# Patent

## Title
Recombinant human factor IX and use thereof

## Abstract

The present invention aims at converting factor IX into a molecule with enhanced activity which provides an alternative for replacement therapy and gene therapy for hemophilia B. Using recombinant techniques, factor IX having substitution of amino acid residue of SEQ ID NO: 7 at amino acid position selected from the group consisting of 86, 277, and 338 (exclude the circumstance of a single substitution at amino acid position 338) exhibits better clotting activity than recombinant wild type factor IX.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims priority to a Provisional Application (Application No. 60/884,129) filed on Jan. 9, 2007, which is hereby incorporated by reference in its entirety.


Although incorporated by reference in its entirety, no arguments or disclaimers made in the parent application apply to this Non-provisional application. Any disclaimer that may have occurred during the prosecution of the above-referenced application(s) is hereby expressly rescinded. Consequently, the Patent Office is asked to review the new set of claims in view of all the prior art of record and any search that the Office deems appropriate.
FIELD OF THE INVENTION
The present invention relates to a recombinant human factor IX protein, and a nucleic acid sequence encoding thereof. The present invention also relates to a method for treating hemophilia.
BACKGROUND OF THE INVENTION
In the developed world, the current therapeutic choices for treatment of hemophilia patients comprise prophylactic and on-demand replacement therapy (Lofqvist T. et al., J. Intern. Med. 1997; 241:395-400) with either plasma-derived or recombinant coagulation factor concentrate (Lippert B. et al., Blood Coagul. Fibrinolysis. 2005; 16:477-485). Standard treatment for Hemophilia is infusions of protein concentrates to replace the defective clotting factor. The amount infused depends upon the severity of bleeding, the site of the bleeding, and the body size of the patient. People with severe forms of the disease may be treated by regular prophylactic infusions. The outcome is good with treatment and management so most people with hemophilia are able to lead relatively normal lives. However, the high cost and limited availability of the recombinant protein make dosing of clotting factors a crucial issue in the treatment of hemophilia. In addition, the plasma-derived products run the risk for HIV and hepatitis B and C transmission, and the half-life of the infused protein in a patient is short, which results in the necessity for fairly frequent infusions (White G. C. et al., Transfus. Sci. 1998; 19:177-189).
Other treatments, such as gene therapy and tissue implant techniques are also under study as possible treatments (Hough C. et al., J. Thromb. Haemost., 2005; 3:1195-1205). One clinical trial of gene therapy in hemophilia patients showed only transient therapeutic increments of clotting factor expression due to generation of antibody against delivering vehicle (Manno C. S. et al., Nat. Med. 2006; 12:342-347). Therefore, gene therapy remains an investigational method with many obstacles to overcome before it can be widely used as treatment for hemophilia.
Hemophilia B is caused by a deficiency of a blood plasma protein called factor IX that affects the clotting property of blood. The disorder is caused by an inherited X-linked recessive trait, with the defective gene located on the X chromosome. Thus, the disorder occurs primarily in males. Hemophilia B occurs in about 1 out of 30,000 men.
Human factor IX is a vitamin K-dependent zymogen which plays an important role in blood coagulation. Factor IX circulates as a 415-amino acid single chain zymogen with a molecular mass of 55,000 daltons and is present in normal plasma at approximately 5 μg/ml.
Recombinant factor IX products offer greatly reduced risk for HIV and hepatitis B and C transmission. If recombinant factor IX with enhanced clotting activity can be generated through genetic engineering of factor IX DNA, it will not only lower the cost for the clotting factor but also reduce the dose of it in managing patients with hemophilia. Moreover, this method will also provide a more efficient tool for gene therapy trials in patients with hemophilia.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the SDS-PAGE analysis of purified recombinant factor IX. Purified proteins (4 μg/lane) from Wild type (IX-7) and mutants IX-1, IX-2, IX-8, IX-3, IX-4, IX-5 and IX-6 were subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Samples were run under non-reducing conditions. Factor IX protein bands were visualized by Commassie blue staining. The concentration of affinity-purified recombinant wild type and alanine-replaced factor IX was determined by the BCATM protein assay kit (Pierce, Rockford, Ill., USA) using bovine γ-globulin (cat.#23212, Pierce) to generate a standard curve for calculating the protein concentrations.
FIG. 2 shows human factor IX levels in hemophilia B mice at 24 hours after hydrodynamic treatment with pBS-HCRHP1-A-FIX (see “Method”). Male hemophilia B mice (20 μg body weight) were subjected to hydrodynamic shock by tail vein injection of 2 ml of 50 μg DNA in 6-8 seconds. The mice were recovered and sacrificed 24 h after injection for collection of blood plasma for clotting activity and protein level determination (IX:Ag) by Enzyme-linked ImmunoSorbent assay (ELISA). Each bar represents the data of individual mouse. Standard curves for ELISA and for clotting activity were derived in parallel experiments from serial dilutions of normal plasma pooled from 20 healthy donors. The factor IX protein level and clotting activity in the pooled plasma were assumed to be 5 μg/ml.
FIG. 3 shows results of factor IX expression by adeno-associated virus (AAV)-mediated gene transfer to hemophilia B mice. Construction of the rAAV2/8 vector carrying, individually, IX-6 and IX-7 was described in “Methods”. Homozygous female hemophilia B mice (n=6, aged 8 ̃14 weeks, weighing 16 ̃18 g) were respectively injected intravenously with 4×1012 vg/kg (a) 4×1011 and 8×1010 vg/kg (b) of the rAAV2/8 vehicles carrying IX-6 and IX-7 as indicated. Blood was collected 2 weeks after injection for measurement of factor IX protein level and clotting activity. Each group of mice was numbered according to age. Specific clotting activity presented as percentage was defined as the clotting activity measured for each sample divided by its mass (IX:Ag) measured by ELISA. Standard curves for ELISA and for clotting activity were derived in parallel experiments from serial dilutions of normal plasma pooled from 20 healthy donors. Factor IX protein level and clotting activity in the normal pooled plasma was assumed to be 5 μg/ml.



SUMMARY OF THE INVENTION
The present invention provides a recombinant human factor IX protein having substitution of amino acid residue of SEQ ID No: 7 at amino acid position selected from the group consisting of 86, 277 and 338, provided that a single substitution at amino acid position 338 is excluded.
The present invention further provides an isolated nucleic acid encoding a recombinant human factor IX protein having nucleic acid sequence shown in SEQ ID NO: 9, 10, 11, 12, 13 or 14.
The present invention further provides a pharmaceutical composition comprising: (a) a human factor IX protein of the present invention, and (b) a pharmaceutically acceptable carrier, excipient, or diluent.
The present invention further provides a method for generating a human factor IX protein of the present invention in vivo comprising: (a) constructing a vector carrying a nucleic acid encoding the human factor IX protein; and (b) administering the vector to a mammalian.
The present invention further provides a method for treating hemophilia comprising administering to a patient in need of such treatment with an effective amount of the protein of the present invention.
DETAILED DESCRIPTION OF THE INVENTION
The present invention provides a recombinant factor IX with higher activity than wild type factor IX, and it allows less protein injection than the latter into hemophilia to reach the therapeutic level.
The present invention provides a new factor IX DNA sequence that would express a factor IX protein with a higher clotting activity than the DNA sequence expressing wild type factor IX when delivered into animals by various means such as viral vectors.
Using recombinant techniques, factor IX with simultaneously double or triple alanine replacement at positions 86, 277, and 338 exhibited 2 ̃14 times better clotting activity than wild type recombinant factor IX (IX-7). In an attempt to understand the causes contributing to the increased clotting activity of these factor IX variants, several functional parameters were determined. Table 1 demonstrates that the increased clotting activity was factor VIIIa-dependent and was attributed to the enhanced affinity of factor IX for factor VIII and an increased kcat and decreased KM for factor X.
Accordingly, the present invention provides a recombinant human factor IX protein having substitution of amino acid residue of SEQ ID No: 7 at amino acid position selected from the group consisting of 86, 277 and 338, provided that a single substitution at amino acid position 338 is excluded. The present proteins have alanine residue substitution at amino acid sequence of wild type factor IX, wherein the substitution is at the amino acid position selected from the group consisting of 86, 277, and 338, provided that a single substitution at amino acid position 338 is excluded.
The term “amino acid” used herein is a molecule that contains both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent. In the alpha amino acids, the amino and carboxyl groups are attached to the same carbon, which is called the α-carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. In general, the standard amino acids such as alanine, asparagine, aspartic acid, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, methionine, phenylalanine, serine, threonine, tryptophan, tyrosine or valine can be used as a substituted amino acid. In a preferred embodiment, the substituted amino acid residue is alanine.
In a more preferred embodiment, the protein of the present invention has SEQ ID No: 1, 2, 3, 4, 5 or 6. In the most preferred embodiment, the protein of the present invention has SEQ ID No: 6.
The substitution creates the non-naturally occurring human factor IX exhibiting from 2 to 14 folds more than wild type factor IX protein's clotting activity (Table 1). The protein has enhanced affinity for cofactor, factor VIIIa. In an embodiment, the recombinant human factor IX protein has Kd values of 0.1 ̃0.5 nM. In an embodiment, the recombinant human factor IX protein has KM values of 32 ̃128 nM, preferably 32 ̃56 nM (Table 2).
The present invention also provides an isolated nucleic acid encoding a recombinant human factor IX protein having nucleic acid sequence shown in SEQ ID NO: 9, 10, 11, 12, 13 or 14. In a preferred embodiment, the nucleic acid has SEQ ID NO: 11, 12 or 13. In a more preferred embodiment, the nucleic acid has SEQ ID NO: 14.
The present invention further provides a pharmaceutical composition comprising: (a) a human factor IX protein of the present invention; and (b) a pharmaceutically acceptable carrier, excipient, or diluent.
Besides in vitro expression and analysis of their biological properties, the present invention also relates to using mouse model to evaluate the potential role of the alanine variants. The hemophilia B mouse offers a model that allows the physiological role of these variant factor IXs to be studied. To estimate the degradation pathway of factor IX, these human factor IX proteins is injected into the tail vein of hemophilia mouse and the characteristics of these mutant proteins is observed.
Hydrodynamics-based delivery of naked plasmid DNA to liver can generate therapeutic plasma levels of transgene products in mice. This technology is used to deliver the DNA encoding the wild type and variant factor IX genes to hemophilia B mice.
Systemic delivery of therapeutic transgenes by viral vectors can potentially lead to long-term transgene expression (Miao C. H. et al., Mol. Ther. 2001; 3:947-957). But the efficiency of gene transfer to hepatocytes is poor. The recombinant AAV delivery system garnered enthusiastic support when it demonstrated efficacy in initial preclinical studies in the hemophilia B animal models (Davidoff A. M. et al., Mol. Ther. 2005; 11:875-888). Two clinical studies were initiated using an AAV serotype 2 vector to deliver factor IX to the muscle (Manno C. S. et al., Blood. 2003; 101:2963-2972) by direct intro muscular injection and to the liver via hepatic artery infusion (Manno C. S. et al., Nat. Med. 2006; 12:342-347). In the muscle trial, plasma level of factor IX generally did not raise above 1%, whereas levels of up to 12% were detected in the plasma of single patient treated by hepatic artery delivery of the AAV vector. However the increase was followed by a transient rise in serum transaminase levels and loss of factor IX expression, probably due to pre-existing host immunity to AAV capsid proteins that targeted the transduced cells. Because the recombinant IX-6 has higher activity than wild type (IX-7) in our mouse model, it could be possible to reduce the injection quantity of viral particles and reach the same factor IX activity.
Accordingly, the present invention also provides a method for generating a human factor IX protein of the present invention in vivo comprising:

    (a) constructing a vector carrying a nucleic acid encoding the human factor IX protein; and
    (b) administering the vector to a mammalian.


In a preferred embodiment, the mammalian is human.
The term “administration” used herein is not limited but includes via vector, plasmid, liposome, DNA injection, electroporation, gene gun, intravenously injection or hepatic artery infusion.
The present invention further provides a method for treating hemophilia comprising administering to a patient in need of such treatment with an effective amount of a protein of the present invention.
While the invention has been described and exemplified in sufficient detail for those skilled in this art to make and use it, various alternatives, modifications, and improvements should be apparent without departing from the spirit and scope of the invention.
One skilled in the art readily appreciates that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. The embryos, animals, and processes and methods for producing them are representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Modifications therein and other uses will occur to those skilled in the art. These modifications are encompassed within the spirit of the invention and are defined by the scope of the claims.
EXAMPLE
The examples below are non-limiting and are merely representative of various aspects and features of the present invention.
Materials
Purified human factors VIa, XIa, Xa, and X, and polyclonal goat anti-human factor IX antibodies (cat. #GAFIX-AP) were purchased from Enzyme Research Laboratory (ERL, South Bend, Ind., USA). Phosphatidylcholine (PC), phosphatidylserine (PS) and ITS (Insulin-Transferrin-Sodium selenite) media supplements used in serum free media were from Sigma Chemical Co. (St. Louis, Mo., USA). Preparation of tissue factor and PCPS phospholipids were described previously (Chang Y J, et al., Biochemistry, 1999:10940-10948). Factor IX deficient plasma, Spectrozyme FXa, and Spectrozyme FIXa were purchased from American Diagnostica Inc. (Greenwich, Conn., USA). All the restriction endonucleases and polymerases were products of the New England Biolabs, Inc. (Beverly, Mass., USA). Geneticin (G418) was from CalBiochem (Merck KGaA, Darmstadt, Germany). A Vmax microtiter plate reader equipped with a thermal controller (Molecular Devices Corp., Menlo Park, Calif., USA) was used for all spectrophotometric assays. QAE-Sephadex A50, and Resource Q were from Amersham (Amersham Pharmacia BioTech, UK, Bucks, England).
Methods
In-Vitro Mutagenesis, Expression and Purification of Factor IX
Site-specific mutagenesis was performed on the human factor IX CDNA by a PCR-based method (QuickChange, Stratagene, Boston, USA) using primer pairs for replacing the codons at residues 86, 277 or 338 with those for alanine. The sequences of the primers are IX86 (5′GTGAATTAGATGCAACATGTA3′) pairing with IX86T7 (5′GTTACATGTTGCATCTAATTCAC3′) for replacing residue 86; IX277 (5′GAACTGGACGCACCCTTAGTGC3′) pairing with IX277-2 (5′CTAAGGGTGCGTCCAGTTCCAG3′) for replacing residue 277, and IX338 (5′CATGTCTTGCATCTACAAAG3′) pairing with IX338D (5′CTTTGTAGATGCAAGACATG3′) for residue 338. With these primer pairs, 7 different factor IX cDNA's were generated, fully sequenced, and together with wild type factor IX (IX-7) subcloned into pCR3TM-Uni (Invitrogen, Calif., USA) for expression in human 293 cells under the control of cytomegalovirus. Of the 7 recombinant factor IX mutants, three are single replacement mutants with alanine substitution at residues 86, 277 or 338 (SEQ ID NO:1, SEQ ID NO: 2 or SEQ ID NO: 8, respectively), another three are double replacement mutants with alanine substitutions at 86 plus 277 (SEQ ID NO: 3), 86 plus 338 (SEQ ID NO: 4) and 277 plus 338 (SEQ ID NO: 5), and the other is triple replacement mutant with 86, 277 and 338 all replaced by alanine (SEQ ID NO: 6). Identification of cell clones expressing the recombinant proteins was by ELISA (see below) using the commercially available factor IX specific antibodies. Expansion of the correct cell clones in serum free media to large quantity and purification of the recombinant proteins were performed as described previously. Briefly, one liter of the cultured supernatant was adjusted to 5 mM benzamidine and 4 mM EDTA and subjected to centrifugation at 4,350 rpm (HA6000, Sorvall RC-3C Plus, DuPont) for 30 mm at 4° C. After removal of cell debris, the supernatant was passed through a QAE-Sephadex A50 column (30 ml, 5×2.5 cm) equilibrated with IBS/EDTA (20 mM Tris-Cl, pH 7.5, and 150 mM NaCl/4 mM EDTA). After washing the column with 1 liter of TBS containing 5 mM benzamidine, factor IX was eluted with a gradient of 0 ̃30 mM CaCl2 in TBS/1 mM benzamidine. Fractions containing factor IX were identified by ELISA (see below), pooled, dialyzed against 100-fold excess volumes of 50 mM Tris-Cl, pH 7.5, and filtered through a 0.22-μm syringe filter (Millipore, Cork, Ireland). Approximately 100 ml of the QAE-eluent was loaded on to a Resource Q column (1 ml, Akta FPLC purifier, Amersham Biosciences). After washing in buffer containing 50 mM Tris-Cl, pH 7.5, the column was eluted with a gradient of NaCl (0 ̃1 M) in 50 mM Tris-Cl, pH 7.5. Factor IX was eluted at fractions of approximate 250 mM NaCl. The purified recombinant factor IX proteins were verified by SDS-PAGE followed by staining with Coomassie blue.
Enzyme-Linked Immunosorbent Assay (ELISA) and Clotting Activity Assay.
The protein mass of wild type and the alanine-replaced human factor IX (hFIX) in cultured supernatant and in mouse plasma was determined by ELISA using polyclonal antibodies to human factor IX. The antibodies are species-specific polyclonal anti-hFIX antibodies that do not cross-react with murine factor IX. Pooled plasmas of at least 20 healthy individuals were used in serial dilutions in parallel experiments to prepare standard curves for calculation of the level of factor IX. The standard curves from the pooled plasma paralleled to those derived from the purified plasma factor IX (IMMUNINE, Baxter AG, Vienna, Austria).
The function of the recombinant factor IX proteins was determined by their clotting activities in the one-stage activated partial thromboplastin time (aPTT) assays. Pooled normal plasma in serial dilutions was used as assay standards. The standard curves of the clotting assays parallel to those derived from the purified plasma factor IX (IMMUNINE) and the recombinant factor IX (BeneFIX, Genetics Institute, Inc. Cambridge Mass., USA). The specific activity of a sample was defined as the clotting activity divided by its mass. The factor IX protein mass and clotting activity in pooled normal human plasma was assumed to be 5 μg/ml.
Activation of Factor IX by Factor XIa and by Factor VIIa and Tissue Factor (VIIa·TF) Complex
The activation of factor IX by factor XIa in the presence of TBS/5 mM CaCl2 was performed at an enzyme to substrate ratio of 1:200. Aliquots from the reaction mixtures were withdrawn at timed-intervals, placed in a solution containing 1% SDS and 2 mM EDTA to stop the reaction, adjusted in gel loading buffer (final concentrations: 50 mM Tris-Cl, pH 6.8, 2 mM EDTA, 1% SDS, 8% glycerol, and 0.025% Bromophenol blue), and subsequently subjected to SDS-PAGE analysis. The activation of factor IX by the VIIa·TF complex was performed at an enzyme to substrate ratio of 1:80 and in TBS/5 mM of CaCl2. Aliquots from the reaction mixtures were withdrawn at timed-intervals and resolved by SDS-PAGE analysis.
Interaction of Factor IXa with Factor X
Factor IXa was prepared by activation with factor XIa as described above. The concentration of the factor IXa molecules was determined by titration with antithrombin III (ATIII) as described previously (Chang Y J, et al., Journal of Biological Chemistry. 2002; 277:25393). Interaction of factor IXa with factor X was analyzed by monitoring kinetically the hydrolysis of Spectrozyme FXa by activated factor X generated by factor IXa in the absence and presence of factor VIIIa. Briefly, when without factor VIIIa, factor IXa (10 nM) was incubated with PCPS at room temperature for 5 min before different concentrations of factor X (0-1 μM) and 0.5 mM Spectrozyme FXa were added and the reaction was recorded as the absorbance change of the mixture according to the incubation time. The final volume was 100 μl and the reaction was performed at 37° C. in buffers containing 0.01% BSA and 40 μM PCPS in TBS/5 mM CaCl2 (TBS/CaCl2/BSA/PCPS). The interaction of factor IXa with factor X in the presence of factor VIIIa was performed by incubation of 25 μl of factor VIIIa (freshly prepared) with an equal volume of FIXa diluted and preincubated in TBS/CaCl2/BSA/PCPS, and a 50 μl of a reaction mixture containing PCPS, Spectrozyme FXa and factor X added subsequently. The factor Xa activity generated by the factor IXa-factor VIIIa complex (the intrinsic tenase activity) in the mixture was detected kinetically on the microtiter plate reader. Final concentrations were 0.25 nM for wild type or mutant factor IXa, 0.4 nM for factor VIIIa, 40 μM for PCPS, 0-200 nM for factor X, and 0.5 mM for Spectrozyme FXa. The factor IXa activity was calculated by the following equation as described previously. Absorbance (A405)=at2+bt+c
Interaction of Factor IXa with Factor VIIIa
Binding experiments were performed by monitoring the intrinsic tenase activity at limiting concentrations of factor VIIIa. Twenty-five microliters of freshly prepared factor VIIIa (0.4 nM) were incubated with 25 μl of different concentrations of wild type or mutant factor IXa (0-20 nM) to form the intrinsic tenase complex. Activity of the intrinsic tenase complex formed by binding of factor VIIIa to factor IXa was then measured by the addition of 50 μl of a mixture of factor X and Spectrozyme FXa in a reaction buffer containing TBS/Ca/PCPS/BSA. Final concentrations were factor VIIIa, 0.1 nM, PCPS, 40 μM, factor X, 100 nM, Spectrozyme FXa, 0.5 mM, and factor IXa, 0 ̃15 nM. Experiments were performed in duplicate for 3 independent reactions, and curves were fitted using all data points. The Kd values were derived by calculations according to the following equation as described previously (Chang Y J, et al., Journal of Biological Chemistry. 2002; 277:25393).




  
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Interaction of Factor IX with Antithrombin III (ATIII)

The inhibition of factor IXa by ATIII was performed by gel analysis of the enzyme-inhibitor complex. 0.53 μM factor IXa and 0.53 μM ATIII were incubated at 37° C. in 100 μl of TBS/5 mM CaCl2 with or without 0.01 unit/ml heparin. Aliquots (20 μl) of the reaction mixtures were withdrawn at different time intervals (0, 5, 10, 20, and 30 min), mixed with gel loading buffer (final concentration: 50 mM Tris-Cl, pH 6.8, 2 mM EDTA, 1% SDS, 8% glycerol, and 0.025% Bromophenol blue) and developed by SDS-PAGE followed by staining with silver.
Animal Experiments
All the animal experiments described below followed standard procedures. Animals were treated according to the guidelines of the National Taiwan University in Taiwan or the National Institutes of health guidelines for animal care and the guidelines of the Children's Hospital and Regional Medical Center at Seattle, USA. Hemophilia B mice of C57BL/6 strain background were originally obtained from Dr. Darrel Stafford (Biology Department, University of North Carolina at Chapel Hill, N.C., USA) and Dr. Katherine High (The Children's Hospital of Philadelphia, Pa., USA).
Protein Infusion into Hemophilia B Mice
Mice were anesthetized with 2.5% Avertin and injected intravenously with 0.25 μg/g body weight of recombinant proteins IX-6 (SEQ ID NO. 6), IX-7 (SEQ ID NO. 7) and IX-8 (SEQ ID NO. 8) to reach a hypothetical circulating level of 5 μg/ml, assuming the total plasma volume of a mouse be estimated by 1/10 of body weight. At 5 min, 15 min and 2 h after injections, mice were sacrificed and blood was collected into 3.8% sodium citrate (9:1 v/v) from the inferior vena cava. Plasma were prepared by centrifugation at 8,000 rpm (Eppendorf, 5415R) at room temperature for 10 minutes and subjected to analyses for protein mass by ELISA and clotting activity by aPTT assay.
Hydrodynamic Injection and Measurement of Human Factor IX Expression in Hemophilia B Mice
The cDNA's coding for recombinant factor IX (SEQ ID Nos. 9-16) were individually subcloned into pBS-HCRHP1-A (Miao C. H. et al., Mol. Ther. 2001; 3:947-957), for optimal expression in the liver of hemophilia B mice under the control of the human apolipoprotein E/C-I gene locus control region and the human alpha-1 antitrypsin promoter, as well as the truncated human factor IX intron 1 and the bovine growth hormone polyadenylation signal sequence for improved protein expression. Mice were anesthetized with 2.5% Avertin and aliquots (50-100 μg) of these expression plasmids (pBS-HCRHP1-A-FIX) were dissolved in 2 ml PBS (phosphate-buffered saline) and injected into the tail vein of 17 ̃24 g mice over a period of 6 ̃8 seconds. Each experiment with respective plasmid was repeated several times with at least two different batches of plasmid DNA prepared at different times. Blood samples were taken from inferior vena cava when necessary and made into plasma by dilution with 1/10 (v/v) of 3.8% sodium citrate. Human factor IX protein levels and clotting activity expressed and present in the mouse plasma were measured by ELISA and aPTT, respectively. Liver tissues were also prepared and measured for factor IX expression by ELISA. Total liver (1 ̃1.7 g) were homogenized in the presence of 2 ml of T-PER tissue protein extraction reagent (cat. #78510, Pierce) containing 5 μl/ml of protease inhibitor cocktail (Sigma). After centrifugation, the total protein in the supernatant of the extract was about 31.8±3.5 mg/ml which was subjected to ELISA for human factor IX levels.
Gene Transfer Experiments Using Pseudotyped ssAAV2/8 Vector
The coding sequences of IX-6 (SEQ ID NO: 14), and IX-7 (SEQ ID NO: 15) cDNA (1.4-kb in length, without 3′ untranslated region) were individually subcloned into pBS-HCRHP1-A, subsequently excised as a 4.3-kb SpeI fragment containing the entire expression cassette (enhancer, promoter, factor IX coding region and intron 1, and bovine growth hormone polyadenylation signal) and subcloned into pAAV-MCS (Stratagene, La Jolla, Calif.) at the NotI site converted to XbaI by ligation with linkers. The resultant plasmids consist of the entire expression cassette (4.3-kb SpeI fragment) flanked by the inverted terminal repeats (ITRs) of AAV2. The ssAAV2/8 vector carrying individual IX-6 and IX-7 expression cassettes were used to produce AAV viral particles by the Triple transfection method as previously described (Xiao X, et al. J. Virol. 1998; 72:2224-2232). The vector titers were determined by quantitative polymerase chain reaction (LightCycler 480, Roche Applied Science, Mannheim, Germany) using factor IX specific primers (forward: 5′-GGAAGCAGTATGTTGATGG-3′ and reversed: 5′-TGGTTCACAGGACTTCTGGT-3′) and expressed as vector genome (vg)/ml. Tail vein administration of viral particles into hemophilia B mice was performed with vector doses of 4×1012, 4×1011 or 8×1010 vg/kg body weight. These mice were sacrificed 2 weeks after tail vein injection of AAV particles. Blood samples were collected from inferior vena cava for plasma preparation. Human factor IX protein levels and clotting activities expressed and present in the mouse plasma were measured by ELISA and aPTT, respectively.
Results
Engineered Recombinant Factor IX Proteins Exhibited Higher Clotting Activity than Wild Type Factor IX (IX-7)
To search for factor IX variants with augmented clotting function, we selected 3 amino acid positions 86, 277, and 338, of human factor IX and replaced them singly or in combination with alanine. We expressed a total of 7 alanine-replaced factor IX variants in human 293 kidney cells. The expression levels of the mutated factor IX were quite equivalent to that of the wild type factor IX (IX-7) and approximated 0.08 ̃0.5 μg/24 h/106 cells. After purification, all the recombinant factor IX proteins revealed as a single band in SDS-PAGE with a mobility similar to that of plasma derived factor IX (FIG. 1). The identity of the recombinant proteins were verified and confirmed by amino acid sequence analysis revealing the first 5 residues of each recombinant (data not shown). The integrity of the IX-7 and alanine mutants was further investigated by activation of the recombinant factor IX proteins with factor XIa and with the factor VIa and tissue factor (VIIa·TF) complex, and inhibition by antithrombin III in the presence and absence of heparin. These experiments revealed no apparent differences between IX-7 and all the 7 alanine recombinants (data not shown). We conclude that alanine substitutions at positions 86, 277 and 338 did not alter the global structure of factor IX.
The clotting activity of the purified factor IX recombinants was shown in Table 1. Recombinant IX-7 was fully active and had a specific activity of 94%. All the factor IX mutants were also functional and had 1.1 ̃13 times more clotting activity than IX-7. Among all, factor IX-6 was the most active and had 13 times better than IX-7's clotting activities.







TABLE 1







Specific Clotting activity of purified factor IX.a










Clotting act.
Sp. Act.



(μg/ml)
(%)













IX-7
4.72 ± 0.81
 94 ± 16


IX-1
5.38 ± 0.50
115 ± 10


IX-2
5.96 ± 0.77
130 ± 15


IX-8
18.08 ± 0.14 
362 ± 3 


IX-3
6.34 ± 0.34
122 ± 7 


IX-4
8.51 ± 2.06
199 ± 41


IX-5
9.38 ± 3.30
188 ± 66


IX-6
66.04 ± 2.84 
1293 ± 57 





aThe recombinant factor IX was purified from 0.5~1 liters cultured supernatant of stably-transfected HEK 293 cells. The purified factor IX concentration was determined by Biuret method (BCA protein assay kit, Pierce) as described in legend to FIG. 1 and diluted to 5 μg/ml. The clotting activity was determined by the aPTT assays. Pooled normal human plasma in serial dilutions was used to generate the standard curves. The factor IX concentration in the pooled plasma was estimated to be 5 μg/ml. The specific activity of a sample was defined as the clotting activity divided by its mass in concentration and presented as percentage. The experiments were repeated 2 times.






The Increased Clotting Activity of IX-6 Correlated with its Affinity for Factor VIIIa.

Enzymatic kinetics parameters were measured with the factor IXa recombinants to investigate the influence of the alanine substitution on the clotting function of factor IXa. We assume that factor tenase activity is proportional to the concentration of the factor IXa in complex with factor VIIIa (FIXa·FVIIIa). Therefore, one could monitor the generation of factor Xa by the FIXa·FVIIIa complex as an indication for the binding affinity of factor IXa for factor VIIIa and calculate the apparent dissociation constant (Kd). As shown in Table 2, the Kd's for the three variants with single alanine mutations (IX-1, IX-2 and IX-8) and one of the variants with double mutations (IX-3) (1.20 nM ̃1.95 nM) are approaching that for IX-7 (2.44 nM). Surprisingly, the Kd's for the two with double mutations (IX-4 and IX-5) and the one with triple mutations (IX-6) (0.4 nM, 0.34 nM and 0.19 nM, respectively) were significantly lower than those for the IX-7 or the three single mutations. There is a 10-fold dramatic difference in Kd between IX-6 and IX-7. Moreover, it appears that IX-6 and factor VIIIa can form an efficient enzyme complex (0.144 nM) as compared with IX-7 and factor VIIIa (0.033 nM). These consequences, together with the better affinity between IX-6 and factor VIIIa than IX-7 and factor VIIIa, seem to justify the increased clotting activity of IX-6.
In the absence of factor VIIIa, the kinetic parameters, i.e., KM and kcat for all the recombinant mutants and IX-7 were very similar (Table 2), with kcat/KM around 240.59 ̃726.81 M−1sec−1. The result indicates that without factor VIIIa, factor IXa is a rather inefficient enzyme in cleaving factor X, which has been observed for activated IX-7 and so does for these factor IXa mutants.







TABLE 2





Kinetic parameters of factor Xa generation in the absence and presence of factor VIIIa.






















KM
Vmax
Enzymea
Kcatb ×
kcat/KM
Kd


Without FVIIIa
nM
nM FXa/min
nM
10−4
(M−1sec−1)
nM





IX-7
756.8 ± 102.6
0.16 ± 0.04
10
2.62 ± 0.59
352.95 ± 109.17


IX-1
531.9 ± 130.2
0.14 ± 0.03
10
2.25 ± 0.50
426.54 ± 35.84 


IX-2
395.3 ± 43.0 
0.07 ± 0.05
10
1.22 ± 0.86
303.54 ± 204.5 


IX-8
479.8 ± 44.0 
0.08 ± 0.04
10
1.37 ± 0.61
280.05 ± 108.00


IX-3
290.1 ± 54.58
0.12 ± 0.05
10
1.95 ± 0.77
726.81 ± 298.62


IX-4
479.0 ± 87.5 
0.08 ± 0.02
10
1.35 ± 0.41
278.40 ± 36.18 


IX-5
681.4 ± 151.1
0.10 ± 0.07
10
1.64 ± 1.11
240.59 ± 161.64


IX-6
742.8 ± 18.0 
0.17 ± 0.05
10
2.82 ± 0.85
380.68 ± 121.26






KM
Vmax
Enzymea
Kcatb ×
kcat/
Kd


With 0.4 nM FVIIIac
nM
nM FXa/min
nM
1
KM × 108
nM





IX-7
54.04 ± 5.25 
27.81 ± 0.66 
0.033
14.17 ± 0.34 
2.64 ± 0.21
2.44


IX-1
55.39 ± 10.57
15.11 ± 0.90 
0.049
5.09 ± 0.30
0.93 ± 0.12
1.42


IX-2
44.27 ± 2.15 
29.74 ± 0.42 
0.056
8.89 ± 0.13
2.01 ± 0.07
1.20


IX-8
44.79 ± 8.33 
28.41 ± 3.34 
0.052
9.08 ± 1.07
2.04 ± 0.14
1.32


IX-3
35.17 ± 3.19 
34.12 ± 1.13 
0.039
14.56 ± 0.48 
4.16 ± 0.28
1.95


IX-4
80.95 ± 13.15
46.78 ± 8.02 
0.106
7.36 ± 1.26
0.91 ± 0.04
0.40


IX-5
116.53 ± 12.45 
148.81 ± 14.03 
0.114
17.93 ± 6.72 
2.12 ± 0.44
0.34


IX-6
46.01 ± 10.53
52.26 ± 10.22
0.144
6.07 ± 1.19
1.33 ± 0.10
0.19





aThe concentration of factor IXa-VIIIa complex was derived from experimental conditions and observed Kd


bkcat = Vmax/[enzyme], the unites are M FXa, M−1FIXa(or FIXa-FVIIIa), s−1


cThe reaction was incubated with 0.4 nM factor VIIIa and 0.25 nM factor IXa to activate 0-200 nM factor X in the presence of 0.5 mM Spectrozyme FXa, 40 μM PCPS and 5 mM Ca2+.


# ND: not determined






Recombinant IX-6 was More Active than IX-7 In Vivo.

To evaluate the effectiveness of the recombinant factor IX in vivo, we infused IX-6, IX-7, and IX-8 proteins into hemophilia B mice and followed the protein levels and clotting function of the proteins by analyzing the plasma samples at timed intervals. As shown in Table 3, when approximately 1 μg/ml of IX-7 protein was detected in the plasma of the hemophilia B mice at 5 min after tail vein injection of 10 μg recombinant protein in 20 g mice, the level decreased to 76% initial levels at 15 min and to 18% initial at 2 h. The circulating factor IX-7's clotting activity at each timepoint ranged around 121 ̃483% protein mass. Parallel experiments with IX-6 and IX-8 revealed that while comparable to IX-7's protein levels were detected at each time point in mice infused with IX-8 and IX-6, the mice infused with recombinant IX-8 exhibited 2.4 (5 min's sample)  ̃3.67 (2 h's) times, respectively, more clotting function than those infused with IX-7. In consistent with in-vitro's experimental findings with IX-6, hemophilia B mice infused with IX-6 exhibited a much higher than IX-7's activity, approximately 2.6 ̃7.5 times more than IX-7's specific activity throughout each time point [IX-7 versus IX-6, (2.91/1.15) versus (12.05/0.72) for 5 min's data as an example].







TABLE 3







Time course study of plasma factor IX levels in mice infused with


recombinant factor IX proteins.*











IX-7 (n = 4)
IX-8 (n = 2)
IX-6














Clotting act.
IX:Ag
Clotting act.
IX:Ag
Clotting act.
IX:Ag







μg/ml (% of first time point)
















 5 min.
2.91 ± 1.2
 1.15 ± 0.2 (100)
6.98 ± 1.4
 0.92 ± 0.1 (100)
12.05 ± 4.4 
 0.72 ± 0.1 (100) (n = 5)


 15 min.
2.63 ± 1.0
0.88 ± 0.3 (76)
5.24 ± 2.7
0.86 ± 0.1 (94)
6.74 ± 1.4
0.55 ± 0.2 (77) (n = 4)


120 min
0.64 ± 0.4
0.21 ± 0.2 (18)
2.35 ± 0.2
0.36 ± 0.0 (39)
4.80 ± 3.1
0.45 ± 0.1 (62) (n = 3)





*Approximately 10 μg factor IX was injected into each mouse to reach hypothetical protein concentration of 5 μg/ml plasma. Blood samples were taken at different time points after injection and subjected to ELISA and clotting assay. Standard curves were derived from serial dilutions of normal plasma in parallel experiment. ELISA system used pAb from ERL (Gafix-AP160) as coating antibody and ERL pAb-HRP (Gafix-HRP) as detecting antibody. Normal plasma factor IX concentration is assumed to be 5 μg/ml.






Gene Delivery to Hemophilia B Mice by Hydrodynamic Injection Method

The efficacy of the factor IX mutants for the treatment of hemophilia B was also evaluated by the method of hydrodynamic injection of expression plasmids carrying individual cDNAs into hemophilia B mice for expression of the factor IX mutants predominantly by the liver. The expression levels were measured 24 h after DNA injection and shown in FIG. 2 and Table 4. Recombinant IX-7 and all the alanine replacement mutants except IX-6 were expressed and secreted into plasma at a protein level of 0.7 ̃1.17 μg/ml and clotting activity of 0.46 ̃2.26 μg/ml. IX-6 had reproducibly higher protein levels (3.22±0.58 μg/ml, n=4) and clotting activities (12.34±2.87 μg/ml, n=4) than IX-7 and the other alanine mutants. Interestingly, IX-6 also had 6 times (clotting activity) and 2 times (specific activity, i.e., IX:Ag/clotting) higher activity than IX-8. The higher factor IX protein levels found in mice injected with IX-6 DNA than with IX-7 and the other mutants was not observed with the cell culturing expression system which indicated that IX-7 and IX-6 were synthesized to similar levels. To further investigate possible explanations for the higher plasma factor IX protein levels in the mice injected with IX-6 than with IX-7 DNA, we extracted and quantified the intracellular and circulating factor IX in the liver and plasma, respectively. As shown in Table 4 approximately equal amount of factor IX was extracted from the liver of mice treated with IX-6 and IX-7 DNA (1.18 and 1.36 μg/g liver, respectively, p=0.43). These data indicated that IX-6 DNA- and IX-7 DNA-injected mice had comparable amount of intracellular factor IX in the liver. Interestingly, the IX-6 DNA-treated mice had statistically more circulating factor IX than IX-7 DNA-treated mice (1.5 times difference, p<0.01, n=7 ̃10). More importantly, the plasma clotting activity of IX-6 DNA-mice is 15 times higher than that of the IX-7 DNA-treated mice (4.88±2.12 μg/ml vs 0.31±0.15 μg/ml, Table 4).







TABLE 4







Factor IX levels in mice hydrodynamically injected with plasmids.*











plasma











Liver

Clotting act. (μg/ml)












Total protein (mg)
IX:Ag (μg)
IX:Ag (μg/ml)
(Sp. Act. %)















IX-7 (n = 7)
60.92 ± 7.02
1.34 ± 0.76
0.20 ± 0.08
0.31 ± 0.15 (154 ± 33)


IX-6 (n = 10)
65.73 ± 7.76
1.60 ± 0.61
0.34 ± 0.10
4.88 ± 2.12 (1411 ± 357)





*Hydrodynamic delivery of factor IX expression plasmids into hemophilia B mice. Male hemophilia B mice of 20 μg were subjected to hydrodynamic shock by tail vein injection of 2 ml of 100 μg DNA in 6-8 s. The mice were recovered and sacrificed 24 h after injection for collection of blood plasma for clotting assay by aPTT and protein levels by ELISA (IX:Ag). For ELISA system, plates were coated with pAb from ERL (Gafix-AP160) and ERL pAb-HRP (Gafix-HRP) was used as detecting antibody. Standard curve was derived from serial dilutions of normal plasma. Normal plasma factor IX concentration is assumed to be 5 ug/ml.






Gene Transfer Experiments Using Pseudotyped ssAAV2/8 Vector

The efficacy of IX-6 in gene therapy was further investigated using viral vectors. The hemophilia B mice were injected intravenously with recombinant adeno-associated viral vectors (rAAV2/8) carrying individual IX-6, and IX-7 at a dose of 4×1012 vg/kg. At two weeks after injection, the plasma factor IX protein level expressed by rAAV2/8 carrying IX-7 was about 2.3 ̃7.8 μg/ml (n=5) (FIG. 3a). Compared with IX-7, the factor IX level expressed by rAAV2/8 carrying IX-6 reached 1.58 ̃4.23 μg/ml (n=6). It appears that rAAV2/8 carrying IX-6 had lower factor IX protein level in mouse plasma than those carrying IX-7. In contrast, the specific clotting activity of IX-6 (495±109%) is 5 times higher than that of IX-7 (94±34%). We also evaluate the efficacy of IX-6 when delivered at lower doses of viral vectors (at 4×1011 vg/kg and 8×1010 vg/kg, respectively). As shown in FIG. 3b, the specific activity measured from mice injected with rAAV2/8 carrying IX-6 reach 1236±418% (4×1011 vg/kg) and 1129±479% (8×10 vg/kg), and the specific activity measured in those mice injected with rAAV2/8 carrying IX-7 is approximately 192±24% (4×10 vg/kg) and 246±116% (8×10 vg/kg) for the two doses. At the lowest dose, one of the mice injected with IX-6 had 38% normal clotting activity and all 4 mice are above or nearly above the 10% therapeutic level. In contrast, the mice injected with IX-7 had only 5.6% and 7.4% normal clotting activity. The result further demonstrated that IX-6 can be an effective reagent when low dose of viral vector is preferred to reduce the formation of anti-viral antibodies.
The foregoing is illustrative of the present invention, and is not to be construed as limiting thereof. The invention is defined by the following claims, with equivalents of the claims to be included therein.

## Claims

1. A recombinant human Factor IX (FIX) protein comprising the amino acid sequence of SEQ ID NO: 7, except for amino acid substitution(s) at one or more positions of SEQ ID NO: 7 selected from the group consisting of: substitution at position 86, substitution at position 277, substitution at positions 86 and 277, substitution at positions 86 and 338, substitution at positions 277 and 338, and substitution at positions 86, 277 and 338.

2. The recombinant human FIX protein of claim 1, wherein the amino acid substitution(s) is at least one residue selected from the group consisting of: alanine, asparagine, aspartic acid, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, methionine, phenylalanine, serine, threonine, tryptophan, tyrosine and valine.

3. The recombinant human FIX protein of claim 2, wherein the residue is alanine.

4. The recombinant human FIX protein of claim 1, comprising the amino acid sequence of SEQ ID NO: 6.

5. The recombinant human FIX protein of claim 1, wherein said protein comprises a 2 fold to 14 fold more blood clotting activity compared to the wild type human Factor IX protein.

6. The recombinant human FIX protein of claim 1, said protein comprising enhanced affinity with Factor VIIIa.

7. The recombinant human FIX protein of claim 4, said protein comprising a Kd value of 0.1 to 0.5 nM.

8. The recombinant human FIX protein of claim 4, said protein comprising a Km value of 32 to 128 nM.

9. A pharmaceutical composition comprising the recombinant human FIX protein of claim 1 and a pharmaceutically acceptable carrier, excipient or diluent.

10. A method for treating hemophilia comprising administering to a patient in need thereof an effective amount of the recombinant human FIX protein of claim 1.

11. The method of claim 10, wherein the administering is by injection.