insufficient, e.g., where circulating factors are necessary for diagnostic switch promoter activity to occur. In this embodiment, cells are isolated from a subject and the polynucleotides are introduced into the cells in culture as described above. At some point after the introduction of the polynucleotides into the cells, the cells are introduced back into the subject. Reintroduction may be carried out by any method known in the art, e.g., intravenous infusion or direct injection into a tissue or cavity. In one embodiment, the presence of the polynucleotides in the cells is determined prior to introducing the cells back into the subject. In another embodiment, cells containing the polynucleotides are selected (e.g., based on the presence of a selectable marker in the polynucleotides) and only those cells containing the polynucleotides are reintroduced into the subject. After the cells are reintroduced to the subject, ligand is administered to the subject and reporter gene expression is assayed. The ligand may be administered by any suitable method, either systemically (e.g., orally, intravenously) or locally (e.g., intraperitoneally, intrathecally, intraventricularly, direct injection into the tissue or organ where the cells were reintroduced). The optimal timing of ligand administration can be determined for each type of cell and disease or disorder using only routine techniques. In one embodiment, the ligand may be administered, reporter gene expression determined, the ligand removed, and the process repeated one or more times to obtain multiple diagnostic measurements of the cells. In another embodiment, ligand is continuously administered and reporter gene expression is measured periodically. The detection of reporter gene expression after ligand is administered can occur in vivo or ex vivo. For example, if the reporter gene encodes a secreted protein that circulates in the blood, detection of the protein can occur in a blood sample removed from the patient. If the reporter gene encodes a protein that produces a luminescent or fluorescent signal, the signal may be detected in vive. In another embodiment, a sample of the modified cells can be removed and expression of the reporter gene detected ex vivo.
The second in vivo diagnostic embodiment of the invention involves direct in vivo introduction of the polynucleotides into the cells of the subject. The polynucleotides may be introduced into the subject systemically or locally (e.g., at the site of the suspected disease or disorder). Once the polynucleotides have been introduced to the subject, the ligand may be administered and reporter gene expression assayed. The ligand may be administered by any suitable method, either systemically (e.g., orally, intravenously) or locally (e.g., intraperitoneally, intrathecally, intraventricularly, direct injection into the tissue or organ where the suspected disease or disorder is occurring). The optimal timing of ligand administration can be determined for each type of cell and disease or disorder using only routine techniques. In one embodiment, the ligand may be added, reporter gene expression determined, the ligand removed, and the process repeated one or more times to obtain multiple diagnostic measurements of the cells containing the polynucleotides. In another embodiment, ligand is continuously administered and reporter gene expression is measured periodically. The detection of reporter gene expression after ligand is administered can occur in vivo or ex vivo. For example, if the reporter gene encodes a secreted protein that circulates in the blood, detection of the protein can occur in a blood sample removed from the patient. If the reporter gene encodes a protein that produces a luminescent or fluorescent signal, the signal may be detected in vivo. In another embodiment, a sample of the modified cells can be removed and expression of the reporter gene detected ex vivo.
When non-autologous cells are used in the diagnostic methods, the cells may be obtained from any source, e.g., other subjects, cell lines, or animals. The non-autologous cells may be any cells that are viable after transplantation, such as fibroblasts or stem cells (e.g., embryonic stem cells, hematopoietic stem cells). The non-autologous cells are isolated and the polynucleotides are introduced into the cells in culture as described above. At some point after the introduction of the polynucleotides into the cells, the cells are introduced into the subject. Introduction may be carried out by any method known in the art, e.g., intravenous infusion or direct injection into a tissue or cavity. In one embodiment, the presence of the polynucleotides in the cells is determined prior to introducing the cells back into the subject. In another embodiment, cells containing the polynucleotides are selected (e.g., based on the presence of a selectable marker in the polynucleotides) and only those cells containing the polynucleotides are introduced into the subject. In one embodiment, the non-autologous cells are surrounded by a barrier (e.g., encapsulated) prior to introduction into the subject. After the cells are introduced to the subject, ligand is administered to the subject and reporter gene expression is assayed. The ligand may be administered by any suitable method, either systemically (e.g., orally, intravenously) or locally (e.g., intraperitoneally, intrathecally, intraventricularly, direct injection into the tissue or organ where the cells were introduced). The optimal timing of ligand administration can be determined for each type of cell and disease or disorder using only routine techniques. In one embodiment, the ligand may be administered, reporter gene expression determined, the ligand removed, and the process repeated one or more times to obtain multiple diagnostic measurements of the cells. In another embodiment, ligand is continuously administered and reporter gene expression is measured periodically. The detection of reporter gene expression after ligand is administered can occur in vivo or ex vivo. For example, if the reporter gene encodes a secreted protein that circulates in the blood, detection of the protein can occur in a blood sample removed from the patient. If the reporter gene encodes a protein that produces a luminescent or fluorescent signal, the signal may be detected in vivo. In another embodiment, a sample of the modified cells can be removed and expression of the reporter gene detected ex vivo.
In all in vivo embodiments, the polynucleotides or vector comprising the polynucleotides may comprise a sequence encoding a lethal polypeptide that can be turned on to express a product that will kill a cell containing the polynucleotides or vector. Lethal polypeptide expression can be used to eliminate the modified cells from a subject, either because diagnostic tests are no longer needed or because of a problem with the modified cells (e.g., hyperproliferation or toxicity). A lethal polypeptide, as used herein, is a polypeptide that, when expressed, is lethal to the cell that expresses the polypeptide, either because the polypeptide itself is lethal or the polypeptide produces a compound that is lethal. As used herein, a lethal polypeptide includes polypeptides that induce cell death in any fashion, including but not limited to, necrosis, apoptosis and cytotoxicity. Examples of lethal polypeptides include, but are not limited to, apoptosis inducing tumor suppressor genes such as, but not limited to, p53, Rb and BRCA-1, toxins such as diphtheria toxin (DTA), shigella neurotoxin, botulism toxin, tetanus toxin, cholera toxin, CSE-V2 and other variants of scorpion protein toxins to name a few, suicide genes such as cytosine deaminase and thymidine kinase, and cytotoxic genes, e.g., tumor necrosis factor, interferon-alpha. The present invention is not limited by the identity of the lethal polypeptide, provided that the polypeptide is capable of being lethal to the cell in which it is expressed. If the modified cells are short-lived cells (e.g., cells with a limited lifespan (e.g., about 10 days or less, such as dendritic cells), it may not be necessary to include a lethal polypeptide in the polynucleotides or vector as the cells will be naturally removed over a short period of time.
Another aspect of the invention relates to methods of monitoring progression of a disease or disorder by administering to cells of the subject the diagnostic gene switches of the invention and measuring reporter gene expression to monitor progression of the disease or disorder. In one embodiment, the invention relates to methods of monitoring the progression of a disease or disorder in a subject, comprising:

    (a) introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) administering ligand to said modified cells; and
    (c) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates progression of said disease or disorder in said subject.
Progression may be indicated by increasing or decreasing reporter gene expression depending on whether the diagnostic switch promoters are responsive to factor(s) that increase or decrease during progression of the disease or disorder. These methods may be carried out using any of the variants of the diagnostic methods described above (i.e., ex vivo cells, modification of cells ex vivo followed by reintroduction of the cells in vivo, or in vivo). A disease or disorder is monitored by measuring reporter gene expression at least twice as an indication of the state of the disease or disorder and noting any change in the level of expression. In one embodiment, the monitoring can be carried out by exposing the cells to ligand continuously and measuring reporter gene expression intermittently. In another embodiment, the monitoring can be carried out by exposing cells to ligand intermittently and measuring reporter gene expression during each exposure.
One embodiment of the invention relates to methods of preparing modified cells for monitoring the progression of a disease or disorder in a subject, comprising introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells.
Another embodiment of the invention relates to methods of monitoring the progression of a disease or disorder in a subject, comprising:

    (a) administering ligand to modified cells of said subject; and
    (b) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates progression of said disease or disorder in said subject; and
wherein said modified cells of said subject comprise (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor.
In a further embodiment, the methods of monitoring progression of a disease or disorder are carried out using non-autologous cells, e.g., cells that are allogeneic or xenogeneic to the subject, and the modified non-autologous cells are introduced into the subject. In one embodiment, the non-autologous cells are surrounded by a barrier (e.g., encapsulated) prior to being introduced into the subject. One embodiment of the invention relates to methods of monitoring the progression of a disease or disorder in a subject, comprising:

    (a) introducing into non-autologous cells (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) introducing said modified cells into said subject;
    (c) administering ligand to said modified cells; and
    (d) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates progression of said disease or disorder in said subject.
A further aspect of the invention relates to methods of monitoring the effectiveness of a treatment for a disease or disorder in a subject, comprising administering to the subject a treatment and carrying out the diagnostic methods of the invention at least twice to determine if reporter gene expression is increasing, decreasing, or remaining the same. In one embodiment, the invention relates to methods of monitoring the effectiveness of a treatment for a disease or disorder in a subject, comprising:

    (a) administering said treatment to said subject;
    (b) introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (c) administering ligand to said modified cells; and
    (d) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates the effectiveness of said treatment.
A change in the level of expression of the reporter gene after the treatment is administered is an indication of the effectiveness of the treatment. A decrease in reporter gene expression indicates the treatment is effective if the diagnostic switch promoter(s) are responsive to factor(s) that are elevated in the disease or disorder. An increase in reporter gene expression indicates the treatment is effective if the diagnostic switch promoter(s) are responsive to factor(s) that are reduced in the disease or disorder. If reporter gene expression does not change after administration of the treatment, it may indicate that the treatment has halted the progression of the disease or disorder. These methods may be carried out using any of the variants of the diagnostic methods described above (i.e., ex vive cells, modification of cells ex vive followed by reintroduction of the cells in vivo, in vivo).
For the ex vive embodiment of the invention, cells may be isolated from the subject before treatment to determine baseline levels of reporter gene expression. After the treatment is administered to the subject, cells may be isolated from the subject at various intervals to determine reporter gene expression.
For the in vivo embodiments of the invention, modified cells or the polynucleotides can be introduced into a subject before, during, or after administration of the treatment. If the cells or polynucleotides are administered prior to the treatment, a baseline level of reporter gene expression can be obtained.
The measurement of reporter gene expression may be carried out ex vivo or in vivo. In one embodiment, the monitoring can be carried out by exposing the cells to ligand continuously and measuring reporter gene expression intermittently. In another embodiment, the monitoring can be carried out by exposing cells to ligand intermittently and measuring reporter gene expression during each exposure.
In one embodiment, one or both of the polynucleotides encoding a gene switch and a reporter gene may be part of a therapeutic vector that is being administered to a subject (e.g., a vector encoding a therapeutic protein or nucleic acid for gene therapy). In this embodiment, the therapeutic treatment and the diagnostic test for monitoring effectiveness of the treatment are administered together in one unit, ensuring that all cells that receive the treatment also receive the diagnostic gene switch.
One embodiment of the invention relates to methods of preparing modified cells for monitoring the effectiveness of a treatment for a disease or disorder in a subject, comprising introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells.
Another embodiment of the invention relates to methods of monitoring the effectiveness of a treatment for a disease or disorder in a subject, comprising:

    (a) administering said treatment to said subject;
    (b) administering ligand to modified cells of said subject; and
    (c) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates the effectiveness of said treatment; and
wherein said modified cells of said subject comprise (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor.
In a further embodiment, the methods of monitoring the effectiveness of a treatment for a disease or disorder are carried out using non-autologous cells, e.g., cells that are allogeneic or xenogeneic to the subject, and the modified non-autologous cells are introduced into the subject. In one embodiment, the non-autologous cells are surrounded by a barrier (e.g., encapsulated) prior to being introduced into the subject. In one embodiment the invention relates to methods of monitoring the effectiveness of a treatment for a disease or disorder in a subject, comprising:

    (a) introducing into non-autologous cells (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) introducing said modified cells into said subject;
    (c) administering ligand to said modified cells; and
    (d) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates the effectiveness of said treatment.
Another aspect of the invention relates to methods of monitoring the potential toxicity of an administered treatment for a disease or disorder in a subject. In one embodiment, the invention relates to methods of monitoring the potential toxicity of an administered treatment for a disease or disorder in a subject, comprising: administering said treatment to said subject;

    (a) introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by factors found in cells that are being exposed to toxic conditions, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) administering ligand to said modified cells; and
    (c) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates the toxicity of said treatment.
In one embodiment, this aspect involves polynucleotides in which the transcription factor sequence(s) are under the control of promoters that are regulated by factors found in cells that are being exposed to toxic conditions, e.g., cells that are stressed or dying. Examples include, without limitation, promoters responsive to apoptosis signals, necrosis signals, hypoxia, reactive oxygen species, DNA or chromatin modification, protein degradation, oxidative/reductive state, changes in pH, etc. Suitable stress promoters include those disclosed in U.S. Published Application No. 2003/0027127 (incorporated herein by reference) and include, without limitation, promoters from the following genes: CYP1A1, GST Ya, GADD45, GRP78, JUN, FOS, XHF, HSP70, MT IIA, GADD153, ALDH 1, HMO, CRE, XRE, NFrxBRE, RARE, ThRE, PPRE, TRE, ERE, and p53RE. Suitable apoptosis-responsive promoters include, without limitation, Fas/CD95, TRAMP, TNF RI, DR1, DR2, DR3, DR4, DR5, DR6, FADD, RIP, TNFα, Fas ligand, TRAILR1, TRAILR2, TRAILR3, Bcl-2, p53, BAX, BAD, Akt, CAD, PI3 kinase, PP1, and caspase proteins. Detection of an increase in reporter gene expression following administration of a treatment is an indication that the treatment is harmful to the cells. By making the gene switch responsive to stress or death signals, it can be used to monitor the effects of a treatment and detect toxic effects on the cellular level long before the subject exhibits overt symptoms of toxicity.
These methods may be carried out using any of the variants of the diagnostic methods described above (i.e., ex vivo cells, modification of cells ex vivo followed by reintroduction of the cells in vivo, in vivo).
For the ex vivo embodiment of the invention, cells may be isolated from the subject before treatment to determine baseline levels of reporter gene expression. After the treatment is administered to the subject, cells may be isolated from the subject at various intervals to determine reporter gene expression.
For the in vivo embodiments of the invention, modified cells or the polynucleotides can be introduced into a subject before, during, or after administration of the treatment. If the cells or polynuclcotides are administered prior to the treatment, a baseline level of reporter gene expression can be obtained.
The measurement of reporter gene expression may be carried out er vive or in vivo. In one embodiment, the monitoring can be carried out by exposing the cells to ligand continuously and measuring reporter gene expression intermittently. In another embodiment, the monitoring can be carried out by exposing cells to ligand intermittently and measuring reporter gene expression during each exposure.
One embodiment of the invention relates to methods of preparing modified cells for monitoring the potential toxicity of an administered treatment for a disease or disorder in a subject, comprising introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by factors found in cells that are being exposed to toxic conditions, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells.
Another embodiment of the invention relates to methods of monitoring the potential toxicity of an administered treatment for a disease or disorder in a subject, comprising:

    (a) administering said treatment to said subject;
    (b) administering ligand to modified cells of said subject; and
    (c) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates the toxicity of said treatment; and
wherein said modified cells of said subject comprise (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by factors found in cells that are being exposed to toxic conditions, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor.
In a further embodiment, the methods of monitoring the potential toxicity of an administered treatment for a disease or disorder are carried out using non-autologous cells, e.g., cells that are allogeneic or xenogeneic to the subject, and the modified non-autologous cells are introduced into the subject. In one embodiment, the non-autologous cells are surrounded by a barrier (e.g., encapsulated) prior to being introduced into the subject. In one embodiment, the invention relates to methods of monitoring the potential toxicity of an administered treatment for a disease or disorder in a subject, comprising:

    (a) introducing into non-autologous cells (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by factors found in cells that are being exposed to toxic conditions, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) introducing said modified cells into said subject;
    (c) administering ligand to said modified cells; and
    (d) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates the toxicity of said treatment.
In another embodiment of the invention, the polynucleotide comprises transcription factor sequence(s) that are under the control of promoters that are activated by the factor which is being administered as the treatment (e.g., gene therapy treatment with a therapeutic protein or nucleic acid). By making the gene switch responsive to the administered treatment, it can be used to monitor expression of the gene therapy treatment and detect undesirably high or low levels of the treatment long before the subject exhibits overt symptoms of overexpression or underexpression of the therapeutic factor. In one embodiment, the invention relates to methods of monitoring the level of a factor that is being administered to a subject for treatment for a disease or disorder, comprising: administering said treatment to said subject;

    (a) introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by said factor that is being administered for treatment, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) administering ligand to said modified cells; and
    (c) detecting reporter gene expression;


wherein the level of expression of said reporter gene indicates the level of the factor being administered for treatment.
These methods may be carried out using any of the variants of the diagnostic methods described above (i.e., ex vivo cells, modification of cells ex vivo followed by reintroduction of the cells in vivo, in vivo).
For the ex vivo embodiment of the invention, cells may be isolated from the subject before treatment to determine baseline levels of reporter gene expression. After the treatment is administered to the subject, cells may be isolated from the subject at various intervals to determine reporter gene expression.
For the in vivo embodiments of the invention, modified cells or the polynucleotides can be introduced into a subject before, during, or after administration of the treatment. If the cells or polynucleotides are administered prior to the treatment, a baseline level of reporter gene expression can be obtained.
The measurement of reporter gene expression may be carried out ex vivo or in vivo. In one embodiment, the monitoring can be carried out by exposing the cells to ligand continuously and measuring reporter gene expression intermittently. In another embodiment, the monitoring can be carried out by exposing cells to ligand intermittently and measuring reporter gene expression during each exposure.
One embodiment of the invention relates to methods of preparing modified cells for monitoring the level of a factor that is being administered to a subject for treatment for a disease or disorder, comprising introducing into cells of said subject (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by said factor that is being administered for treatment, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells.
Another embodiment of the invention relates to method of monitoring the level of a factor that is being administered to a subject for treatment for a disease or disorder, comprising:

    (a) administering said treatment to said subject;
    (b) administering ligand to modified cells of said subject; and
    (c) detecting reporter gene expression;


wherein the level of expression of said reporter gene indicates the level of the factor being administered for treatment; and
wherein said modified cells of said subject comprise (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by said factor that is being administered for treatment, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor.
In a further embodiment, the methods of monitoring the level of a factor that is being administered to a subject for treatment for a disease or disorder are carried out using non-autologous cells, e.g., cells that are allogeneic or xenogeneic to the subject, and the modified non-autologous cells are introduced into the subject. In one embodiment, the non-autologous cells are surrounded by a barrier (e.g., encapsulated) prior to being introduced into the subject. A method of monitoring the level of a factor that is being administered to a subject for a disease or disorder in a subject, comprising:

    (a) introducing into non-autologous cells (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by said factor that is being administered for treatment, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) introducing said modified cells into said subject;
    (c) administering ligand to said modified cells; and
    (d) detecting reporter gene expression;


wherein the level of expression of said reporter gene indicates the level of the factor being administered for treatment.
Another aspect of the invention relates to methods of detecting transplant rejection in a subject that has received an organ or tissue transplant, comprising:

    (a) introducing into cells of said organ or tissue transplant (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during transplant rejection, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) administering ligand to said modified cells; and
    (c) detecting reporter gene expression;


wherein expression of the reporter gene indicates that transplant rejection has been detected.
An additional embodiment of the invention relates to methods of monitoring the progression of transplant rejection in a subject that has received an organ or tissue transplant, comprising:

    (a) introducing into cells of said organ or tissue transplant (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during transplant rejection, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
    (b) administering ligand to said modified cells; and
    (c) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates progression of said transplant rejection in said subject.
The methods for detecting and monitoring transplant rejection in a transplant recipient can be used to monitor the viability of transplanted organs or tissues. The ability to detect the onset of transplant rejection will allow a medical practitioner to adjust treatment of the transplant patient accordingly, e.g., by adjusting the level of immunosuppression therapy. The sensitivity of the present methods may allow for earlier detection of rejection than is possible with the current method of taking periodic tissue biopsies to look for tissue damage. The earlier detection of the occurrence of rejection in a subject will allow for a more rapid response and avoidance of further damage to the transplanted organs or tissues. The methods may be used for any organ or tissue transplant, including, without limitation, heart, kidney, lung, liver, pancreas, small and large intestine, skin, cornea, bone marrow, bone, ligament, tendon, neural tissue, and stem cell transplants.
In the methods of the invention the gene switch comprises one or more diagnostic switch promoters that are activated during transplant rejection, i.e., rejection promoters. A rejection promoter is any promoter that is activated in a transplanted organ or tissue when the rejection process begins to occur. Examples of rejection promoters that are useful in the present invention include, without limitation, promoters from the genes listed in Table 4, along with the organs in which increased expression has been detected during rejection.








TABLE 4





Gene
Organ/Tissue







A Disintegrin And Metalloproteinase 17 (ADAM17)
Kidney


A Disintegrin And Metalloproteinase 19 (ADAM19)
Kidney


AGT
Kidney


Allograft Inflammatory Factor-1 (AIF-1)
Liver


Angiotensin II Type 1 Receptor (AGTR1)
Heart


APAF1
Intestine


β2-Defensin
Lung


Brain Natriuretic Peptide
Heart


C-Reactive Protein (CRP)
Liver


C3
Kidney


CCL1
Heart


CCL3
Heart


CCL4
Heart


CCL5
Heart


CCR5
Heart


CD3
Kidney


CD95
Liver


CD95 Ligand
Liver, Heart


CD103
Kidney


Cellular Mediator of Immune Response (MIR)
Heart


CFLAR
Heart


Chemokine (C—X—C motif) Ligand 9 (CXCL9)
Heart


Collagen Type IX α3
Kidney


Collagenase
Lung


Connective Tissue Growth Factor (CTGF)
Kidney


CX3CR1
Heart


CXCR3
Pancreas, Heart,



Kidney


Cyclooxygenase-2 (COX-2)
Kidney, Heart


Early Growth Response Gene-1 (EGR-1)
Lung, Heart


ENA 78
Heart


Eotaxin
Cornea


Epidermal Growth Factor Receptor (EGFR)
Kidney


EPST11
Intestine


Fas
Heart


Fas Ligand
Kidney, Heart,



Pancreas


Fork-Head Activin Signal Transducer-1 (FAST-1)
Heart


FOXP3
Kidney


Fractalkine
Kidney, Heart


Gamma 2
Kidney


Granulysin
Kidney


Granzyme B
Kidney, Pancreas,



Intestine,



Heart, Lung


Heat Shock Protein-60 (HSP-60)
Intestine


Heat Shock Protein-70 (HSP-70)
Intestine


Hepatocyte Growth Factor (HGF)
Heart


IF127
Intestine


Integrin-α4 (ITGA4)
Heart


Interferon-γ
Kidney, Intestine,



Heart


Interferon-Inducible Protein 10 (IP-10; CXCL10)
Kidney, Heart,



Pancreas


Interleukin-2 (IL-2)
Heart


Interleukin-2 Receptor (IL-2R)
Intestine


Interleukin-4 (IL-4)
Kidney


Interleukin-15 (IL-15)
Heart, Lung


Interleukin-18 (IL-18)
Kidney


Intracellular Adhesion Molecule-1 (ICAM-1)
Kidney


Laminin
Kidney


LAP3
Intestine


Macrophage Inflammatory Protein-2 (MIP-2)
Cornea


MADCAM-1
Intestine


Matrix Metalloproteinase-2 (MMP-2)
Intestine, Kidney


Matrix Metalloproteinase-9 (MMP-9)
Kidney, Intestine


Matrix Metalloproteinase-11 (MMP-11)
Kidney


Matrix Metalloproteinase-12 (MMP-12)
Kidney


Matrix Metalloproteinase-14 (MMP-14)
Kidney


MDK
Intestine


MIG
Pancreas, Heart


MIP-1α
Cornea, Pancreas,



Heart, Kidney


MIP-1β
Cornea, Heart


Monocyte Chemotactic Protein-1 (MCP-1)
Cornea, Pancreas,



Heart


Monocyte Chemotactic Protein-2 (MCP-2)
Heart


MUC2
Intestine


MUC4
Intestine


NKG2D
Kidney


p16 (INK4a)
Kidney


p21 (WAF/CIP1)
Kidney


p27 (Kip1)
Kidney


Perforin
Kidney, Pancreas,



Intestine, Heart


Programmed Cell Death (PDCD1)
Heart


RANTES
Cornea, Pancreas,



Kidney, Heart


RAS Homolog Gene Family, Member U (RHOU)
Heart


Semaphorin 7A (SEMA7A)
Heart


Serine Proteinase Inhibitor-9 (PI-9)
Kidney


SOD2
Heart


STK6
Intestine


Surfactant Protein-C (SP-C)
Kidney


TIAF-1
Kidney, Liver


TIM-3
Kidney


Tissue Inhibitor of Metalloproteinase-1 (TIMP-1)
Kidney


Tissue Inhibitor of Metalloproteinase-2 (TIMP-2)
Kidney


Transforming Growth Factor-β1 (TGF-β1)
Intestine, Kidney,



Heart


Transforming Growth Factor Type I Receptor
Intestine


Tumor Necrosis Factor-α (TNF-α)
Intestine, Heart,



Kidney


Urokinase Plasminogen Activator (uPA)
Kidney


Urokinase Plasminogen Activator Receptor (uPAR)
Kidney


Vascular Cell Adhesion Molecule-1 (VCAM-1)
Kidney, Lung


Vasoactive Intestinal Peptide (VIP)
Intestine


WD Repeat Dommoain 40A (WDR40A)
Heart


XCL1
Heart









In one embodiment of the invention, the polynucleotides comprising the rejection promoters are administered to the organ or tissue to be transplanted prior to the transplantation process. Organs and tissues that are used for transplantation typically must be transplanted into a recipient within 24-48 hours after removal from the donor. In one embodiment, the polynucleotides of the invention are administered to the organ or tissue within 48 hours of removal from the donor, e.g., within 36, 24, 18, 12, or 6 hours of removal from the donor. In another embodiment, the polynucleotides are administered to the organ or tissue at least 48 hours prior to transplantation into the recipient, e.g., at least 36, 24, 18, 12, or 6 hours prior to transplantation. The polynucleotides may be introduced into the organ or tissue to be transplanted in one location or in more than one location within the organ or tissue, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or more locations.
In another embodiment, the polynucleotides are administered to the organ or tissue after it has been transplanted into a subject, e.g., 2, 4, 6, 8, 10, 12, or 18 hours, 1, 2, 3, 4, 5, or 6 days, or 1, 2, 3, or 4 weeks or more after the transplantation.
The polynucleotides may be administered to the organ or tissue by any means as discussed above, including direct injection, electroporation, viral delivery, etc. In other embodiments, the polynucleotides may be administered as part of transgenic cells, e.g., transgenic stem cells. The cells may be isolated from either the transplant donor or the transplant recipient. For example, stem cells may be isolated from a patent in need of a transplant and the polynucleotides of the invention introduced into the stem cells. The transgenic cells may then be stored (e.g., frozen) until an organ or tissue is available for transplantation. The transgenic cells may then be administered to the organ or tissue before or after transplantation.
In a further embodiment, the methods of detecting transplant rejection may be carried out by introducing the polynucleotides of the invention into non-autologous cells, e.g., cells that are allogeneic or xenogeneic to the organ or tissue being transplanted, and the modified non-autologous cells are introduced to the organ or tissue prior to transplantation. In one embodiment, the modified non-autologous cells are surrounded by a barrier (e.g., encapsulated) prior to being introduced into the organ or tissue.
In one embodiment of the invention, the gene switch comprises a single rejection promoter operably linked to a transcription factor sequence. In another embodiment, the gene switch comprises two rejection promoters that are operably linked to two different transcription factor sequences that together encode a ligand-dependent transcription factor. The two rejection promoters may be the same or different.
In another embodiment, the gene switch may further comprise a promoter that regulates expression of a control protein that is useful for monitoring the function of the gene switch, i.e., to show that the gene switch is operating properly in its environment, e.g., has not been subjected to gene silencing. The expression of the control protein may be used to limit false negative results from the diagnostic switch. In one embodiment, the promoter linked to the control protein is a constitutive promoter so that the control protein is always expressed. In a different embodiment, the promoter linked to the control protein is a switch promoter which is different from the rejection promoter(s) present in the gene switch. The control protein may be a ligand-dependent transcription factor that binds to a promoter operably linked to a second reporter gene that is different from the first reporter gene. For example, the control protein may be a ligand-dependent transcription factor having a different DNA binding domain than the transcription factor expressed from the rejection promoter(s), and that recognizes the response elements in the promoter operably linked to the second reporter gene as shown in FIG. 4.
In one embodiment of the methods for detecting or monitoring transplant rejection, the reporter gene is any reporter gene described above. In another embodiment, the reporter gene encodes a secreted protein, e.g., one that can be readily detected in a blood or urine sample of a transplant recipient. In another embodiment, the reporter gene encodes a protein that is endogenous to the transplant recipient, e.g., a protein that is normally expressed at low levels so that an increase in reporter gene expression upon the onset of rejection can be detected.
Once the polynucleotides of the invention have been administered to the organ or tissue transplant, the methods of detecting or monitoring transplant rejection may be carried out by detecting reporter gene expression. In one embodiment, the level of reporter gene expression may be measured once. In another embodiment, the level of reporter gene expression may be measured more than once, e.g., regularly, such as once every 1, 2, 3, 4, 5, 6 days, 1, 2, 3, 4 weeks, or every 1, 2, 3, 4, 5, 6 or more months. At each time point to be measured, a measurement of reporter gene expression may be made in the absence of ligand to get a background level of expression and in the presence ligand to obtain the level of reporter gene expression due to activation of the rejection promoter(s). In one embodiment, the level of reporter gene expression in the presence of ligand is determined shortly after transplantation (e.g., within 1, 2, 3, 4, 5, 6 days or 1, 2, 3, or 4 weeks) to obtain the ligand-induced baseline level of reporter gene expression prior to the occurrence of any transplant rejection. The initial timepoint (or any subsequent timepoint) can be used to determine how much ligand must be administered to the subject and how long the ligand must be present to obtain measurable reporter gene expression. Both the dose and time may be adjusted as needed for each subject. Regular monitoring of ligand-induced reporter gene expression may then be carried out to detect any increase in reporter gene expression, which is indicative of transplant rejection.
If a polynucleotide encoding a control protein (either constitutive or inducible) is present in the gene switch, the level of the control protein or the reporter gene induced by the control protein may be measured at the same time to confirm that the gene switch is functioning properly. If the gene switch is not functioning optimally, it may be necessary to increase the ligand concentration or the amount of time between ligand administration and reporter gene detection to increase the signal from the gene switch. In another embodiment, if the gene switch is no longer functioning, additional polynucleotides may be administered to the organ or tissue transplant so that monitoring of transplant rejection can be continued.
In a further embodiment, once an increase in reporter gene expression has been detected indicating the presence of transplant rejection, the diagnosis may be confirmed using traditional means, e.g., by obtaining a biopsy of the transplanted tissue.
One embodiment of the invention relates to methods of preparing on organ or tissue transplant for detecting transplant rejection in a subject, comprising introducing into cells of said organ or tissue transplant (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during transplant rejection, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells.
Another embodiment of the invention relates to methods of detecting transplant rejection in a subject that has received an organ or tissue transplant, comprising:

    (a) administering ligand to said subject; and
    (b) detecting reporter gene expression;


wherein expression of the reporter gene indicates that transplant rejection has been detected; and
wherein said organ or tissue transplant comprises one or more cells comprising (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during transplant rejection, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor.
One embodiment of the invention relates to methods of preparing an organ or tissue transplant for monitoring the progression of transplant rejection in a subject, comprising introducing into cells of said organ or tissue transplant (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during transplant rejection, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells.
Another embodiment of the invention relates to methods of monitoring the progression of transplant rejection in a subject that has received an organ or tissue transplant, comprising:

    (a) administering ligand to said subject; and
    (b) detecting reporter gene expression at least twice;


wherein a change in the level of expression of said reporter gene indicates progression of said transplant rejection in said subject, and
wherein said organ or tissue transplant comprises one or more cells comprising (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during transplant rejection, and (2) a polynucleotide encoding a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor.
In a further embodiment, the methods of monitoring transplant rejection may be carried out by introducing the polynucleotides of the invention into non-autologous cells, e.g., cells that are allogeneic or xenogeneic to the organ or tissue being transplanted, and the modified non-autologous cells are introduced to the organ or tissue prior to transplantation. In one embodiment, the modified non-autologous cells are surrounded by a barrier (e.g., encapsulated) prior to being introduced into the organ or tissue.
In one embodiment of the methods described above, one or both of the polynucleotides encoding a gene switch and a reporter gene may be part of a therapeutic vector that is being administered to a subject (e.g., a vector encoding a therapeutic factor (protein or nucleic acid) for gene therapy). In this embodiment, the factor and the diagnostic test for monitoring the level of the factor are administered together in one unit, ensuring that all cells that receive the treatment also receive the diagnostic gene switch.
For each of the methods described above, in one embodiment, the polynucleotide encoding the gene switch and the polynucleotide encoding the reporter gene linked to a promoter are part of one larger polynucleotide, e.g., a vector. In another embodiment, the polynucleotide encoding the gene switch and the polynucleotide encoding the reporter gene linked to a promoter are separate polynucleotides.
In one aspect, the invention relates to polynucleotides that may be used in the methods of the invention. In one embodiment, the polynucleotide encodes a gene switch, the gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during said disease or disorder. In another embodiment, the polynucleotide further encodes a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor. In one embodiment, the gene switch is an EcR-based gene switch. In another embodiment, the gene switch comprises a first transcription factor sequence under the control of a first diagnostic switch promoter and a second transcription factor sequence under the control of a second diagnostic switch promoter, wherein the proteins encoded by said first transcription factor sequence and said second transcription factor sequence interact to form a protein complex which functions as a ligand-dependent transcription factor. In one embodiment, the first diagnostic switch promoter and the second diagnostic switch promoter are different. In another embodiment, the first diagnostic switch promoter and the second diagnostic switch promoter are the same. In another embodiment, the first transcription factor sequence encodes a protein comprising a heterodimer partner and a transactivation domain and the second transcription factor sequence encodes a protein comprising a DNA binding domain and a ligand-binding domain. In a further embodiment, the polynucleotide also encodes a lethal polypeptide operably linked to an inducible promoter.
In one aspect, the invention relates to polynucleotides encoding a gene switch, the gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by factors found in cells that are being exposed to toxic conditions. In another embodiment, the polynucleotide further encodes a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor. In one embodiment, the gene switch is an EcR-based gene switch. In another embodiment, the gene switch comprises a first transcription factor sequence under the control of a first diagnostic switch promoter and a second transcription factor sequence under the control of a second diagnostic switch promoter, wherein the proteins encoded by said first transcription factor sequence and said second transcription factor sequence interact to form a protein complex which functions as a ligand-dependent transcription factor. In one embodiment, the first diagnostic switch promoter and the second diagnostic switch promoter are different. In another embodiment, the first diagnostic switch promoter and the second diagnostic switch promoter are the same. In another embodiment, the first transcription factor sequence encodes a protein comprising a heterodimer partner and a transactivation domain and the second transcription factor sequence encodes a protein comprising a DNA binding domain and a ligand-binding domain. In a further embodiment, the polynucleotide also encodes a lethal polypeptide operably linked to an inducible promoter.
In one aspect, the invention relates to polynucleotides encoding a gene switch, the gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated by said factor that is being administered for treatment. In another embodiment, the polynucleotide further encodes a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor. In one embodiment, the gene switch is an EcR-based gene switch. In another embodiment, the gene switch comprises a first transcription factor sequence under the control of a first diagnostic switch promoter and a second transcription factor sequence under the control of a second diagnostic switch promoter, wherein the proteins encoded by said first transcription factor sequence and said second transcription factor sequence interact to form a protein complex which functions as a ligand-dependent transcription factor. In one embodiment, the first diagnostic switch promoter and the second diagnostic switch promoter are different. In another embodiment, the first diagnostic switch promoter and the second diagnostic switch promoter are the same. In another embodiment, the first transcription factor sequence encodes a protein comprising a heterodimer partner and a transactivation domain and the second transcription factor sequence encodes a protein comprising a DNA binding domain and a ligand-binding domain. In a further embodiment, the polynucleotide also encodes a lethal polypeptide operably linked to an inducible promoter.
In one aspect, the invention relates to polynucleotides encoding a gene switch, the gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, linked to a diagnostic switch promoter, wherein the activity of the promoter is modulated during transplant rejection. In another embodiment, the polynucleotide further encodes a reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor. In one embodiment, the gene switch is an EcR-based gene switch. In another embodiment, the gene switch comprises a first transcription factor sequence under the control of a first diagnostic switch promoter and a second transcription factor sequence under the control of a second diagnostic switch promoter, wherein the proteins encoded by said first transcription factor sequence and said second transcription factor sequence interact to form a protein complex which functions as a ligand-dependent transcription factor. In one embodiment, the first diagnostic switch promoter and the second diagnostic switch promoter are different. In another embodiment, the first diagnostic switch promoter and the second diagnostic switch promoter are the same. In another embodiment, the first transcription factor sequence encodes a protein comprising a heterodimer partner and a transactivation domain and the second transcription factor sequence encodes a protein comprising a DNA binding domain and a ligand-binding domain. In a further embodiment, the polynucleotide also encodes a lethal polypeptide operably linked to an inducible promoter.
Another aspect of the invention relates to vectors comprising any of the polynucleotides described above. In one embodiment, the vector is a plasmid vector or a viral vector. In one embodiment, the polynucleotides are present on the same vector. In a further embodiment, each of the polynucleotides is on a separate vector. The separate vectors may be the identical vector (e.g., the same plasmid), the same type of vector (e.g., both are plasmids but not the same plasmid), or different types of vectors (e.g., one vector is a plasmid, the other vector is a virus).
In another aspect, the invention provides kits that may be used in conjunction with methods the invention. Kits according to this aspect of the invention may comprise one or more containers, which may contain one or more components selected from the group consisting of one or more nucleic acid molecules, restriction enzymes and one or more cells comprising such nucleic acid molecules. Kits of the invention may further comprise one or more containers containing cell culture media suitable for culturing cells of the invention, one or more containers containing antibiotics suitable for use in culturing cells of the invention, one or more containers containing buffers, one or more containers containing transfection reagents, one or more containers containing substrates for enzymatic reactions, and/or one or more ligands for gene switch activation.
Kits of the invention may contain a wide variety of nucleic acid molecules that can be used with the invention. Examples of nucleic acid molecules that can be supplied in kits of the invention include those that contain promoters, sequences encoding gene switches, enhancers, repressors, selection markers, transcription signals, translation signals, primer hybridization sites (e.g., for sequencing or PCR), recombination sites, restriction sites and polylinkers, sites that suppress the termination of translation in the presence of a suppressor tRNA, suppressor tRNA coding sequences, sequences that encode domains and/or regions, origins of replication, telomeres, centromeres, and the like. In one embodiment, kits may comprise a polynucleotide comprising a gene switch without any diagnostic switch promoters, the polynucleotide being suitable for insertion of any diagnostic switch promoters of interest. Nucleic acid molecules of the invention may comprise any one or more of these features in addition to polynucleotides as described above.
Kits of the invention may comprise cells. The cells may comprise the polynucleotides of the invention, or the cells and the polynucleotides may be in separate containers. In one embodiment the cells may be autologous cells, e.g., as part of a kit designed for a specific subject. In another embodiment, the cells may be non-autologous cells, e.g., as part of a kit designed for any subject. In a further embodiment, the non-autologous cells may be surrounded by a barrier (e.g., encapsulated).
Kits of the invention may comprise containers containing one or more recombination proteins. Suitable recombination proteins include, but are not limited to, Cre, Int, IHF, Xis, Flp, Fis, Hin, Gin, Cin, Tn3 resolvase, ΦC31, TndX, XerC, and XerD. Other suitable recombination sites and proteins are those associated with the GATEWAYTM Cloning Technology available from Invitrogen Corp., Carlsbad, Calif., and described in the product literature of the GATEWAYTM Cloning Technology (version E, Sep. 22, 2003), the entire disclosures of which are incorporated herein by reference.
Kits of the invention can also be supplied with primers. These primers will generally be designed to anneal to molecules having specific nucleotide sequences. For example, these primers can be designed for use in PCR to amplify a particular nucleic acid molecule. Sequencing primers may also be supplied with the kit.
One or more buffers (e.g., one, two, three, four, five, eight, ten, fifteen) may be supplied in kits of the invention. These buffers may be supplied at working concentrations or may be supplied in concentrated form and then diluted to the working concentrations. These buffers will often contain salt, metal ions, co-factors, metal ion chelating agents, etc. for the enhancement of activities or the stabilization of either the buffer itself or molecules in the buffer. Further, these buffers may be supplied in dried or aqueous forms. When buffers are supplied in a dried form, they will generally be dissolved in water prior to use.
Kits of the invention may contain virtually any combination of the components set out above or described elsewhere herein. As one skilled in the art would recognize, the components supplied with kits of the invention will vary with the intended use for the kits. Thus, kits may be designed to perform various functions set out in this application and the components of such kits will vary accordingly.
The present invention further relates to instructions for performing one or more methods of the invention. Such instructions can instruct a user of conditions suitable for performing methods of the invention. Instructions of the invention can be in a tangible form, for example, written instructions (e.g., typed on paper), or can be in an intangible form, for example, accessible via a computer disk or over the internet.
It will be recognized that a full text of instructions for performing a method of the invention or, where the instructions are included with a kit, for using the kit, need not be provided. One example of a situation in which a kit of the invention, for example, would not contain such full length instructions is where the provided directions inform a user of the kits where to obtain instructions for practicing methods for which the kit can be used. Thus, instructions for performing methods of the invention can be obtained from internet web pages, separately sold or distributed manuals or other product literature, etc. The invention thus includes kits that direct a kit user to one or more locations where instructions not directly packaged and/or distributed with the kits can be found. Such instructions can be in any form including, but not limited to, electronic or printed forms.
Having now fully described the invention, it will be understood by those of ordinary skill in the art that the same can be performed within a wide and equivalent range of conditions, formulations and other parameters without affecting the scope of the invention or any embodiment thereof. All patents, patent applications and publications cited herein are fully incorporated by reference herein in their entirety.
EXAMPLES
Example 1
The vector shown in FIG. 5 includes IL-24/mda-7 promoter (SEQ ID NO.: 5). Adenovirus produced using the adenoviral shuttle vector is used to transduce cells isolated from lymphatic samples. The transduces cells are split into two groups and cultured either in the presence or absence of activator ligand. Both sets of cells are then disrupted, and the resulting cell lysates are used in luciferase assays.
Example 2
The vector shown in FIG. 6 includes TRPM4 and TRGC1/TARP promoters (SEQ ID NO.: 6). The DNA vector is used to transduce a prostate biopsy using non-viral transduction systems. The transduced biopsy is split into two groups and cultured either in the presence or absence of an activator ligand. Both sets of biopsied tissues are homogenized, and the resulting lysates are used in luciferase assays.
Example 3
The vector shown in FIG. 7 includes the ADAM-17 promoter (SEQ ID NO.: 7) and the CD95-ADAM8 reporter (SEQ ID NOs: 10-11). Adenovirus produced using the adenoviral shuttle vector is used to transduced a portion of a donor kidney before transplantation. Following transplantation, serum samples are assayed for the reporter gene for a period defined by the physician. The assay protocol consists of assaying reporter expression from samples not exposed to activator ligand. Immediately after blood draw of the non-activated group, ligand is administered for 24 hours and then discontinued; another blood sample is acquired within one hour before the ligand treatment is completed. Reporter assay results are compared between the ligand-treated and untreated samples. A period of 60 hours must pass before this procedure is performed again.
Example 4
The vector shown in FIG. 8 includes the CXCL9 and SEMA7A promoters (SEQ ID NO.: 8) and the CD40-CD3 reporter (SEQ ID NOs.: 12-13). This vector is used to transduce a portion of a donor heart before transplantation via direct needle injection. Following transplantation, serum samples are assayed for the reporter gene for a period defined by the physician. The assay protocol consists of assaying reporter expression from samples not exposed to an activator ligand. Immediately after the blood draw of the “non-activated” group, ligand is administered for 24 hours and then discontinued; another blood sample is acquired within one hour before the ligand treatment is completed. Reporter assay results are compared between the ligand-treated and untreated samples. A period of 60 hours must pass before this procedure can be performed again.
Example 5
The vector shown in FIG. 9 includes the ADAM-17 promoter and the alkaline phosphatase—c terminal CD40 reporter (SEQ ID NO.: 14). Adenovirus produced using this adenoviral shuttle vector is used to transduce primary porcine kidney cells. The resulting cells are encapsulated in alginate (see WO 2007/046719A2), and then implanted into a donor kidney before transplantation. Following transplantation, serum samples are assayed for the reporter gene for a period defined by the physician. The assay protocol consists of assaying reporter expression from samples not exposed to activator ligand. Immediately after the blood draw of the “non-activated” group, ligand is administered for 24 hours and then discontinued; another blood sample is acquired within one hour before the ligand treatment is completed. Reporter assay results are compared between the ligand-treated and untreated samples. A period of 60 hours must pass before this procedure can be performed again.

## Claims

1. A method of detecting kidney transplant rejection in a subject that has received a kidney transplant, comprising:
introducing into cells of said organ or tissue transplant (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a ligand-dependent transcription factor, operably linked to a diagnostic ADAM-17 switch promoter, wherein the activity of the promoter is modulated during transplant rejection, and (2) a polynucleotide encoding a CD95-ADAM8 dual reporter or a alkaline phosphatase—c terminal CD40 reporter gene linked to a promoter which is activated by said ligand-dependent transcription factor, to produce modified cells;
administering ligand to said modified cells; and
detecting reporter gene expression;
wherein expression of the CD95-ADAM8 dual reporter or the alkaline phosphatase—c terminal CD40 reporter gene indicates that transplant rejection has been detected.

2. The method of claim 1, wherein said polynucleotides are introduced into said cells prior to transplantation.

3. The method of claim 1, wherein said polynucleotides are introduced into said cells after transplantation.

4. The method of claim 1, wherein said gene switch is an ecdysone receptor (EcR)-based gene switch.

5. The method of claim 4, wherein said ligand binds to the EcR ligand binding domain.

6. The method of claim 5, wherein said ligand is a diacylhydrazine.

7. The method of claim 6, wherein said ligand is selected from the group consisting of RG-115819, RG-115830, and RG-115932.

8. The method of claim 1, wherein one of said polynucleotides further encodes a lethal polypeptide operably linked to an inducible promoter.