WO2015054439A2 - Hybrid factor viii polypeptides for use to treat hemophilia a - Google Patents

Hybrid factor viii polypeptides for use to treat hemophilia a Download PDF

Info

Publication number
WO2015054439A2
WO2015054439A2 PCT/US2014/059787 US2014059787W WO2015054439A2 WO 2015054439 A2 WO2015054439 A2 WO 2015054439A2 US 2014059787 W US2014059787 W US 2014059787W WO 2015054439 A2 WO2015054439 A2 WO 2015054439A2
Authority
WO
WIPO (PCT)
Prior art keywords
hrfviii
amino acid
fviii
seq
naturally occurring
Prior art date
Application number
PCT/US2014/059787
Other languages
French (fr)
Other versions
WO2015054439A3 (en
Inventor
Tommy E. Howard
Vincent La Terza
Original Assignee
Haplomics, Inc.
The Regents Of The University Of California
Department Of Veterans Affairs
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Haplomics, Inc., The Regents Of The University Of California, Department Of Veterans Affairs filed Critical Haplomics, Inc.
Publication of WO2015054439A2 publication Critical patent/WO2015054439A2/en
Publication of WO2015054439A3 publication Critical patent/WO2015054439A3/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/745—Blood coagulation or fibrinolysis factors
    • C07K14/755—Factors VIII, e.g. factor VIII C (AHF), factor VIII Ag (VWF)

Definitions

  • HYBRID FACTOR VIII POLYPEPTIDES FOR USE TO TREAT HEMOPHILIA
  • the present disclosure is directed to hybrid recombinant factor VIII polypeptides (hrFVIII), nucleic acids, including cDNAs, encoding said recombinant factor VIII polypeptides, cells comprising nucleic acids encoding hrFVIII polypeptides, and methods of using such hrFVIII polypeptides.
  • FVIII factor VIII replacement therapies
  • pdFVIII extracted and pooled human plasma-derived FVIII
  • rFVIII recombinant FVIII
  • inhibitors which reduces the effectiveness of the FVIII replacement or, in the worst case, renders the replacement ineffective (Lacroix-Desmazes et al., Pathophysiology of inhibitors to FVIII in patients with haemophilia A. Haemophilia 2002: 8: 273-9). In hemophilia A patients of African- American descent, inhibitors occur in approximately 50% of individuals following FVIII replacement therapy.
  • a recombinant r-porcine FVIII product is in late stage clinical testing sponsored by Ipsen and Inspiration Biopharmaceuticals.
  • OBI r-porcine FVIII product
  • plasma derived porcine FVIII Hyate:C®
  • OBI may be immunogenic and induce neutralizing antibodies after multiple infusions.
  • Hybrid recombinant factor VIII polypeptides (hrFVIII) disclosed herein provide effective functionality of a FVIII protein, sufficiently reduce or eliminate antigenicity in HA patients, and restore hemostasis would be a useful treatment for HA patients.
  • the hrFVIII disclosed herein provides an valuable alternative for the treatment of HA.
  • hybrid recombinant FVIII polypeptides comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring nonsynonymous -Single Nucleotide Polymorphisms (ns-SNP); cDNAs encoding such hrFVIII; expression vectors comprising nucleic acids encoding such hrFVIII, cells comprising expression vectors comprising nucleic acids encoding such hrFVIII; and methods of treating subjects having hemophilia A by administering to the subject such hrFVIII.
  • ns-SNP nonsynonymous -Single Nucleotide Polymorphisms
  • the hrFVIII disclosed herein have non-naturally occurring combinations of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, or 15 amino acid modifications selected from the group consisting of: Glul 13Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser.
  • the hrFVIII can be full length, having a B-domain deletion (BDD), having a B- domain deletion 2 (BDD-2), or having a B-domain deletion 3 (BDD-3).
  • an expression vector comprising a complementary DNA (cDNA) encoding a hrFVIII comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns-SNP.
  • cDNA complementary DNA
  • the cDNA encodes a hrFVIII comprising non-naturally occurring combination comprising between 2 and 15 amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser, as described above.
  • a mammalian cell comprising a nucleic acid encoding a hrFVIII described herein.
  • the cell comprises a complementary DNA (cDNA) encoding a hrFVIII comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns-SNP.
  • cDNA complementary DNA
  • the cDNA encodes a hrFVIII comprising non-naturally occurring combination comprising between 2 and 15 amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser, as described above.
  • the cDNA encodes a hrFVIII lacking the B-domain of wild-type FVIII as described above.
  • the cDNA is contained in an expression vector.
  • the cell is a Chinese Hamster Ovary (CHO) cell.
  • the cell is an African green monkey (COS -7) cell.
  • the cell is a human cell.
  • the human cell is a selected from the group consisting of Hek293, Per-C6, CAP, HKB-11 , and HT-1080 cells.
  • a method for treating a subject suffering from Hemophilia A comprising administering to the subject an effective amount of a hrFVIII described herein.
  • the immunoreactivity of hrFVIII polypeptide described herein in a subject containing inhibitors to an existing FVIII replacement product is determined.
  • hybrid recombinant FVIII polypeptides comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns-SNP; cDNAs encoding such hrFVIII; expression vectors comprising nucleic acids encoding such hrFVIII, cells comprising expression vectors comprising nucleic acids encoding such hrFVIII.
  • Figure 1 depicts the polymorphisms within the human F8 gene, which encode several structurally distinct FVIII proteins referred to as haplotypes. As illustrated, existing FVIII therapeutics only target the HI and H2 forms.
  • Figure 2 illustrates that several polymorphic FVIII ns-SNPs reside within the B-cell immunodominant inhibitor (IDI)-epitopes of alio- and auto-antibodies found commonly in plasma from inhibitor patients with congenital and acquired HA.
  • IDI B-cell immunodominant inhibitor
  • A The variable residues R484H and M2238V, which are encoded by the two common Black-restricted ns-SNPs (G1679A and A6940G), are located in the A2- & C2-domain IDI-epitopes respectively.
  • B The alleles of three ns-SNPs define the primary amino acid sequence of hrFVIII products disclosed herein.
  • Figure 3 illustrates an expression vector capable of expressing the hrFVIII described herein.
  • Figure 4 illustrates the construction of Human FVIII B-Domain Deleted-2 (BDD-2) polypeptides for FVIII Haplotypes HI, H3, H4, and H3/H4.
  • Figure 5 illustrates the construction of the Human FVIII Haplotype H3 B-Domain Deleted-2 (BDD-2) polypeptide.
  • Figure 6 illustrates the construction of the Human FVIII Haplotype HI B-Domain Deleted-2 (BDD-2) polypeptide.
  • Figure 7 illustrates the construction of the Human FVIII Haplotype H3/H4 B-Domain Deleted-2 (BDD-2) polypeptide.
  • Figure 8 illustrates the construction of the Human FVIII Haplotype H4 B-Domain Deleted-2 (BDD-2) polypeptide.
  • subject can include domesticated animals, such as cats, dogs, etc., livestock (e.g., cattle, horses, pigs, sheep, goats, etc.), laboratory animals (e.g., mouse, rabbit, rat, guinea pig, etc.) and birds.
  • livestock e.g., cattle, horses, pigs, sheep, goats, etc.
  • laboratory animals e.g., mouse, rabbit, rat, guinea pig, etc.
  • the subject is a mammal such as a primate, for example, a human.
  • Amount effective and "effective amount” in the context of a composition or dosage form for administration to a subject refers to an amount of the composition or dosage form that produces one or more desired responses in the subject, for example, provide effective functionality of a FVIII protein, sufficiently reduce or eliminate antigenicity in HA patients, and restore hemostasis. Therefore, in some embodiments, an amount effective is any amount of a composition provided herein that produces one or more of these desired hemostasis responses with minimal immunogenicity. The amount are one that a clinician believe to have a clinical benefit for a subject in need of FVIII replacement.
  • Effective amount can involve only improving the patient's hemostasis with minimal immunogenicity, although in some embodiments, it involves restoring hemostasis completely.
  • An amount that is effective can also be an amount of a composition provided herein that produces a desired therapeutic endpoint or a desired therapeutic result. Effective amount result in hemostasis of a subject after the administration of hrFVIII. The achievement of any of the foregoing are monitored by routine methods.
  • the effective amount is one in which the desired hemostasis response persists in the subject for at least 1 week, at least 2 weeks, at least 1 month, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 9 months, at least 1 year, at least 2 years, at least 5 years, or longer.
  • the effective amount is one which produces a measurable desired hemostasis response, for example, a measurable increase in hemostasis in the patient for at least 1 week, at least 2 weeks, at least 1 month, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 9 months, at least 1 year, at least 2 years, at least 5 years, or longer.
  • Effective amount will depend, of course, on the particular subject being treated; the severity of a condition, disease or disorder; the individual patient parameters including age, physical condition, size and weight; the duration of the treatment; the nature of concurrent therapy (if any); the specific route of administration and like factors within the knowledge and expertise of the health practitioner.
  • Dosage form means a pharmacologically and/or immunologically active material in a medium, carrier, vehicle, or device suitable for administration to a subject.
  • “Pharmaceutically acceptable excipient” means a pharmacologically inactive material used together with the hrFVIII and carriers to formulate the inventive compositions.
  • Pharmaceutically acceptable excipients comprise a variety of materials known in the art, including but not limited to saccharides (such as glucose, lactose, and the like), preservatives such as antimicrobial agents, reconstitution aids, colorants, saline (such as phosphate buffered saline), and buffers.
  • Protocol refers to any dosing regimen of one or more substances to a subject.
  • a dosing regimen may include the amount, frequency and/or mode of administration.
  • such a protocol may be used to administer one or more compositions disclosed herein to one or more subjects. Hemostasis responses in these subjects can then be assessed to determine whether or not the protocol was effective in restoring hemostasis with minimal immunogenicity. Any other therapeutic and/or prophylactic effect may also be assessed instead of or in addition to the aforementioned hemostasis responses. Whether or not a protocol had a desired effect are determined using any of the methods provided herein or otherwise known in the art.
  • a blood sample may be obtained from a subject to which a composition provided herein has been administered according to a specific protocol in order to determine whether or not hemostasis has been restored.
  • Useful methods for detecting the presence and/or number of inhibitors include a haplotype-specific version of the Nijmegen-modified Bethesda assay, Bethesda assay, ELISA assays, ELISPOT assays, and other similar type assays.
  • haplotype refers to a combination of DNA sequences that are closely linked on one chromosome and are commonly inherited together.
  • the gene encoding FVIII (F8) is polymorphic in the human population, yet there are four common non- synonymous single nucleotide polymorphisms (nsSNPs), that together with two infrequent nsSNPs define eight haplotypes of the F8 gene, referred to as haplotype (H)l , H2, H3, H4, H5, H6, H7, and H8.
  • haplotype (H)l haplotype
  • H2 H3, H4 H5 H6, H7
  • H8 haplotype
  • B-domain deleted FVIII (BDD-FVIII or BDDFVIII) or the like refers to a protein that by virtue of recombinant genetic engineering comprises a FVIII protein in which the B domain of FVIII or some portion of the B domain of FVIII has been removed from the sequence of FVIII resulting in a functional recombinant FVIII protein.
  • Toole, J. J. et al. A large region (approximately equal to 95 kDa) of human factor VIII is dispensable for in vitro procoagulant activity. Proc Natl Acad Sci U S A 83, 5939-5942 (1986)).
  • Synthetic linker refers to a sequence of DNA that by virtue of recombinant DNA techniques is introduced into the gene-encoding sequence of a gene, which DNA sequence is not present in the naturally -occurring sequence of the gene, and which DNA sequence serves the purpose of tying together an upstream and downstream portion of the gene and is necessitated when using recombinant DNA techniques to delete a domain or a portion of a domain of the gene.
  • Single nucleotide polymorphism refers to a variation of one nucleotide (Adenine, Guanine, Cytosine, or Thymine) in the DNA sequence on a chromosome in the genome of an individual that differs from the nucleotide in the DNA sequence of either another chromosome of that individual or a chromosome of another individual.
  • nsSNP non-synonymous single nucleotide polymorphism
  • SNP refers to a SNP in the gene -encoding region of a chromosome that by the nature of its position in the gene-encoding region of a chromosome yields a change in the amino acid sequence of the protein encoded by the gene.
  • immunogen A substance that is capable of initiating an immune response that is directed against that substance is referred to as an immunogen.
  • immunogen refers to the ability of any particular substance to induce an immune response, where a substance that is highly immunogenic in turn easily induces an immune response.
  • An antigen is a substance that can be bound with specificity by molecules of the immune system. While all immunogens are antigens, not all antigens are immunogens; this is to say that some substances, while not capable of initiating an immune response, are nonetheless capable of being bound by molecules of the immune system.
  • antigenicity refers to the ability of any particularly substance be bound by molecules of the immune system.
  • the human F8 gene is polymorphic and encodes several structurally distinct FVIII proteins referred to as haplotypes. Sequencing studies of the F8 gene have revealed four common nsSNPs that, together with two infrequent ns-SNPs, encode eight distinct wild-type FVIII proteins referred to as haplotype HI, H2, H3, H4, H5, H6, H7, and H8. The variants, their associated ns-SNP, their distribution in black, Chinese, and white populations, and inhibitor development are illustrated in Figure 1 , panel A&B.
  • hrFVIII polypeptides are provided herein that provide lower immunogenicity as compared to the current replacement FVIII product, and may allow the evasion of previously developed inhibitors.
  • the treatment of subjects with inhibitors using the hrFVIII of disclosed herein provide an alternative replacement product and to the induction of immune tolerance therapy, which is currently done through laborious and expensive methods requiring multiple administrations of high levels of replacement FVIII.
  • HA patients with haplotypes that deviate from H 1 or H2 may be more prone to the development of neutralizing antibodies upon administration of recombinant FVIII products due to the presence of differing amino acid attributable to haplotype differences. It is particularly noteworthy that most neutralizing anti-FVIII alloantibodies in many congenital HA inhibitor patients are directed against two regions of the human FVIII protein that are variable among individuals of Black African descent ( Figure 1 & Figure 2A), which comprise a particularly vulnerable portion of the HA patient population.
  • the hrFVIII disclosed herein have combinations of modifications based on naturally-occurring human haplotypes, allowing for the generation of functional FVIII.
  • Antibodies directed against the currently available recombinant FVIII product's A2- domain IDI-epitope, which is bounded by and inclusive of the Arginine at residue -484 (R484) and the Isoleucine at residue-508 (1508), are noncompetitive inhibitors of the FVIIIa/FIXa intrinsic-Xase enzyme complex.
  • FVIII antibodies directed against the C2- domain IDI-epitope block the binding of FVIIIa to phospholipid. Inhibitor neutralization studies indicate that the effects of anti-A2 and anti-C2 inhibitors are additive.
  • inhibitors to a given domain appear to act independently of inhibitors to other domains.
  • the FVIII IDI -epitopes of alloantibody and autoantibody inhibitors appear to be the same, though autoantibody plasmas are more likely to be specific for an epitope in either the A2-domain or the C2- domain.
  • FVIII epitopes some have domain specific antibodies.
  • electrostatic effects, hydrogen bonding and steric considerations may impact protein -protein (antibody-antigen) interactions.
  • protein -protein antibody-antigen
  • meaningful distinctions may be made between the a-side chains of arginine and histidine as well as of methionine and valine (Met2238Val) with respect to these criteria.
  • Arginine possesses a guanidinium functional group that is highly basic with a pKa of >12. It has a delocalized positive charge and can make multiple hydrogen bonds.
  • Histidine, with its imidazole side chain is only weakly basic with a pKa of 6.5.
  • the hrFVIII polypeptides disclosed herein provide functional FVIII polypeptides that avoid specific antibody-antigenic interactions at specific domains wherein a subject could or has previously developed antibodies.
  • a recombinant FVIII polypeptide in which all of the known and suspected antigenic FVIII ns-SNP are replaced by alanine is designed and termed "Low immunogenicity universal donor No. 1" in Table 1 below.
  • Alanine is the simplest chiral amino acid, consisting of a single methyl side -chain group, the lack of chemical reactivity of which is thought to contribute to a lower immunogenicity profile than all other amino acids.
  • ns-SNPs non-naturally occurring amino acid modifications encoded by the ns-SNPs could be combined into a large number of possible hybrids that would have fewer changes than, for example, the porcine FVIII replacement products, leading to a less immunogenic recombinant FVIII for replacement therapy.
  • the hrFVIII polypeptides disclosed herein contain significant and distinct amino acid modifications compared to the HI and H2 F8 haplotypes and thus provide important alternatives to current replacement therapies.
  • These hybride FVIII can therefore be used as an initial replacement FVIII product, or as alternative FVIII product that can be administered to inhibitor patients (patients with antibodies to the currently marketed HI or H2 Haplotype products).
  • hydrid recombinant FVIII polypeptides comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns-SNP.
  • the recombinant FVIII polypeptides provided herein have non-naturally occurring combinations of two to fifteen amino acid modifications, for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 amino acid modifications, selected from the group consisting of: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser.
  • amino acid modifications for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 amino acid modifications, selected from the group consisting of: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl24
  • the hrFVIII polypeptides contemplated herein contain combinations of modifications at least 2 or more of the naturally occurring ns-SNP sites, creating non- naturally occurring hrFVIII polypeptides.
  • the 2 or more modifications are selected from the following: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser, wherein the remainder of the full length hrFVIII comprises the HI wild -type sequence, provided in SEQ ID No: 101.
  • the remainder of the full length hrFVIII comprises amino acid sequence that are homologous to the HI wild -type sequence, for example, at least about 90%, 91%, 92%>, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous.
  • additional modifications are made to the HI wild-type amino acid sequence based on ns-SNPs other than those listed, or alanine substitutions at amino acids of particular antigenicity or immuno genicity .
  • Table 1A Examples of hrFVIII polypeptides provided herein comprising various amino acid modifications compared to the FVIII HI wild -type amino acid sequence are summarized in Table 1A below. Specifically, Table 1 discloses 17 separate full-length recombinant FVIII constructs (FL-rFVIII). The first construct listed is HI (Kogenate). HI is the most common haplotype of FVIII in humans, and for these studies the sequence of HI provides the template construct upon which amino acid changes are made to give rise to the other constructs in the table.
  • H4 is identical in sequence over its entire length compared to HI, with the exception of two amino acid modifications: Arg484His and Aspl241Glu. Taking the sum of modifications from H3 and H4, there are three total modifications (as they have a single modification in common) and a chimera is formed by combining these three modifications into a single construct.
  • This particular construct is the tenth entry in the table and is labeled H3/H4.
  • the H3/H4 construct is identical in sequence over its entire length compared to HI, with the exception of three amino acid modifications: Arg484His, Aspl241Glu, and Met2238Val. Other chimeras are also displayed in the table and are constructed from combinations of the modifications present in haplotypes H3-H9.
  • the hrFVIII polypeptides disclosed herein include, for example, H3/H4, H3/H4/H6, H3/H4/H6/H7, H3/H4/H6/H7/H8, H3/H4/H6/H7/H8/H9, low antigenicity universal donor No. 1, low antigenicity universal donor No. 2, and low immunogenicity universal donor No. 1.
  • the amino acid sequences in the naturally occurring HI & H2 forms of FL hFVIII are contained in the existing FL therapeutic FVIII proteins Kogenate® (also known as Helixate®) and Recombinate® (also known as Advate®).
  • the primary amino acid sequences of 10 of the distinct FL hFVIII proteins and the nucleic acid sequences of the cDNAs that encode them are indicated in Table 1A above in the columns designated "SEQ ID NO (protein)" and “SEQ ID NO (cDNA)", respectively.
  • amino acid residue(s) bolded and highlighted grey in the haplotypic forms of the FL h-rFVIII protein listed represent the naturally-occurring variable positions in the human FVIII protein and indicate how each of these sixteen hrFVIII are distinct allelically from the currently used therapeutics, Kogenate® and Recombinate®.
  • the hrFVIII comprises a non-naturally occurring combination comprising two amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising three amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising four amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising five amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising six amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising seven amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising eight amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising nine amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising ten amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising eleven amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising twelve amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising thirteen amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising fourteen amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises a non-naturally occurring combination comprising fifteen amino acid modifications: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser.
  • the hrFVIII comprises the amino acid modifications Arg484His, Aspl241Glu, and Met2238Val, creating an H3/H4 FVIII hybrid, the amino acid sequence of which is provided in SEQ ID NO: 1.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 1.
  • the hrFVIII comprises the amino acid modifications Arg484His and Met2238Val, creating an alternative H3/H4 FVIII hybrid, the amino acid sequence of which is provided in SEQ ID NO: 13.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 13.
  • the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 2.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 2.
  • the hrFVIII comprises the amino acid modifications Arg484His, Arg776Gly, Aspl241Glu, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 15.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 15. The modifications described herein are further illustrated in Table 1 above.
  • the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 16.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 16. The modifications described herein are further illustrated in Table 1 above.
  • the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, Hisl919Asn, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 17.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 17.
  • the modifications described herein are further illustrated in Table 1 above.
  • low antigenicity universal donor hrFVIII polypeptides and nucleic acids encoding said polypeptides are provided.
  • the low antigenicity hrFVIII polypeptide comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, and Met2238Val, and the additional modifications Glul l3Asp, Ala387Thr, Argl l07Trp, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Pro2292Ser, the amino acid sequence of which is provided in SEQ ID NO: 18.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 18.
  • the modifications described herein are further illustrated in Table 1 above.
  • the low antigenicity universal donor hrFVIII polypeptide comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Argl260Lys, and Met2238Val, and the additional modifications Glul l3Asp, Ala387Thr, Argl l07Trp, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Pro2292Ser, the amino acid sequence of which is provided in SEQ ID NO: 19.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 19.
  • the modifications described herein are further illustrated in Table 1 above.
  • a further aspect includes a low immunogenicity universal donor No. 1 hrFVIII polypeptide, and nucleic acids encoding said polypeptides, comprising the amino acid modifications Gln334Ala, Gln334Ala, Arg484Ala, Arg776Ala, Asp 1241 Ala, Argl260Ala, and Met2238Ala, and the additional modifications Glul l3Ala, Argl l07Ala, Leul462Ala, Ilel668Ala, His 1919Ala, Glu2004Ala, Val2223Ala, and Pro2292Ala, the amino acid sequence of which is provided in SEQ ID NO: 20.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 20.
  • the modifications described herein are further illustrated in Table 1 above.
  • an isolated or recombinant polypeptide herein identified as Haplotype 9, and a nucleic acid encoding said polypeptide is provided comprising the amino acid modifications Aspl241Glu and His l919Asn, the amino acid sequence of which is provided in SEQ ID NO: 33.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 33.
  • This Haplotype 9 FVIII polypeptide is further illustrated in Table 1 above.
  • hrFVIII polypeptides comprising a FVIII polypeptide wherein at least a portion of the B-domain has been deleted, further comprising amino acid modifications at ns-SNP positions compared to the currently available BDD- FVIII products.
  • Table IB B-domain-deleted (BDD) human hrFVIII using engineered junction BDD-1.
  • BDD-1 10 distinct BDD FVIII proteins is called BDD-1 and corresponds to that found in the existing therapeutic BDD-1 rFVIII protein known as Refacto® or Xyntha® (Moroctocog alfa).
  • BDD- 1 is an engineered junction created by linking (via peptide bond formation) the FVIII serine (Ser [S]) and glutamine (Glu [Q]) residues at positions 743 and 1638, respectively, in the mature circulating form of the FVIII protein (i.e., S 743 - Q 1638 ), which results in a protein containing 1,438 amino acids.
  • BDD-2 10 BDD FVIII proteins is called BDD-2 and corresponds to that found in the existing therapeutic BDD-2 rFVIII protein known as Novo8® (Turoctocog alfa).
  • BDD-2 is an engineered junction created by linking (via peptide bond formation) the FVIII serine (Ser [S]) and glutamine (Glu [Q]) residues at positions 750 and 1638, respectively, in the mature circulating form of the FVIII protein (i.e., S 750 - Q 1638 ), which results in a protein containing 1,445 amino acids.
  • BDD-3 the BDD junction in these 10 BDD rFVIII proteins is called BDD-3 and corresponds to that found in the existing therapeutic BDD-3 rFVIII protein known as Octopharma8® (Simoctocog alfa).
  • BDD-3 is an engineered junction created by linking (via 2 peptide bond formations) the FVIII histidine (His [H]) and glutamate (Glu [E]) residues at positions 748 and 1649, respectively, in the circulating mature FVIII protein to the N- and C-terminal ends of the synthetic, non-FVIII octapeptide sequence QAYRYRRG (i.e., H 748 - QAYRYRRG - E 1649 ), which results in a protein containing 1,440 amino acids.
  • QAYRYRRG i.e., H 748 - QAYRYRRG - E 1649
  • the amino acid residue(s) bolded and highlighted grey in the haplotypic forms of the BDD-3 rFVIII protein listed represent the naturally-occurring variable positions in the human FVIII protein and indicate how each of these nine hrFVIII are distinct allelically from the currently used therapeutic, which is referred to as Octopharma8®.
  • the hrFVlll comprises the amino acid sequence of SEQ ID NO: 3, provided herewith.
  • a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 3.
  • the hrFVlll comprises the amino acid sequence of SEQ ID NO: 4 provided herewith.
  • a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 4.
  • the hrFVlll comprises the amino acid modification Gln334Pro (H7). In one embodiment, the hrFVlll comprises the amino acid sequence of SEQ ID NO: 5 provided herewith. In one embodiment, a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 5. In one embodiment, the hrFVlll comprises the amino acid modifications Arg484His and Met2238Val (H3/H4). In one embodiment, the hrFVlll comprises the amino acid sequence of SEQ ID NO: 6 provided herewith.
  • a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 6.
  • the hrFVlll comprises the amino acid modifications Gln334Pro, Arg484His, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 21.
  • a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 21.
  • the hrFVlll comprises the amino acid modifications Gln334Pro, Arg484His, His l919Asn, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 22.
  • a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 22.
  • the hrFVlll comprises the amino acid modifications Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser, the amino acid sequence of which is provided in SEQ ID NO: 23.
  • a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 23.
  • the hrFVlll comprises the amino acid modifications Glul l3Ala, Gln334Ala, Arg484Ala, Ilel668Ala, His l919Ala, Glu2004Ala, Val2223Ala, Met2238Ala, and Pro2292Ala, the amino acid sequence of which is provided in SEQ ID NO: 24.
  • a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 24.
  • additional hrFVIII polypeptides comprising a
  • the linker region in the B -domain deleted constructs can be varied to include additional or fewer amino acids from the N -terminus and C-terminus of the B domain.
  • the linker comprises the linker sequence SFSQNSRHPSQNPPVLK HQR, comprising ten amino acids from the N-terminus of the B- domain followed by eleven amino acids from the C-terminus of the B-domain.
  • the hrFVIII comprises the amino acid sequence of SEQ ID NO: 25 provided herewith.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 25.
  • the hrFVIII comprises the amino acid sequence of SEQ ID NO: 26 provided herewith. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 26. In one embodiment, the hrFVIII comprises the amino acid modification Gln334Pro (H7). In one embodiment, the hrFVIII comprises the amino acid sequence of SEQ ID NO: 27 provided herewith.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 27.
  • the hrFVIII comprises the amino acid modifications Arg484His and Met2238Val (H3/H4).
  • the hrFVIII comprises the amino acid sequence of SEQ ID NO: 28 provided herewith.
  • a hrFVIII is provided that is at least about 90%>, 91%>, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 28.
  • the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 29.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 29.
  • the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, His l919Asn, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 30.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 30.
  • the hrFVIII comprises the amino acid modifications Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser, the amino acid sequence of which is provided in SEQ ID NO: 31.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 31.
  • the hrFVIII comprises the amino acid modifications Glul l3Ala, Gln334Ala, Arg484Ala, Ilel668Ala, His l919Ala, Glu2004Ala, Val2223Ala, Met2238Ala, and Pro2292Ala, the amino acid sequence of which is provided in SEQ ID NO: 32.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 32.
  • nucleic acids that encode the hrFVIII polypeptides described herein including, for example, SEQ ID NOs: 1-6, 13, 15-33, 52, and 53. This would include all degenerate sequences related to a specific polypeptide sequence, i.e. all nucleic acids having a sequence that encodes one particular polypeptide sequence as well as all nucleic acids, including degenerate nucleic acids, encoding the disclosed variants and derivatives of the polypeptide sequences.
  • each particular nucleic acid sequence may not be written out herein, it is understood that each and every sequence is in fact disclosed and described herein through the disclosed polypeptide sequence.
  • a complementary DNA (cDNA) encoding a hrFVIII comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns- SNP.
  • the cDNA encodes a hrFVIII comprising a non-naturally occurring combination comprising 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, or 15 amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser.
  • the encoded hrFVIII comprises the amino acid modifications Arg484His, Aspl241Glu, and Met2238Val.
  • the cDNA comprises the nucleic acid sequence of SEQ ID NO: 7 provided herewith. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 7.
  • the encoded hrFVIII comprises the amino acid modifications Arg484His and Met2238Val, creating an alternative H3/H4 FVIII hybrid.
  • the cDNA comprises the nucleic acid sequence of SEQ ID NO: 14 provided herewith.
  • the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 14.
  • the encoded hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, and Met2238Val.
  • the cDNA comprises the nucleic acid sequence of SEQ ID NO: 8, provided in Table 30 below.
  • the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 8.
  • the cDNA encodes a hrFVIII lacking a B-domain of wild-type FVIII. In one embodiment, the cDNA encodes a hrFVIII comprising the amino acid modification Met2238Val (H3/H5). In one embodiment, the cDNA comprises the nucleic acid sequence of SEQ ID NO: 9 provided herewith wherein the gap in the sequence indicates the B-domain deleted sequence. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 9.
  • the cDNA encodes a hrFVIII comprising the amino acid modification Arg484His (H4/H8).
  • the cDNA comprises the nucleic acid sequence of SEQ ID NO: 10 provide herewith wherein the gap in the sequence indicates the B-domain deleted sequence.
  • the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 10.
  • the cDNA encodes a hrFVIII comprising the amino acid modification Gln334Pro (H7).
  • the cDNA comprises the amino acid sequence of SEQ ID NO: 11 provided herewith wherein the gap in the sequence indicates the B-domain deleted sequence. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 1 1. In one embodiment, the cDNA encodes a hrFVIII comprising the amino acid modifications Arg484His and Met2238Val (H3/H4). In one embodiment, the cDNA comprises the nucleic acid sequence of SEQ ID NO: 12 provided herewith wherein the gap in the sequence indicates the B-domain deleted sequence. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 12.
  • the cDNA encoding the hrFVIII comprises the amino acid modifications Arg484His, Arg776Gly, Aspl241Glu, and Met2238Val.
  • the cDNA comprises the nucleic acid sequence of SEQ ID NO: 34 provided herewith.
  • the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 34.
  • the cDNA encodes a hrFVIII polypeptide comprising the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, and Met2238Val, the cDNA sequence of which is provided herewith in SEQ ID NO: 35.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 35.
  • the cDNA encodes a hrFVIII polypeptide comprising the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, Hisl919Asn, and Met2238Val, the cDNA sequence of which is provided herewith in SEQ ID NO: 36.
  • a hrFVIII is provided that is at least about 90%>, 91%>, 92%>, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 36.
  • the cDNA encodes a low antigenicity hrFVIII polypeptide comprising the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, and Met2238Val, and the additional modifications Glul l3Asp, Ala387Thr, Argl l07Trp, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Pro2292Ser, the cDNA sequence of which is provided herewith in SEQ ID NO: 37.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 37.
  • the cDNA encodes a low antigenicity universal donor hrFVIII polypeptide comprising the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Argl260Lys, and Met2238Val, and the additional modifications Glul l3Asp, Ala387Thr, Argl l07Trp, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Pro2292Ser, the cDNA sequence of which is provided herewith in SEQ ID NO: 38.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 38.
  • the cDNA encoding hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, and Met2238Val, the cDNA sequence of which is provided herewith in SEQ ID NO: 39.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 39.
  • the cDNA encoding hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, His l919Asn, and Met2238Val, the cDNA sequence of which is provided herewith in SEQ ID NO: 40.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 40.
  • the cDNA encoding hrFVIII comprises the amino acid modifications Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser, the cDNA sequence of which is provided herewith in SEQ ID NO: 41.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 41.
  • hrFVIII polypeptides comprising a FVIII polypeptide wherein at least a portion of the B -domain has been deleted, further comprising amino acid modifications at ns-SNP positions compared to the currently available BDD-FVIII products.
  • the linker region in the B-domain deleted constructs can be varied to include additional or fewer amino acids from the N-terminus and C-terminus of the B domain.
  • the linker comprises the linker cDNA sequence encoding the amino acid sequence SFSQNSRHPSQNPPVLK HQR, comprising ten amino acids from the N-terminus of the B- domain followed by eleven amino acids from the C-terminus of the B-domain.
  • BDD-2 B-domain deleted 2
  • the hrFVIII comprises the amino acid modification Met2238Val (H3/H5).
  • the hrFVIII comprises the amino acid sequence of SEQ ID NO: 42 provided herewith.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 42.
  • the hrFVIII comprises the amino acid modification Arg484His (H4/H8).
  • the hrFVIII comprises the amino acid sequence of SEQ ID NO: 43, provided in Table 44 below.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 43.
  • the hrFVIII comprises the amino acid modifications Arg484His, Aspl241Glu, and Met2238Val (H3/H4). In one embodiment, the hrFVIII comprises the amino acid sequence of SEQ ID NO: 44 provided herewith. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 44. In one embodiment, the hrFVIII comprises the amino acid modification Gln334Pro (H7). In one embodiment, the hrFVIII comprises the amino acid sequence of SEQ ID NO: 45 provided herewith.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 45.
  • the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, and Met2238Val, the amino acid sequence of which is provided herewith in SEQ ID NO: 46.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 46.
  • the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, Hisl919Asn, and Met2238Val, the amino acid sequence of which is provided herewith in SEQ ID NO: 47.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 47.
  • the hrFVIII comprises the amino acid modifications Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser, the amino acid sequence of which is provided herewith in SEQ ID NO: 48.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 48.
  • an isolated cDNA encoding Haplotype 9 polypeptide comprising the amino acid modifications Asp 1241 Glu and His l919Asn, the cDNA sequence of which is provided herewith in SEQ ID NO: 49.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 49.
  • an isolated cDNA encoding a Haplotype 9 B- domain deleted (BDD) polypeptide is provided comprising the amino acid modification Hisl919Asn, the cDNA sequence of which is provided herewith in SEQ ID NO: 50.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 50.
  • an isolated cDNA encoding a Haplotype 9 B -domain deleted-2 (BDD-2) polypeptide is provided comprising the amino acid modification Hisl919Asn, the cDNA sequence of which is provided herewith in SEQ ID NO: 51.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 51.
  • an isolated Haplotype 9 B-domain deleted (BDD) polypeptide comprising the amino acid modification Hisl919Asn, the amino acid sequence of which is provided herewith in SEQ ID NO: 52.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 52.
  • an isolated Haplotype 9 B-domain deleted-2 (BDD-2) polypeptide is provided comprising the amino acid modification Hisl919Asn, the amino acid sequence of which is provided herewith in SEQ ID NO: 53.
  • a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 53.
  • the expression vectors can be used to express the hrFVIIIs described herein in a eukaryotic host cell, for example a mammalian cell, wherein the hrFVIII can subsequently be isolated, purified, and processed into a form suitable for administration to a subject.
  • the expression vector is a viral vector.
  • the expression vector is a non-viral vector.
  • the nucleic acids that are delivered to cells typically contain expression controlling systems.
  • the inserted genes in viral and retroviral systems usually contain promoters, and/or enhancers to help control the expression of the desired gene product.
  • a promoter is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site.
  • a promoter contains core elements required for basic interaction of RNA polymerase and transcription factors, and may contain upstream elements and response elements.
  • Promoters controlling transcription from vectors in mammalian host cells may be obtained from various sources, for example, the genomes of viruses such as: polyoma, Simian Virus 40 (SV40), adenovirus, retroviruses, hepatitis-B virus and cytomegalovirus (CMV), or from heterologous mammalian promoters, e.g. beta actin promoter.
  • the early and late promoters of the SV40 virus are conveniently obtained as an SV40 restriction fragment which also contains the SV40 viral origin of replication (Fiers et al, Nature, 273 : 1 13 (1978)).
  • the immediate early promoter of the human cytomegalovirus is conveniently obtained as a Hindlll E restriction fragment (Greenway, P. J. et al, Gene 18: 355-360 (1982)).
  • promoters from the host cell or related species also are useful herein.
  • Enhancer generally refers to a sequence of DNA that functions at no fixed distance from the transcription start site and can be either 5' (Laimins, L. et al, Proc. Natl. Acad. Sci. 78: 993 (1981)) or 3' (Lusky, M. L., et al, Mol. Cell Bio. 3: 1 108 (1983)) to the transcription unit. Furthermore, enhancers can be within an intron (Banerji, J. L. et al, Cell 33 : 729 (1983)) as well as within the coding sequence itself (Osborne, T. F., et al, Mol. Cell Bio. 4: 1293 (1984)).
  • Enhancers function to increase transcription from nearby promoters. Enhancers also often contain response elements that mediate the regulation of transcription. Promoters can also contain response elements that mediate the regulation of transcription. Enhancers often determine the regulation of expression of a gene. While many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, -fetoprotein and insulin), typically one will use an enhancer from a eukaryotic cell virus for general expression. Examples are the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
  • the promoter and/or enhancer may be specifically activated either by light or specific chemical events which trigger their function.
  • Systems can be regulated by reagents such as tetracycline and dexamethasone.
  • reagents such as tetracycline and dexamethasone.
  • irradiation such as gamma irradiation, or alkylating chemotherapy drugs.
  • the promoter and/or enhancer region can act as a constitutive promoter and/or enhancer to maximize expression of the region of the transcription unit to be transcribed.
  • the promoter and/or enhancer region are active in all eukaryotic cell types, even if it is only expressed in a particular type of cell at a particular time.
  • a promoter of this type for example is the CMV promoter (650 bases).
  • Other example promoters are SV40 promoters, cytomegalovirus (full length promoter), and retroviral vector LTR.
  • Expression vectors used in eukaryotic host cells may also contain sequences necessary for the termination of transcription which may affect mRNA expression. These regions are transcribed as polyadenylated segments in the untranslated portion of the mRNA encoding tissue factor protein. The 3' untranslated regions also include transcription termination sites.
  • the transcription unit also contain a polyadenylation region. One benefit of this region is that it increases the likelihood that the transcribed unit will be processed and transported like mRNA.
  • the identification and use of polyadenylation signals in expression constructs is well established. For instance, homologous polyadenylation signals can be used in the transgene constructs.
  • the polyadenylation region is derived from the SV40 early polyadenylation signal and consists of about 400 bases.
  • the polyadenylation signal is derived from the human growth hormone poly-A signal (hGH-pA).
  • the transcribed units can contain other standard sequences alone or in combination with the above sequences improve expression from, or stability of, the construct.
  • the expression vectors can include nucleic acid sequence encoding a marker product.
  • This marker product is used to determine if the gene has been delivered to the cell and once delivered is being expressed.
  • the marker genes can be the E. Coli lacZ gene, which encodes ⁇ -galactosidase, and green fluorescent protein.
  • the marker may be a selectable marker.
  • Suitable selectable markers for mammalian cells are dihydrofolate reductase (DHFR), thymidine kinase, neomycin, neomycin analog G418, hydromycin, and puromycin.
  • DHFR dihydrofolate reductase
  • thymidine kinase thymidine kinase
  • neomycin neomycin analog G418, hydromycin
  • puromycin puromycin.
  • These cells lack the ability to grow without the addition of nutrients such as thymidine or hypoxanthine. Because these cells lack certain genes necessary for a complete nucleotide synthesis pathway, they cannot survive unless the missing nucleotides are provided in a supplemented media.
  • An alternative to supplementing the media is to introduce an intact DHFR or TK gene into cells lacking the respective genes, thus altering their growth requirements. Individual cells which were not transformed with the DHFR or TK gene will not be capable of survival in non-supplemented media.
  • the second category is dominant selection which refers to a selection scheme used in any cell type and does not require the use of a mutant cell line. These schemes typically use a drug to arrest growth of a host cell. Those cells which have a novel gene would express a protein conveying drug resistance and would survive the selection. Examples of such dominant selection use the drugs neomycin, (Southern P. and Berg, P., J. Molec. Appl. Genet. 1 : 327 (1982)), mycophenolic acid, (Mulligan, R. C. and Berg, P. Science 209: 1422 (1980)) or hygromycin, (Sugden, B. et al, Mol. Cell. Biol. 5 : 410-413 (1985)).
  • the three examples employ bacterial genes under eukaryotic control to convey resistance to the appropriate drug G418 or neomycin (geneticin), xgpt (mycophenolic acid) or hygromycin, respectively. Others include the neomycin analog G418 and puramycin.
  • the disclosed vectors thus provide DNA molecules which are capable of integration into a mammalian chromosome without substantial toxicity.
  • the FVIII constructs disclosed herein are created using standard molecular cloning techniques (Sambrook, J. & Green, M. R. Molecular cloning: a laboratory manual, Cold Spring Harbor Laboratory Press, 2012).
  • the starting material for cloning the constructs can consist of a cDNA construct that encodes for full-length H3 FVIII (FL-H3-FVIII), named HOW1 as shown in Figure 3.
  • Several restriction endonuclease sites have been identified in the HOW1 cDNA construct to allow for digestion of the construct and subsequent ligation of replacement or insert construct into the construct.
  • a HI BDD-2 construct is created.
  • the H3 BDD-2 construct can in turn be digested with Kpnl and Xbal followed by insertion of insert construct entitled Fragment A-H to create a H3/H4 BDD-2 construct as shown in Figure 7.
  • the HI BDD-2 construct can in turn be digested with Kpnl and Xbal followed by insertion of insert construct entitled Fragment A-H to create a H4 BDD-2 construct as shown in Figure 8.
  • the FVIII constructs created can then be used to produce corresponding hrFVIII.
  • the H3/H4 BDD-2 construct shown in Figure 7 comprises cDNA having a SEQ ID No: 44 can be used to create the hrFVIII having a SEQ ID NO: 28.
  • insert constructs that have restriction endonuclease sites that are complementary to the sites in HOW1, a variety of combinations of modifications can be made to the FVIII constructs.
  • These insert constructs can be synthesized to specifications in terms of sequence to form the cDNAs disclosed herein.
  • the insert construct is obtained through commercial sources.
  • a cDNA construct that encodes for full-length H3 FVIII is used as an example, cDNA constructs that encodes other full length haplotype FVIIIs can also be used as the starting sequences.
  • the digestion and subsequent insert construct ligation procedures outlined in Figures 4-8 can be used on these cDNA constructs that encodes other full length haplotype FVIIIs to produce the hrFVIII disclosed herein.
  • an expression vector comprising a nucleic acid encoding a hrFVIII described herein.
  • the expression vector comprises a complementary DNA (cDNA) encoding a hrFVIII comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns-SNP.
  • the cDNA encodes a hrFVIII comprising non-naturally occurring combination comprising between 2 and 15 amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser, as described above.
  • the cDNA encodes a hrFVIII lacking the B-domain of wild-type FVIII, as described above.
  • the expression vector comprises a cDNA selected from the group consisting of SEQ ID NOs: 7-12, 14, and 34-51.
  • the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NOs. 7-12, 14, and 34-51.
  • the expression vector further comprises a CMV promoter operably linked to the cDNA sequence.
  • the expression vector further comprises a human growth hormone poly -A signal 3' operably linked to the 3' end of the cDNA sequence.
  • the expression vector further comprises a neomycin resistance gene.
  • An example expression vector capable of expressing the hrFVIII described herein is illustrated in Figure 3. Specifically, transient transfection of COS-7 cells validated the expression of the F8 cDNA encoding the full-length H3 haplotype FVIII and established the functionality of the: human growth hormone poly-A signal (hGH-pA); CMV promoter; and neomycin resistance cassette (Neo'). H3 has a "G" at 3591, coding Glu at translated residue 1260, which is residue 1241 in plasma FVIII and at 6940, coding Val at residue 2257, which is residue 2238 in plasma FVIII.
  • the cell comprises a nucleic acid encoding the hrFVIII polypeptides described herein. In one embodiment, the cell comprises a cDNAs encoding the hrFVIII polypeptides described herein. In one embodiment, the nucleic acid is contained within an expression construct.
  • Cells contemplated herein include eukaryotic cell lines suitable for recombinant protein production.
  • the cell is a mammalian cell that has the ability to synthesize proteins that are similar to those naturally occurring in humans with respect to molecular structures and biochemical properties.
  • Contemplated cells include COS- 7, CHO, baby hamster kidney cells (BHK), mouse cells such as NSO (myeloma), Hek293, Per-C6, CAP (CEVEC's Aminocyte Production) cell lines, HKB-1 1, and HT-1080 cells.
  • Suitable cell lines and recombinant protein production methods are known in the art and described in, for example, Swiech et al, Protein Expression and Purification 84 (2012); 147- 153; Zhu, Biotechnology Advances 30 (2012); 1 158-1 170; hacker et al, Biotechnology Advances 27 (2009); 1023-1027.
  • the nucleic acids encoding the hrFVIIIs described herein can be delivered through a number of direct delivery systems such as, electroporation, lipofection, calcium phosphate precipitation, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, or via transfer of genetic material in cells or carriers such as cationic liposomes.
  • direct delivery systems such as, electroporation, lipofection, calcium phosphate precipitation, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, or via transfer of genetic material in cells or carriers such as cationic liposomes.
  • Appropriate means for transfection, including viral vectors, chemical transfectants, or physico -mechanical methods such as electroporation and direct diffusion of DNA, are described by, for example, Wolff, J. A., et al, Science, 247, 1465 -1468,
  • Transfer vectors can be any nucleotide construction used to deliver genes into cells (e.g., a plasmid), or as part of a general strategy to deliver genes, e.g., as part of recombinant retrovirus or adenovirus (Ram et al. Cancer Res. 53 :83-88, (1993)).
  • Nucleic acids that are delivered to cells which are to be integrated into the host cell genome typically contain integration sequences. These sequences are often viral related sequences, particularly when viral based systems are used. These viral intergration systems can also be incorporated into nucleic acids which are to be delivered using a non-nucleic acid based system of deliver, such as a liposome, so that the nucleic acid contained in the delivery system can become integrated into the host genome.
  • Other general techniques for integration into the host genome include, for example, systems designed to promote homologous recombination with the host genome. These systems typically rely on sequence flanking the nucleic acid to be expressed that has enough homology with a target sequence within the host cell genome that recombination between the vector nucleic acid and the target nucleic acid takes place, causing the delivered nucleic acid to be integrated into the host genome. These systems and the methods necessary to promote homologous recombination are known to those of skill in the art.
  • the hrFVIII polypeptides described herein are suitable for treating a patient suffering from Hemophilia A. Accordingly, provided herein is a method of treating a subject suffering from hemophilia A with a suitable amount of a hrFVIII polypeptide described herein.
  • the level of inhibitors present in the subject is determined prior to administration of a hrFVIII polypeptide described herein. If a significant level of inhibitors is present, for example, a Bethesda Unit titer of about 10 or greater, then a neutralization assay is performed on the hrFVIII polypeptide. If the subject's inhibitors do not significantly neutralize the ability of the hrFVIII polypeptide, then the polypeptide is administered to the patient. If the hrFVIII polypeptide is neutralized, then an alternative hrFVIII described herein is administered. Bethesda Unit neutralization assays are well known in the art, for example, as described further below and in US 2010/0256062.
  • Inhibitor to FVIII is screened for by mixing test plasma with a known amount of FVIII. After a 2 hour incubation period at 37° C, the residual FVIII activity is determined in a FVIII assay. By comparing the difference in the FVIII activity of the patient incubation mixture and a control mixture, the absence or presence of a FVIII inhibitor can be demonstrated. Some antibodies will only prolong the Protein Truncation Test (PTT) after incubation.
  • PTT Protein Truncation Test
  • the assay disclosed herein can utilize blood plasma that contains only one of the 6 wild type forms of FVIII protein.
  • FVIII inhibitors IgG antibodies directed against FVIII, can occur in alloimmunized patients with congenital FVIII deficiency (Hemophilia A) or as autoantibodies. The latter are associated with pregnancy, autoimmune disease, or drugs but most often occur spontaneously, particularly among elderly persons.
  • Serial subject plasma dilutions in citrated saline are prepared, from 1 :1 up to 1 :160 (or higher if necessary for high-titer factor inhibitors). The purpose of these dilutions is to dilute out the inhibitor.
  • the patient plasma dilutions are then mixed with an equal volume of normal plasma containing a normal amount of coagulation factors.
  • the mixed dilutions are usually incubated for up to 2 hours, because certain inhibitors show an inhibitory effect only after prolonged incubation (particularly factor V and FVIII inhibitors).
  • FVIII assays are then performed on each mixed dilution.
  • the dilution that inhibits 50% of FVIII in the assay defines the titer of the inhibitor. For example, if the 1 :40 dilution inhibits 50% of the FVIII in the assay, the patient is reported to have a titer of 40 BU of FVIII inhibitor.
  • the assay can be used to determine if the FVIII inhibitor cross-reacts with hrFVIII polypeptide. If there is little or no cross-reactivity, the hrFVIII can be used to treat bleeding due to a FVIII inhibitor.
  • hrFVIII that has the lowest immunogenicity risk for initiating replacement therapy in previously -untreated patients (PUPs) with hemophilia-A (HA) caused by pharmaco genetically relevant F8 mutation types (e.g., the intron-22 inversion, missense mutations, and the intron-1 inversion) can be personalized.
  • HA hemophilia-A
  • F8 mutation types e.g., the intron-22 inversion, missense mutations, and the intron-1 inversion
  • tFVIIIs a new biomarker for the risk of immunogenicity with therapeutic FVIII proteins
  • I- FVIII-CRM intracellular FVIII cross-reactive material
  • P-FVIII- CRM plasma FVIII cross-reactive material
  • This FVIII expression characteristic no doubt contributes to the relatively low (-20%) overall risk of inhibitor development that has been associated with the 1221 (i.e., only about one in every five 1221 patients develops an inhibitor) and is likely associated with other HA-causing F8 gene abnormalities, including missense mutations, which considered together have an even lower immunogenicity risk (i.e., 5-10%). Because this biomarker identifies patients who may have a preexisting tolerance to tFVIIIs, we have coined the term pharmacogenetically-relevant mutation types to descriptively characterize this relatively large subgroup of null -type F8 gene abnormalities as defining the group of patients for whom pharmaco genomics may be most helpful.
  • selecting the FVIII replacement product that has the lowest immunogenicity risk to initiate therapy in previously-untreated patients (PUPs) with severe HA involves first employing non-sequencing- and sequencing-based F8 mutation detection assays to identify and characterize the specific HA-causing abnormality as being either pharmacogenetically-relevant or -irrelevant. For those patients that are found to have pharmacogenetically-relevant abnormalities, e.g.
  • the remaining protein-encoding F8 exonic segments are sequenced to predict which amino acid residues are encoded by the specific alleles present at the multiple known (and any previously unknown) ns-SNP sites so as to guide the selection of the FVIII therapeutic that is most closely matched to the patient's endogenously expressed FVIII protein as it is believed to confer the lowest overall risk of triggering an allogeneic immune- response.
  • selecting the hrFVIII product that has the lowest immunogenicity risk for initiating replacement therapy in previously -untreated patients (PUPs) with hemophilia-A (HA) caused by pharmacogenetically-irre levant F8 mutation types can be personalized based on the following disclosure.
  • the method of treatment for patients whose I-FVIII-CRM status is completely negative also involves first employing non-sequencing- and sequencing-based F8 mutation detection assays to identify and characterize the specific HA-causing abnormality as being pharmacogenetically-irrelevant.
  • one of the BDD hrFVIII proteins disclosed in Tables IB, 1C and ID are believed to be associated with lower immunogenicity risk than the FL hrFVIII proteins disclosed in Tables 1A as they contain almost one-third less of the entire tFVIII protein, which is the source for one or more foreign peptides that might trigger an alloimmune response and lead to inhibitor development, and thus may have an approximately 33% reduced overall immunogenicity risk.
  • HLA-II HLA-class-II
  • a given haplotype of one class of BDD h-rFVIII proteins such as the BDD-2 family may have a lower immunogenicity risk in a given patient than the same haplotype of another class such as the BDD-1 family.
  • the H7 BDD-2 h-rFVIII may have a lower immunogenicity risk than the H7 BDD-1 h-rFVIII, or vice versa, again depending on their specific highly -restricted and individually- limited HLA-II repertoire.
  • selecting the hrFVIII product for initiating immune-tolerance induction therapy in previously-treated alloimmunized patients (PTPs) with severe HA caused by pharmacogenetically -re levant F8 mutation types i.e., choosing the FVIII product with the greatest likelihood of successfully eradicating (or reducing the titer of) a neutralizing anti-FVIII antibody in a so called "inhibitor patient" is as follows.
  • a pharmacogenomics-based strategy is also more likely to be successfully devised and implemented for selecting the optimal FVIII product for eradicating (or reducing the titer of) neutralizing anti-FVIII antibodies in PTPs who have already developed a clinically relevant inhibitor when the patients have pharmacogenetically-relevant F8 mutations.
  • pharmacogenomics-guided immune-tolerance-induction ( ⁇ )- therapy may be more difficult to design and/or less likely to be successful when applied to PTPs with inhibitors and whose severe HA and completely negative I-FVIII-CRM status is caused by pharmacogenetically-irrelevant F8 mutation types— which again would obviously be the case for the rare individuals who have a complete F8 gene deletion from their genome, the pathognomonic gene abnormality for the class of mutations— the method of treatment, as detailed below, can help to select the optimal FVIII product to initiate ⁇ -therapy in such PTPs who have traditionally had success rates of inhibitor eradication that are less than 30- 50%.
  • the method of treatment for patients whose I-FVIII-CRM status is completely negative also involves first employing non- sequencing- and sequencing-based F8 mutation detection assays to identify and characterize the specific HA-causing abnormality as being pharmacogenetically-irrelevant.
  • one of the BDD hrFVIII proteins may be associated with a higher success rate for ITI-therapy than the FL hrFVIII proteins (see Tables 1A) as they contain almost one -third less of the entire tFVIII protein, which would be a much less likely source for one or more additional foreign peptides that might trigger an alloimmune response and lead to ongoing stimulation of the alloimmune response and thus a reduced likelihood of successful inhibitor eradication.
  • a given haplotype of one class of BDD h-rFVIII proteins may have a greater likelihood of successfully inducing immune- tolerance in a given patient than the same haplotype of another class (i.e., the BDD-1 family).
  • the H7 BDD-2 hrFVIII may have a greater chance of successfully inducing immune-tolerance and eradicating the inhibitor than the H7 BDD-1 hrFVIII, or vice versa, again depending on the nature of their specific highly-restricted and individually- limited HLA-II repertoire.
  • the hybrid recombinant FVIII polypeptides described herein can be administered in a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable is meant a material that is not biologically or otherwise undesirable, i.e., the material may be administered to a subject without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained.
  • the carrier would naturally be selected to minimize any degradation of the active ingredient and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art.
  • compositions may be administered in any suitable way, for example, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, or the like.
  • compositions required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the disorder being treated, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein.
  • Parenteral administration of the composition is generally characterized by injection.
  • Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions.
  • a more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, e.g., U.S. Pat. No. 3,610,795, which is incorporated by reference herein.
  • the hrFVIII polypeptide may be in solution or suspension (for example, incorporated into microp articles, liposomes, or cells).
  • Suitable carriers and their formulations are described in Remington: The Science and Practice of Pharmacy (19th ed.) ed. A. R. Gennaro, Mack Publishing Company, Easton, Pa. 1995.
  • an appropriate amount of a pharmaceutically - acceptable salt is used in the formulation to render the formulation isotonic.
  • the pharmaceutically-acceptable carrier include, but are not limited to, saline, Ringer's solution and dextrose solution.
  • the pH of the solution is from about 5 to about 8, for example, from about 7 to about 7.5. It will be apparent to those persons skilled in the art that certain carriers may be more preferable depending upon, for instance, the route of administration and concentration of composition being administered.
  • Pharmaceutical carriers are known to those skilled in the art. These most typically would be standard carriers for administration of drugs to humans, including solutions such as sterile water, saline, and buffered solutions at physiological pH. Other compounds will be administered according to standard procedures used by those skilled in the art.
  • Pharmaceutical compositions may include carriers, thickeners, diluents, buffers, preservatives, surface active agents and the like in addition to the molecule of choice.
  • Pharmaceutical compositions may also include one or more active ingredients such as antimicrobial agents, anti-inflammatory agents, anesthetics, and the like.
  • the pharmaceutical composition may be administered in a number of ways depending on whether local or systemic treatment is desired, and on the area to be treated.
  • Preparations for parenteral administration include sterile aqueous or non -aqueous solutions, suspensions, and emulsions.
  • non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate.
  • Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media.
  • Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils.
  • Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like.
  • hrFVIII polypeptides disclosed herein and the compositions necessary to perform the disclosed methods can be made using any method known to those of skill in the art for that particular reagent or compound unless otherwise specifically noted.
  • Recombinant FVIII can be produced through the use of eukaryotic protein expression systems.
  • a eukaryotic cell line which is deficient in a required gene, is transformed with a vector comprising the gene that it has a deficiency for, and the recombinant DNA which one wishes to express. Transformation can be accomplished by techniques such as electroporation or viral delivery.
  • the cell line chosen to produce the polypeptide is selected to be compatible with the polypeptide of interest, capable of continuously expressing the polypeptide of interests, capable of growing on a medium which facilitates purification of the polypeptide of interest, along with other factors known to those skilled in the art. Examples of such techniques are disclosed in European Patent Application 0 302 968 A2 and U.S. Pat. No. 5,149,637 both of which are incorporated by reference in their entirety .u
  • An expression vector encoding a hrFVIII provided herein can be generated and validated.
  • a H3/4-rFVIIIFL expression vector can be generated and confirmed by sequence using an expression vector disclosed in Figure 3. All of the vector's sequences are confirmed by bi-directional DNA sequencing.
  • the vectors are then transfected into a mammalian cell, for example CHO-cells, in order to generate research grade preparations of purified hrFVIII proteins.
  • the expression vectors can be analyzed using standard Western blotting procedures to determine that the vector yields the human hrFVIII polypeptide disclosed herein in the conditioned medium of transiently transfected, for example, CHO cells.
  • the monoclonal antibody FX008 or other similar FVIII antibodies can be used to purify the hrFVIII proteins expressed in CHO-cells. Additional in vitro analyses can be conducted to ensure that the proteins are of high-quality, including peptide -mapping by mass spectrometry. Assessment of the antigenicity of the human hrFVIII Polypeptides
  • the antigenicity of the human hrFVIII polypeptides disclosed herein can be analyzed.
  • the hrFVIII polypeptides can be analyzed using a haplotype- specific version of the Nijmegen-modified Bethesda assay, in accordance with the design outlined in Table 2, below.
  • test antigens and controls can be evaluated for reactivity with domain-epitope-specific mouse antibodies.
  • these types of antibodies can be purchased from Green Mountain Antibodies, or additional FVIII domain specific antibodies.
  • Sample plasmas can be obtained from inhibitor patients with congenital HA. For example, these plasmas are available from George King Biomedical, Inc. and are available with varying FVIII inhibitor titers.
  • the following inhibitory activities can be measured: (i) four monoclonal antibodies with specific reactivity against one of four different epitopes within the FVIII protein; and (ii) plasma from inhibitor patients against each of the FVIII test hybrid antigens.
  • the inhibitor mAb responses in patients are against H I FVIII or H2 FVIII, since no other haplotypes are represented in the current commercially available rFVIII concentrates.
  • Test plasmas containing hrFVIII described herein can be prepared by reconstituting human FVIII deficient plasma (FVIIIdp) to a concentration of 1 U/mL FVIII :C.
  • Each site-specific anti-FVIII monoclonal antibody is reconstituted in FVIIIdp to a concentration determined to be between 5 and 10 BU/mL against the PNP used.
  • each hrFVIII can be mixed 1 :1 individually with each of the mAb -reconstituted inhibitor plasmas for 120 minutes at 37°C (Table 2).
  • Each hrFVIII polypeptide is mixed 1 : 1 with patient plasma having the antibody titer indicated in Table 2.
  • Each incubated mix is assayed for residual FVIILC, using the ACL Elite -Pro coagulation analyzer (Instrumentation Laboratory), or similar analyzers.
  • the percent activity is recorded for each reaction mix and compared to FVIILC of pooled normal plasma (PNP) with no inhibitors.
  • Results from antigenicity assessment of each construct against the individual mAB-reconstituted inhibitor plasmas reveals the extent to which the epitope specific substitution encoded by the ns-SNPs (e.g., A2, C2, both A2 and C2) that define the test antigens contributes to any reduced reactivity observed in the inhibitor patient plasma.
  • the anti-Al and anti-A3 reconstituted inhibitor plasmas serve primarily as controls. Many acquired HA patients frequently have a more targeted antibody response directed only to the A2- and/or C2-epitopes, and do not have a significant antibody response to the Al and A3 epitopes.
  • hrFVIII As the hrFVIII described herein are further characterized, they can be assessed to include pools of sample plasmas from inhibitor patients with congenital HA as well as with acquired HA.
  • Stored plasma samples have been obtained from >700 patients with congenital HA (of which about half are either of Black African or White European descent and a few dozen each are either of Asian or Latino descent) and from 12 patients with the very rare acquired form of HA, who have racial/ethnic ancestries similar to the congenital HA samples.
  • Genomic DNA, RNA, plasma and cell samples from these patients can be characterized at the genetic, molecular, biochemical and cellular level, in order to facilitate the use of these hybrid proteins in the context of the varying naturally occurring haplotypes.
  • a linker can be inserted in the place of the B domain in order to facilitate proper expression.
  • the linker sequence can be SFSQNSRHPSQNPPVLKRHQR, consisting of 10 amino acids from the N-terminus of the B domain followed by 11 amino acids from the C- terminus of the B domain. ⁇ Haemophilia 16, 349-359 (2010)). These constructs containing the 21 amino acid linker are referred to as BDD-2.
  • the design of the FVIII BDD-2 polypeptides can be constructed as highlighted in Figures 4 to 8.
  • the FVIII ORF from HOW 1 -BDD-2 (FVIII Haplotype 3 B-Domain Deleted-2) was translated. It was determined that its calculated mass is 161,381.73 Da, exactly the same as the expected BDD-2 protein.
  • the FVIII Haplotype H3 full length cDNA was used as a starting sequence ( Figure 5). Convenient restriction sites were identified, allowing insertion of the F8 BDD-2 gene into HOWl. The restriction sites that were identified were Aflll, Kpnl and Xbal.
  • the F8 gene sequence was examined to identify good restriction enzymes to allow swapping of V2238 for M2238 and R484 for H484. Based on examination of the F8 sequence, it was determined that there was a Kpnl enzyme cleavage site located fairly close to the middle of the gene. In order to change R484 to H484, Aflll, with a site located approximately 0.3 kb from the start codon, could be used in combination with Kpnl. In order to change V2238 to M2238, Xbal can be chosen on the 3' end, in combination with Kpnl site.
  • the FVIII BDD-2 constructs can be constructed through the use of four fragments that can be combined in different ways to produce the B- domain-deleted-2 constructs.
  • the FVIII Haplotype HI, H3, H4, and H3/H4 BDD-2 constructs can be constructed as depicted in Figures 4 though Figure 8. This method involves obtaining four DNA fragments to be combined into different constructs. In Figure 4, these four fragments are labeled A-R, A-H, C-V, and C-M.
  • Fragments A-H an Aflll-Kpnl fragment containing A1508 (to express the H484 protein)
  • C-V a Kpnl-Xbal fragment with the B domain deleted and containing G6769 (to express the V2238 protein)
  • C-M a Kpnl-Xbal fragment with the B-domain deleted and containing A6769 (to express M2238 protein)
  • Fragment A-R an Aflll-Kpnl fragment containing G1508 (to express R484)
  • the Human FVIII H3 BDD-2 construct can be generated as depicted in Figure 5.
  • the Kpnl-Xbal fragment can be excised from the full length H3 Haplotype sequence and fragment C-V can be inserted.
  • the HI BDD-2 construct can be generated as depicted in Figure 6.
  • the Kpnl-Xbal fragment can be excised from the full length H3 sequence and fragment C-M can be inserted.
  • the H3/H4 BDD-2 hybrid construct can be generated as depicted in Figure 7.
  • the ⁇ - ⁇ fragment can be excised from the H3 BDD-2 construct and fragment A-H can be used to replace the Aflll-Kpnl fragment.
  • the H4 BDD-2 hybrid construct can be generated as depicted in Figure 8.
  • the Aflll-Kpnl fragment from HI BDD-2 can be excised and fragment A-H can be used to replace the Aflll-Kpnl fragment.
  • Human FVIII BDD-2 constructs for Haplotypes HI, H3, H4, and H3/H4 depicted in Figures 4-8 thus can all be obtained.

Abstract

Hybrid recombinant FVIII polypeptides (hrFVIII) comprising non-naturally occurring combinations of amino acid modifications, cDNAs encoding such hrFVIII, expression vectors comprising nucleic acids encoding such hrFVIII, cells comprising expression vectors comprising nucleic acids encoding such hrFVIII, and methods of treating subjects having hemophilia A by administering to the subject such hrFVIII are disclosed herein. The non- naturally occurring amino acid modifications occur at sites of naturally occurring nonsynonymous-Single Nucleotide Polymorphisms (ns-SNP). The hrFVIII can be full length, having a B-domain deletion (BDD), having a B-domain deletion 2 (BDD-2), or having a B-domain deletion 3 (BDD-3). Methods of making the hrFVIIIs, cDNAs, expression vectors, cells are also disclosed.

Description

HYBRID FACTOR VIII POLYPEPTIDES FOR USE TO TREAT HEMOPHILIA A
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority to U.S. provisional patent application serial number 61/888,373, filed on October 8, 2013 to La Terza et al, entitled "Hybrid Factor VIII Polypeptides For Use to Treat Hemophilia A," incorporated herein by reference.
GOVERNMENT RIGHTS
[0002] Development of the inventions described herein was at least partially funded with government support through NIH grant number 1R41MD008156-01A1 and the U.S. government has certain rights in the inventions.
STATEMENT REGARDING SEQUENCE LISTING
[0003] The Sequence Listing associated with this application is part of the description and is provided in the form of an Annex C/ST.25 text file in lieu of a paper copy, and hereby incoporated by reference into the specification. The name of the text file containing the Sequence Listing is 10001_006WO001_SequenceListing_ PatentIn_ST25.txt. The text file is 615kb, was created on October 8, 2014, and is being submitted electronically via EFS-Web.
FIELD OF THE INVENTION
[0004] The present disclosure is directed to hybrid recombinant factor VIII polypeptides (hrFVIII), nucleic acids, including cDNAs, encoding said recombinant factor VIII polypeptides, cells comprising nucleic acids encoding hrFVIII polypeptides, and methods of using such hrFVIII polypeptides.
BACKGROUND
[0005] Patients with hemophilia A (HA) are treated with factor VIII (FVIII) replacement therapies, i.e., infusions of either extracted and pooled human plasma-derived FVIII (pdFVIII) and/or recombinant FVIII (rFVIII) replacement products. In many cases, treatment with FVIII replacements provides efficient management of this chronic disease.
[0006] In approximately 25-30% of cases, however, this treatment leads to the patients developing anti-FVIII neutralizing antibodies, termed inhibitors, which reduces the effectiveness of the FVIII replacement or, in the worst case, renders the replacement ineffective (Lacroix-Desmazes et al., Pathophysiology of inhibitors to FVIII in patients with haemophilia A. Haemophilia 2002: 8: 273-9). In hemophilia A patients of African- American descent, inhibitors occur in approximately 50% of individuals following FVIII replacement therapy. The development of inhibitors leads to the neutralization of the pro- coagulant function of the FVIII replacement or enhances its removal from the plasma (Lacroix-Desmazes et al, Dynamics of factor VIII interactions determine its immunologic fate in hemophilia A. Blood 2008; 1 12 : 240-9). The development of FVIII inhibitors significantly increases the morbidity and lowers the quality of life for patients who develop inhibitors, and represents the greatest limitation to successful FVIII replacement therapy (Darby et al, The incidence of FVIII and factor IX inhibitors in the hemophilia population of the UK and their effect on subsequent mortality, 1977-99. J Throm Haemost 2004: 2: 1047- 54; Ehrenforth et al., Incidence of development of FVIII and factor IX inhibitors in haemophiliacs. Lancet 1992; 339: 594-8; Lusher et al, Recombinant FVIII for the treatment of previously untreated patients with hemophilia A. Safety, efficacy, and development of inhibitors. Kogenate Previously Untreated Patient Study Group. NEJM 1993; 328: 453-9).
[0007] A recombinant r-porcine FVIII product (OBI) is in late stage clinical testing sponsored by Ipsen and Inspiration Biopharmaceuticals. However, experience with a predecessor product, plasma derived porcine FVIII (Hyate:C®), and in clinical studies of OBI, underscore the fact that OBI may be immunogenic and induce neutralizing antibodies after multiple infusions.
[0008] Hybrid recombinant factor VIII polypeptides (hrFVIII) disclosed herein provide effective functionality of a FVIII protein, sufficiently reduce or eliminate antigenicity in HA patients, and restore hemostasis would be a useful treatment for HA patients. For HA patients who have been treated with existing therapies and who had already developed inhibitors, the hrFVIII disclosed herein provides an valuable alternative for the treatment of HA.
SUMMARY
[0009] Provided herein are hybrid recombinant FVIII polypeptides (hrFVIII) comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring nonsynonymous -Single Nucleotide Polymorphisms (ns-SNP); cDNAs encoding such hrFVIII; expression vectors comprising nucleic acids encoding such hrFVIII, cells comprising expression vectors comprising nucleic acids encoding such hrFVIII; and methods of treating subjects having hemophilia A by administering to the subject such hrFVIII. In one embodiment, the hrFVIII disclosed herein have non-naturally occurring combinations of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, or 15 amino acid modifications selected from the group consisting of: Glul 13Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser. The hrFVIII can be full length, having a B-domain deletion (BDD), having a B- domain deletion 2 (BDD-2), or having a B-domain deletion 3 (BDD-3).
[00010] In one embodiment, provided is an expression vector comprising a complementary DNA (cDNA) encoding a hrFVIII comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns-SNP. In one embodiment, the cDNA encodes a hrFVIII comprising non-naturally occurring combination comprising between 2 and 15 amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser, as described above.
[00011] Further provided is a mammalian cell comprising a nucleic acid encoding a hrFVIII described herein. In one embodiment, the cell comprises a complementary DNA (cDNA) encoding a hrFVIII comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns-SNP. In one embodiment, the cDNA encodes a hrFVIII comprising non-naturally occurring combination comprising between 2 and 15 amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser, as described above. In one embodiment, the cDNA encodes a hrFVIII lacking the B-domain of wild-type FVIII as described above. In one embodiment, the cDNA is contained in an expression vector. In one embodiment, the cell is a Chinese Hamster Ovary (CHO) cell. In one embodiment, the cell is an African green monkey (COS -7) cell. In one embodiment, the cell is a human cell. In one embodiment, the human cell is a selected from the group consisting of Hek293, Per-C6, CAP, HKB-11 , and HT-1080 cells.
[00012] In one aspect, disclosed herein is a method for treating a subject suffering from Hemophilia A comprising administering to the subject an effective amount of a hrFVIII described herein. In one embodiment, prior to administration, the immunoreactivity of hrFVIII polypeptide described herein in a subject containing inhibitors to an existing FVIII replacement product is determined.
[00013] In a further aspect, disclosed herein are methods of making the hybrid recombinant FVIII polypeptides (hrFVIII) comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns-SNP; cDNAs encoding such hrFVIII; expression vectors comprising nucleic acids encoding such hrFVIII, cells comprising expression vectors comprising nucleic acids encoding such hrFVIII.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 depicts the polymorphisms within the human F8 gene, which encode several structurally distinct FVIII proteins referred to as haplotypes. As illustrated, existing FVIII therapeutics only target the HI and H2 forms.
Figure 2 illustrates that several polymorphic FVIII ns-SNPs reside within the B-cell immunodominant inhibitor (IDI)-epitopes of alio- and auto-antibodies found commonly in plasma from inhibitor patients with congenital and acquired HA. (A) The variable residues R484H and M2238V, which are encoded by the two common Black-restricted ns-SNPs (G1679A and A6940G), are located in the A2- & C2-domain IDI-epitopes respectively. (B) The alleles of three ns-SNPs define the primary amino acid sequence of hrFVIII products disclosed herein.
Figure 3 illustrates an expression vector capable of expressing the hrFVIII described herein.
Figure 4 illustrates the construction of Human FVIII B-Domain Deleted-2 (BDD-2) polypeptides for FVIII Haplotypes HI, H3, H4, and H3/H4.
Figure 5 illustrates the construction of the Human FVIII Haplotype H3 B-Domain Deleted-2 (BDD-2) polypeptide.
Figure 6 illustrates the construction of the Human FVIII Haplotype HI B-Domain Deleted-2 (BDD-2) polypeptide.
Figure 7 illustrates the construction of the Human FVIII Haplotype H3/H4 B-Domain Deleted-2 (BDD-2) polypeptide.
Figure 8 illustrates the construction of the Human FVIII Haplotype H4 B-Domain Deleted-2 (BDD-2) polypeptide. DETAILED DESCRIPTION
Definitions
[00014] As used throughout, by a "subject" is meant an individual. Thus, the
"subject" can include domesticated animals, such as cats, dogs, etc., livestock (e.g., cattle, horses, pigs, sheep, goats, etc.), laboratory animals (e.g., mouse, rabbit, rat, guinea pig, etc.) and birds. In some embodiments, the subject is a mammal such as a primate, for example, a human.
[00015] "Amount effective" and "effective amount" in the context of a composition or dosage form for administration to a subject refers to an amount of the composition or dosage form that produces one or more desired responses in the subject, for example, provide effective functionality of a FVIII protein, sufficiently reduce or eliminate antigenicity in HA patients, and restore hemostasis. Therefore, in some embodiments, an amount effective is any amount of a composition provided herein that produces one or more of these desired hemostasis responses with minimal immunogenicity. The amount are one that a clinician believe to have a clinical benefit for a subject in need of FVIII replacement.
[00016] Effective amount can involve only improving the patient's hemostasis with minimal immunogenicity, although in some embodiments, it involves restoring hemostasis completely. An amount that is effective can also be an amount of a composition provided herein that produces a desired therapeutic endpoint or a desired therapeutic result. Effective amount result in hemostasis of a subject after the administration of hrFVIII. The achievement of any of the foregoing are monitored by routine methods.
[00017] In some embodiments of any of the compositions and methods provided, the effective amount is one in which the desired hemostasis response persists in the subject for at least 1 week, at least 2 weeks, at least 1 month, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 9 months, at least 1 year, at least 2 years, at least 5 years, or longer. In other embodiments of any of the compositions and methods provided, the effective amount is one which produces a measurable desired hemostasis response, for example, a measurable increase in hemostasis in the patient for at least 1 week, at least 2 weeks, at least 1 month, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 9 months, at least 1 year, at least 2 years, at least 5 years, or longer. [00018] Effective amount will depend, of course, on the particular subject being treated; the severity of a condition, disease or disorder; the individual patient parameters including age, physical condition, size and weight; the duration of the treatment; the nature of concurrent therapy (if any); the specific route of administration and like factors within the knowledge and expertise of the health practitioner.
[00019] "Dosage form" means a pharmacologically and/or immunologically active material in a medium, carrier, vehicle, or device suitable for administration to a subject.
[00020] "Pharmaceutically acceptable excipient" means a pharmacologically inactive material used together with the hrFVIII and carriers to formulate the inventive compositions. Pharmaceutically acceptable excipients comprise a variety of materials known in the art, including but not limited to saccharides (such as glucose, lactose, and the like), preservatives such as antimicrobial agents, reconstitution aids, colorants, saline (such as phosphate buffered saline), and buffers.
[00021] "Protocol" refers to any dosing regimen of one or more substances to a subject. A dosing regimen may include the amount, frequency and/or mode of administration. In some embodiments, such a protocol may be used to administer one or more compositions disclosed herein to one or more subjects. Hemostasis responses in these subjects can then be assessed to determine whether or not the protocol was effective in restoring hemostasis with minimal immunogenicity. Any other therapeutic and/or prophylactic effect may also be assessed instead of or in addition to the aforementioned hemostasis responses. Whether or not a protocol had a desired effect are determined using any of the methods provided herein or otherwise known in the art. For example, a blood sample may be obtained from a subject to which a composition provided herein has been administered according to a specific protocol in order to determine whether or not hemostasis has been restored. Useful methods for detecting the presence and/or number of inhibitors include a haplotype-specific version of the Nijmegen-modified Bethesda assay, Bethesda assay, ELISA assays, ELISPOT assays, and other similar type assays.
[00022] "Haplotype" refers to a combination of DNA sequences that are closely linked on one chromosome and are commonly inherited together. The gene encoding FVIII (F8) is polymorphic in the human population, yet there are four common non- synonymous single nucleotide polymorphisms (nsSNPs), that together with two infrequent nsSNPs define eight haplotypes of the F8 gene, referred to as haplotype (H)l , H2, H3, H4, H5, H6, H7, and H8. (Viel, K. R. et al. A sequence variation scan of the coagulation factor VIII (FVIII) structural gene and associations with plasma FVIII activity levels. Blood 109, 3713-3724 (2007); Howard, T. E. et al. Haemophilia management: time to get personal? Haemophilia 17, 721-728 (2011); Viel, K. R. et al. Inhibitors of factor VIII in black patients with hemophilia. N Engl J Med 360, 1618-1627 (2009))
[00023] "B-domain deleted FVIII" (BDD-FVIII or BDDFVIII) or the like refers to a protein that by virtue of recombinant genetic engineering comprises a FVIII protein in which the B domain of FVIII or some portion of the B domain of FVIII has been removed from the sequence of FVIII resulting in a functional recombinant FVIII protein. (Toole, J. J. et al. A large region (approximately equal to 95 kDa) of human factor VIII is dispensable for in vitro procoagulant activity. Proc Natl Acad Sci U S A 83, 5939-5942 (1986)).
[00024] "Synthetic linker" refers to a sequence of DNA that by virtue of recombinant DNA techniques is introduced into the gene-encoding sequence of a gene, which DNA sequence is not present in the naturally -occurring sequence of the gene, and which DNA sequence serves the purpose of tying together an upstream and downstream portion of the gene and is necessitated when using recombinant DNA techniques to delete a domain or a portion of a domain of the gene.
[00025] "Single nucleotide polymorphism" (SNP) refers to a variation of one nucleotide (Adenine, Guanine, Cytosine, or Thymine) in the DNA sequence on a chromosome in the genome of an individual that differs from the nucleotide in the DNA sequence of either another chromosome of that individual or a chromosome of another individual.
[00026] "Non-synonymous single nucleotide polymorphism" (nsSNP or ns-
SNP) refers to a SNP in the gene -encoding region of a chromosome that by the nature of its position in the gene-encoding region of a chromosome yields a change in the amino acid sequence of the protein encoded by the gene.
[00027] Foreign substances can interact with the immune system in a number of different ways. A substance that is capable of initiating an immune response that is directed against that substance is referred to as an immunogen. The term "immunogenicity" refers to the ability of any particular substance to induce an immune response, where a substance that is highly immunogenic in turn easily induces an immune response. A set of related but distinct terms are found in the notion of antigenicity. An antigen is a substance that can be bound with specificity by molecules of the immune system. While all immunogens are antigens, not all antigens are immunogens; this is to say that some substances, while not capable of initiating an immune response, are nonetheless capable of being bound by molecules of the immune system. The derivative term "antigenicity" refers to the ability of any particularly substance be bound by molecules of the immune system.
[00028] Throughout this application, various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this pertains. The references disclosed are also individually and specifically incorporated by reference herein for the material contained in them that is discussed in the sentence in which the reference is relied upon.
[00029] The present disclosure may be understood more readily by reference to the following detailed description of embodiments and to the Figures and their previous and following description.
General
[00030] The human F8 gene is polymorphic and encodes several structurally distinct FVIII proteins referred to as haplotypes. Sequencing studies of the F8 gene have revealed four common nsSNPs that, together with two infrequent ns-SNPs, encode eight distinct wild-type FVIII proteins referred to as haplotype HI, H2, H3, H4, H5, H6, H7, and H8. The variants, their associated ns-SNP, their distribution in black, Chinese, and white populations, and inhibitor development are illustrated in Figure 1 , panel A&B.
[00031] However, all currently available replacement FVIII are based on either the HI or H2 haplotype variant. Commercially available replacement FVIII and their corresponding haplotype variant and corresponding ns-SNP location are provided for in Figure 1, and include the HI variants Kogenate® (Bayer) and Helix ate® (ZLB Behring), the H2 variants Recombinate® (Baxter) and Advate® (Baxter), and the H1/H2 variant B -domain deleted Refacto® (Pfizer) and Xyntha® (Pfizer). The amino acid sequence of the HI wild- type variant is provided for in SEQ ID NO: 101.
[00032] One of the most important problems in treatment of hemophilia A is the development of inhibitors against the recombinant FVIII proteins used in replacement therapy. Current replacement therapies comprise the haplotype 1 or haplotype 2 background amino acids. Many patients develop antibody inhibitors to these replacement FVIII products, mostly, for example, at the immunodominant regions in the A2 (from amino acids R484 to 1508) and the C2 (from amino acids E2181 to V2243) regions of the protein. Contained within these immunodominant regions are naturally occurring ns-SNPs. Subjects with ns- SNPs that differ with the replacement FVIII product may be prone to the development of inhibitors, which can be directed to these differing ns-SNPs. By deriving non-naturally occurring combinations of ns-SNP, hrFVIII polypeptides are provided herein that provide lower immunogenicity as compared to the current replacement FVIII product, and may allow the evasion of previously developed inhibitors. Thus, the treatment of subjects with inhibitors using the hrFVIII of disclosed herein provide an alternative replacement product and to the induction of immune tolerance therapy, which is currently done through laborious and expensive methods requiring multiple administrations of high levels of replacement FVIII.
[00033] Accordingly, HA patients with haplotypes that deviate from H 1 or H2 may be more prone to the development of neutralizing antibodies upon administration of recombinant FVIII products due to the presence of differing amino acid attributable to haplotype differences. It is particularly noteworthy that most neutralizing anti-FVIII alloantibodies in many congenital HA inhibitor patients are directed against two regions of the human FVIII protein that are variable among individuals of Black African descent (Figure 1 & Figure 2A), which comprise a particularly vulnerable portion of the HA patient population. Specifically, Black HA patients have long been known to experience this devastating alloimmune treatment complication at twice the frequency of White patients cared for at the same specialized Hemophilia Treatment Centers (HTCs) with the same FVIII replacement products. No analogous White- restricted common ns-SNPs have been identified in gene regions encoding either the A2- or C2-domain immunodominant inhibitor (IDI)- epitopes. Since White patients' mutations arise on one of only two endogenous background F8 haplotypes that have F8 coding sequence identity with the F8 cDNAs used to prepare the currently licensed therapeutics Kogenate® (H 1 -rFVIIIFL), Advate® (H2- rFVIIIFL) & Refacto (Hl/H2-rFVIIIBDD) - white HA patients receive FVIII products matched in primary structure to their endogenous FVIII protein. In White HA patients endogenous expression of FVIII that is matched to replacement FVIII products can induce tolerance to them through the in utero processes that mediate induction of tolerance to "self proteins. This is in contrast to the Black HA patient population, of which about 30% are treated with products that are mismatched to their endogenous FVIII sequence at as many as three ns-SNP-encoded regions in addition to the region corresponding to the HA-causing alteration (Figure 1).
[00034] Attempts has made to match patients' hap lo type with the hap lo type of the FVIII replacement product as disclosed in WO 2006/063031, assigned to Haplomics, Inc., describing isolated FVIII proteins having H3, H4, H5, and H6 haplotypic backgrounds and WO 201 1/046568 to Howard et al, describing isolated FVIII proteins having H7 and H8 haplotypic backgrounds. The FVIII replacement products disclosed in these applications, however, do not differ in sequence from the corresponding wild type haplotypes.
[00035] The hrFVIII disclosed herein have combinations of modifications based on naturally-occurring human haplotypes, allowing for the generation of functional FVIII. Antibodies directed against the currently available recombinant FVIII product's A2- domain IDI-epitope, which is bounded by and inclusive of the Arginine at residue -484 (R484) and the Isoleucine at residue-508 (1508), are noncompetitive inhibitors of the FVIIIa/FIXa intrinsic-Xase enzyme complex. FVIII antibodies directed against the C2- domain IDI-epitope block the binding of FVIIIa to phospholipid. Inhibitor neutralization studies indicate that the effects of anti-A2 and anti-C2 inhibitors are additive. Furthermore, inhibitors to a given domain appear to act independently of inhibitors to other domains. Despite the different immunologic settings in which they arise, the FVIII IDI -epitopes of alloantibody and autoantibody inhibitors appear to be the same, though autoantibody plasmas are more likely to be specific for an epitope in either the A2-domain or the C2- domain.
[00036] Although many inhibitor patients appear to have inhibitors to multiple
FVIII epitopes, some have domain specific antibodies. In general, electrostatic effects, hydrogen bonding and steric considerations may impact protein -protein (antibody-antigen) interactions. For example, meaningful distinctions may be made between the a-side chains of arginine and histidine as well as of methionine and valine (Met2238Val) with respect to these criteria. Arginine possesses a guanidinium functional group that is highly basic with a pKa of >12. It has a delocalized positive charge and can make multiple hydrogen bonds. Histidine, with its imidazole side chain, is only weakly basic with a pKa of 6.5. Small changes in pH can change histidine' s charge and it can be a proton acceptor or donor. If, for example, an antibody-antigen interaction involved a salt-bridge, replacement of arginine with histidine could destabilize the bridge. Furthermore, arginine is a large, straight chain aliphatic amino acid, whereas histidine is more compact and has a planar ring. While neither methionine nor valine is charged, methionine has a sulfur atom that can form hydrogen bonds and undergo chemical modifications that valine cannot. The residues encoded by the ns-SNPs that define the FVIII haplotypes therefore possess antigenically important differences. Accordingly, the hrFVIII polypeptides disclosed herein provide functional FVIII polypeptides that avoid specific antibody-antigenic interactions at specific domains wherein a subject could or has previously developed antibodies. Additionally, a recombinant FVIII polypeptide in which all of the known and suspected antigenic FVIII ns-SNP are replaced by alanine is designed and termed "Low immunogenicity universal donor No. 1" in Table 1 below. Alanine is the simplest chiral amino acid, consisting of a single methyl side -chain group, the lack of chemical reactivity of which is thought to contribute to a lower immunogenicity profile than all other amino acids. The rationale behind this design is to replace, in one recombinant product, all of the residues in FVIII that are suspected of promoting an immune response to FVIII with alanine, thereby placing the least immunogenic amino acid in the residue locations known to contain the most immunogenic amino acids.
[00037] The use of non-naturally occurring amino acid modifications encoded by the ns-SNPs could be combined into a large number of possible hybrids that would have fewer changes than, for example, the porcine FVIII replacement products, leading to a less immunogenic recombinant FVIII for replacement therapy. In addition, the hrFVIII polypeptides disclosed herein contain significant and distinct amino acid modifications compared to the HI and H2 F8 haplotypes and thus provide important alternatives to current replacement therapies. These hybride FVIII can therefore be used as an initial replacement FVIII product, or as alternative FVIII product that can be administered to inhibitor patients (patients with antibodies to the currently marketed HI or H2 Haplotype products).
Full Length Hybrid hrFVIII Polypeptides
[00038] Provided herein are hydrid recombinant FVIII polypeptides (hrFVIII) comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns-SNP. In one embodiment, the recombinant FVIII polypeptides provided herein have non-naturally occurring combinations of two to fifteen amino acid modifications, for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 amino acid modifications, selected from the group consisting of: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser.
[00039] The hrFVIII polypeptides contemplated herein contain combinations of modifications at least 2 or more of the naturally occurring ns-SNP sites, creating non- naturally occurring hrFVIII polypeptides. The 2 or more modifications are selected from the following: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser, wherein the remainder of the full length hrFVIII comprises the HI wild -type sequence, provided in SEQ ID No: 101. In certain embodiments, the remainder of the full length hrFVIII comprises amino acid sequence that are homologous to the HI wild -type sequence, for example, at least about 90%, 91%, 92%>, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous. In certain embodiments, additional modifications are made to the HI wild-type amino acid sequence based on ns-SNPs other than those listed, or alanine substitutions at amino acids of particular antigenicity or immuno genicity .
[00040] Examples of hrFVIII polypeptides provided herein comprising various amino acid modifications compared to the FVIII HI wild -type amino acid sequence are summarized in Table 1A below. Specifically, Table 1 discloses 17 separate full-length recombinant FVIII constructs (FL-rFVIII). The first construct listed is HI (Kogenate). HI is the most common haplotype of FVIII in humans, and for these studies the sequence of HI provides the template construct upon which amino acid changes are made to give rise to the other constructs in the table. For constructs that encode each of the 16 other constructs in the table (including other FVIII haplotypes, FVIII haplotype chimeras, or universal donors), 15 separate definite sites in the amino acid sequence of HI FVIII are variously modified to yield these other constructs. For instance, in comparing HI (Kogenate) to H2 (Recombinate), the entirety of the H2 sequence is identical to the HI sequence with the exception of a single amino acid difference at amino acid residue 1241, which in HI is an aspartic acid (Aspl241), while in H2 is a glutamic acid (Glul241). In genetic mutation nomenclature, this is written as "Aspl241Glu" signifying that the aspartic acid at residue 1241 (in HI) is modified to a glutamic acid (in H2) at that site. Likewise, the sequence differences between HI and H3 are displayed in the third line of the table (labeled H3). HI and H3 are identical over the full length of the amino acid sequence, with the exception of two modifications in H3 : Aspl241Glu and Met2238Val. H4, on the other hand, also has two modifications compared to HI, but one of these is at an amino acid residue site distinct from H3. Thus H4 is identical in sequence over its entire length compared to HI, with the exception of two amino acid modifications: Arg484His and Aspl241Glu. Taking the sum of modifications from H3 and H4, there are three total modifications (as they have a single modification in common) and a chimera is formed by combining these three modifications into a single construct. This particular construct is the tenth entry in the table and is labeled H3/H4. The H3/H4 construct is identical in sequence over its entire length compared to HI, with the exception of three amino acid modifications: Arg484His, Aspl241Glu, and Met2238Val. Other chimeras are also displayed in the table and are constructed from combinations of the modifications present in haplotypes H3-H9. Furthermore, modifications are made that are not necessarily derived from naturally occurring FVIII haplotypes. The last three lines of the table contain constructs with such modifications. For instance, "Low antigenicity universal donor No. 1" is identical in sequence over its entire length compared to HI, with the exception of fifteen amino acid modifications, corresponding to every amino acid modification listed in the table. Furthermore, the last entry in the table contains a construct that is identical in sequence over its entire length compared to HI, with the exception that the amino acid alanine replaces every amino acid at the fifteen modification sites listed in the table.
[00041] The hrFVIII polypeptides disclosed herein include, for example, H3/H4, H3/H4/H6, H3/H4/H6/H7, H3/H4/H6/H7/H8, H3/H4/H6/H7/H8/H9, low antigenicity universal donor No. 1, low antigenicity universal donor No. 2, and low immunogenicity universal donor No. 1. In addition, disclosed is an isolated or recombinant FVIII polypeptide identified as hap lo type 9.
Table 1A. Naturally-occurring and engineered Full-length (FL) human (h)-rFVIII proteins.
Figure imgf000015_0001
[00042] Referring to Table 1A, 18 distinct full-length human FVIII (FL hFVIII) proteins, which all contain 2,332 amino acids are presented. These 18 flFVIII comprise either the 9 naturally-occurring haplotype (H) forms of the mature FVIII protein that have been found to date in the plasma of unrelated healthy persons with diverse geographic origins (i.e., HI, H2, H3, H4, H5, H6, H7, H8, & H9), or the 9 hr FVIII proteins, which, while containing only human FVIII amino acid sequences, are encoded by non- naturally occurring combinations of the less frequent alleles of the known ns-SNPs found to date in the human FVIII gene (h-F8). The amino acid sequences in the naturally occurring HI & H2 forms of FL hFVIII are contained in the existing FL therapeutic FVIII proteins Kogenate® (also known as Helixate®) and Recombinate® (also known as Advate®). The primary amino acid sequences of 10 of the distinct FL hFVIII proteins and the nucleic acid sequences of the cDNAs that encode them are indicated in Table 1A above in the columns designated "SEQ ID NO (protein)" and "SEQ ID NO (cDNA)", respectively. The amino acid residue(s) bolded and highlighted grey in the haplotypic forms of the FL h-rFVIII protein listed (i.e., other than in the first one, which is one of the two specific haplotype forms for this therapeutic family that are currently in clinical use, with the other being the second) represent the naturally-occurring variable positions in the human FVIII protein and indicate how each of these sixteen hrFVIII are distinct allelically from the currently used therapeutics, Kogenate® and Recombinate®.
[00043] In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising two amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising three amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising four amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising five amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising six amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising seven amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising eight amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising nine amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising ten amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising eleven amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising twelve amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising thirteen amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising fourteen amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser. In one embodiment, the hrFVIII comprises a non-naturally occurring combination comprising fifteen amino acid modifications: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser. [00044] In one embodiment, the hrFVIII comprises the amino acid modifications Arg484His, Aspl241Glu, and Met2238Val, creating an H3/H4 FVIII hybrid, the amino acid sequence of which is provided in SEQ ID NO: 1. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 1. In one embodiment, the hrFVIII comprises the amino acid modifications Arg484His and Met2238Val, creating an alternative H3/H4 FVIII hybrid, the amino acid sequence of which is provided in SEQ ID NO: 13. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 13. In one embodiment, the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 2. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 2. In one embodiment, the hrFVIII comprises the amino acid modifications Arg484His, Arg776Gly, Aspl241Glu, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 15. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 15. The modifications described herein are further illustrated in Table 1 above. In one embodiment, the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 16. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 16. The modifications described herein are further illustrated in Table 1 above. In one embodiment, the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, Hisl919Asn, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 17. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 17. The modifications described herein are further illustrated in Table 1 above.
[00045] In an additional aspect, low antigenicity universal donor hrFVIII polypeptides and nucleic acids encoding said polypeptides are provided. In one embodiment, the low antigenicity hrFVIII polypeptide comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, and Met2238Val, and the additional modifications Glul l3Asp, Ala387Thr, Argl l07Trp, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Pro2292Ser, the amino acid sequence of which is provided in SEQ ID NO: 18. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 18. The modifications described herein are further illustrated in Table 1 above. In one embodiment, the low antigenicity universal donor hrFVIII polypeptide comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Argl260Lys, and Met2238Val, and the additional modifications Glul l3Asp, Ala387Thr, Argl l07Trp, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Pro2292Ser, the amino acid sequence of which is provided in SEQ ID NO: 19. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 19. The modifications described herein are further illustrated in Table 1 above.
[00046] A further aspect includes a low immunogenicity universal donor No. 1 hrFVIII polypeptide, and nucleic acids encoding said polypeptides, comprising the amino acid modifications Gln334Ala, Gln334Ala, Arg484Ala, Arg776Ala, Asp 1241 Ala, Argl260Ala, and Met2238Ala, and the additional modifications Glul l3Ala, Argl l07Ala, Leul462Ala, Ilel668Ala, His 1919Ala, Glu2004Ala, Val2223Ala, and Pro2292Ala, the amino acid sequence of which is provided in SEQ ID NO: 20. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 20. The modifications described herein are further illustrated in Table 1 above.
Haplotype 9
[00047] In one aspect, an isolated or recombinant polypeptide herein identified as Haplotype 9, and a nucleic acid encoding said polypeptide, is provided comprising the amino acid modifications Aspl241Glu and His l919Asn, the amino acid sequence of which is provided in SEQ ID NO: 33. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 33. This Haplotype 9 FVIII polypeptide is further illustrated in Table 1 above.
BDD-FVII Polypeptides
[00048] Also provided herein are hrFVIII polypeptides comprising a FVIII polypeptide wherein at least a portion of the B-domain has been deleted, further comprising amino acid modifications at ns-SNP positions compared to the currently available BDD- FVIII products. Table IB. B-domain-deleted (BDD) human hrFVIII using engineered junction BDD-1.
Figure imgf000020_0001
[00049] Referring to Table IB, the B-domain deletion (BDD) junction in these
10 distinct BDD FVIII proteins is called BDD-1 and corresponds to that found in the existing therapeutic BDD-1 rFVIII protein known as Refacto® or Xyntha® (Moroctocog alfa). BDD- 1 is an engineered junction created by linking (via peptide bond formation) the FVIII serine (Ser [S]) and glutamine (Glu [Q]) residues at positions 743 and 1638, respectively, in the mature circulating form of the FVIII protein (i.e., S743 - Q1638), which results in a protein containing 1,438 amino acids. Due to the engineered deletion in these BDD-1 containing hrFVIII proteins that removes the 5 variable B-domain residues R776G, R1 107W, D 1241E, R1260K and L1462P, which are coded by the 5 ns-SNPs in exon-14 of the human FVIII gene (F8), there are only 10 distinct haplotypic forms of this protein as several actually have identical primary amino acid (i.e., protein) sequences that are encoded by identical cDNA sequences as follows: (1) HI = H2 = H6; (2) H3 = H5 (protein & cDNA SEQ ID NOs: 3 & 9, respectively); (3) H4 = H8 (protein & cDNA SEQ ID NOs: 4 & 10, respectively); (4) H7 (protein & cDNA SEQ ID NOs: 5 & 11, respectively); (5) H9 (protein & cDNA SEQ ID NOs: 52 & 50, respectively); (6) H3/H4 (+D 1241E) = H3/H4 (-D1241E) = H3/H4/H6 (protein & cDNA SEQ ID NOs: 6 & 12, respectively); (7) H3/H4/ H7 = H3/H4/H6/H7 = H3/H4/H6/H7/H8 (protein & cDNA SEQ ID NOs: 21 & 39, respectively); (8) H3/H4/H7/H9 = H3/H4/H6/H7/H8/H9 (protein & cDNA SEQ ID NOs: 22 & 40, respectively); (9) Low antigenicity (LA) universal donor No. 3 (protein & cDNA SEQ ID NOs: 23 & 41 , respectively); and (10) Low immunogenicity (LI) universal donor No. 2 (protein SEQ ID NOs: 24). The amino acid residue(s) bolded and highlighted grey in the haplotypic forms of the BDD-1 hrFVIII protein listed (i.e., other than in the first one, which is the specific haplotype form for this therapeutic family currently in clinical use) represent the naturally- occurring variable positions in the human FVIII protein and indicate how each of these nine hrFVIII are distinct allelically from the currently used therapeutic, which is referred to as Refacto® or Xyntha® .
Table 1C. B -domain-deleted (BDD) human hrFVIII using engineered junction BDD-2.
Figure imgf000021_0001
[00050] Referring to Table 1C, the B-domain deletion (BDD) junction in these
10 BDD FVIII proteins is called BDD-2 and corresponds to that found in the existing therapeutic BDD-2 rFVIII protein known as Novo8® (Turoctocog alfa). BDD-2 is an engineered junction created by linking (via peptide bond formation) the FVIII serine (Ser [S]) and glutamine (Glu [Q]) residues at positions 750 and 1638, respectively, in the mature circulating form of the FVIII protein (i.e., S750 - Q1638), which results in a protein containing 1,445 amino acids. Due to the engineered deletion in these BDD-2 containing rFVIII proteins that removes the 5 variable B-domain residues R776G, R1107W, D1241E, R1260K and L1462P, which are encoded by the 5 ns-SNPs in exon-14 of the human FVIII gene (F8), there are only 10 distinct ha lotypic forms of this protein as several actually have identical primary amino acid sequences as follows: (1) HI = H2 = H6; (2) H3 = H5 (protein & cDNA SEQ ID NOs: 25 & 42, respectively); (3) H4 = H8 (protein & cDNA SEQ ID NOs: 26 & 43, respectively); (4) H7 (protein & cDNA SEQ ID NOs: 27 & 45, respectively); (5) H9 (protein & cDNA SEQ ID NOs: 53 & 51, respectively); (6) H3/H4 (+D 1241E) = H3/H4 (-D1241E) = H3/H4/H6 (protein & cDNA SEQ ID NOs: 28 & 44, respectively); (7) H3/H4/ H7 = H3/H4/H6/H7 = H3/H4/H6/H7/H8 (protein & cDNA SEQ ID NOs: 29 & 46, respectively); (8) H3/H4/H7/H9 = H3/H4/H6/H7/H8/H9 (protein & cDNA SEQ ID NOs: 30 & 47, respectively); (9) Low antigenicity (LA) universal donor No. 4 (protein & cDNA SEQ ID NOs: 31 & 48, respectively); and (10) Low immunogenicity (LI) universal donor No. 3 (protein SEQ ID NOs: 32). The amino acid residue(s) bolded and highlighted grey in the haplotypic forms of the BDD-2 rFVIII protein listed (i.e., other than in the first one, which is the specific haplotype form for this therapeutic family currently in clinical use) represent the naturally -occurring variable positions in the human FVIII protein and indicate how each of these nine hrFVIII are distinct allelically from the currently used therapeutic, which is referred to as Novo 8®.
Table ID. B -domain-deleted (BDD) human hrFVIII using engineered junction BDD-3.
Figure imgf000023_0001
[00051] Referring to Table ID, the BDD junction in these 10 BDD rFVIII proteins is called BDD-3 and corresponds to that found in the existing therapeutic BDD-3 rFVIII protein known as Octopharma8® (Simoctocog alfa). BDD-3 is an engineered junction created by linking (via 2 peptide bond formations) the FVIII histidine (His [H]) and glutamate (Glu [E]) residues at positions 748 and 1649, respectively, in the circulating mature FVIII protein to the N- and C-terminal ends of the synthetic, non-FVIII octapeptide sequence QAYRYRRG (i.e., H748 - QAYRYRRG - E1649), which results in a protein containing 1,440 amino acids. Due to the engineered deletion in these BDD-3 containing rFVIII proteins that removes the 5 variable B-domain residues R776G, Rl 107W, D 1241E, R1260K and L1462P, which are encoded by the 5 ns-SNPs in exon-14 of the human FVIII gene (F8), there are only 10 distinct haplotypic forms of this protein as several actually have identical primary amino acid sequences indicated in Table ID above. The amino acid residue(s) bolded and highlighted grey in the haplotypic forms of the BDD-3 rFVIII protein listed (i.e., other than in the first one, which is the specific haplotype form for this therapeutic family currently in clinical use) represent the naturally-occurring variable positions in the human FVIII protein and indicate how each of these nine hrFVIII are distinct allelically from the currently used therapeutic, which is referred to as Octopharma8®. [00052] In one embodiment, the hrFVlll comprises the amino acid modification Met2238Val (H3=H5). In one embodiment, the hrFVlll comprises the amino acid sequence of SEQ ID NO: 3, provided herewith. In one embodiment, a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 3. In one embodiment, the hrFVlll comprises the amino acid modification Arg484His.(H4=H8) In one embodiment, the hrFVlll comprises the amino acid sequence of SEQ ID NO: 4 provided herewith. In one embodiment, a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 4. In one embodiment, the hrFVlll comprises the amino acid modification Gln334Pro (H7). In one embodiment, the hrFVlll comprises the amino acid sequence of SEQ ID NO: 5 provided herewith. In one embodiment, a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 5. In one embodiment, the hrFVlll comprises the amino acid modifications Arg484His and Met2238Val (H3/H4). In one embodiment, the hrFVlll comprises the amino acid sequence of SEQ ID NO: 6 provided herewith. In one embodiment, a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 6. In one embodiment, the hrFVlll comprises the amino acid modifications Gln334Pro, Arg484His, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 21. In one embodiment, a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 21. In one embodiment, the hrFVlll comprises the amino acid modifications Gln334Pro, Arg484His, His l919Asn, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 22. In one embodiment, a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 22. In one embodiment, the hrFVlll comprises the amino acid modifications Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser, the amino acid sequence of which is provided in SEQ ID NO: 23. In one embodiment, a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 23. In one embodiment, the hrFVlll comprises the amino acid modifications Glul l3Ala, Gln334Ala, Arg484Ala, Ilel668Ala, His l919Ala, Glu2004Ala, Val2223Ala, Met2238Ala, and Pro2292Ala, the amino acid sequence of which is provided in SEQ ID NO: 24. In one embodiment, a hrFVlll is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 24. [00053] Also provided herein are additional hrFVIII polypeptides comprising a
FVIII polypeptide wherein at least a portion of the B -domain has been deleted, further comprising amino acid modifications at ns-SNP positions compared to the currently available BDD-FVIII products. In some embodiments, the linker region in the B -domain deleted constructs can be varied to include additional or fewer amino acids from the N -terminus and C-terminus of the B domain. In some embodiments, the linker comprises the linker sequence SFSQNSRHPSQNPPVLK HQR, comprising ten amino acids from the N-terminus of the B- domain followed by eleven amino acids from the C-terminus of the B-domain. (Thim, L, et al, Haemophilia 16: 349-359 (2010)). These constructs with the 21 amino acid B-domain linker are referred to as B-domain deleted 2 (BDD-2). In one embodiment, the hrFVIII comprises the amino acid modification Met2238Val (H3=H5). In one embodiment, the hrFVIII comprises the amino acid sequence of SEQ ID NO: 25 provided herewith. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 25. In one embodiment, the hrFVIII comprises the amino acid modification Arg484His (H4=H8). In one embodiment, the hrFVIII comprises the amino acid sequence of SEQ ID NO: 26 provided herewith. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 26. In one embodiment, the hrFVIII comprises the amino acid modification Gln334Pro (H7). In one embodiment, the hrFVIII comprises the amino acid sequence of SEQ ID NO: 27 provided herewith. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 27. In one embodiment, the hrFVIII comprises the amino acid modifications Arg484His and Met2238Val (H3/H4). In one embodiment, the hrFVIII comprises the amino acid sequence of SEQ ID NO: 28 provided herewith. In one embodiment, a hrFVIII is provided that is at least about 90%>, 91%>, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 28. In one embodiment, the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 29. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 29. In one embodiment, the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, His l919Asn, and Met2238Val, the amino acid sequence of which is provided in SEQ ID NO: 30. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 30. In one embodiment, the hrFVIII comprises the amino acid modifications Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser, the amino acid sequence of which is provided in SEQ ID NO: 31. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 31. In one embodiment, the hrFVIII comprises the amino acid modifications Glul l3Ala, Gln334Ala, Arg484Ala, Ilel668Ala, His l919Ala, Glu2004Ala, Val2223Ala, Met2238Ala, and Pro2292Ala, the amino acid sequence of which is provided in SEQ ID NO: 32. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 32.
Nucleic Acids
[00054] Further provided are nucleic acids that encode the hrFVIII polypeptides described herein, including, for example, SEQ ID NOs: 1-6, 13, 15-33, 52, and 53. This would include all degenerate sequences related to a specific polypeptide sequence, i.e. all nucleic acids having a sequence that encodes one particular polypeptide sequence as well as all nucleic acids, including degenerate nucleic acids, encoding the disclosed variants and derivatives of the polypeptide sequences. Thus, while each particular nucleic acid sequence may not be written out herein, it is understood that each and every sequence is in fact disclosed and described herein through the disclosed polypeptide sequence. It is also understood that while no amino acid sequence indicates what particular DNA sequence encodes that polypeptide within an organism, where particular variants of a disclosed polypeptides are disclosed herein, the known nucleic acid sequence that encodes that polypeptide in the particular gene from which that polypeptide arises is also known and herein disclosed and described. cDNAs Encoding hrFVIII Polypeptides
[00055] In one embodiment, provided is a complementary DNA (cDNA) encoding a hrFVIII comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns- SNP. In one embodiment, the cDNA encodes a hrFVIII comprising a non-naturally occurring combination comprising 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, or 15 amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser. [00056] In one embodiment, the encoded hrFVIII comprises the amino acid modifications Arg484His, Aspl241Glu, and Met2238Val. In one embodiment, the cDNA comprises the nucleic acid sequence of SEQ ID NO: 7 provided herewith. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 7. In one embodiment, the encoded hrFVIII comprises the amino acid modifications Arg484His and Met2238Val, creating an alternative H3/H4 FVIII hybrid. In one embodiment, the cDNA comprises the nucleic acid sequence of SEQ ID NO: 14 provided herewith. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 14. In one embodiment, the encoded hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, and Met2238Val. In one embodiment, the cDNA comprises the nucleic acid sequence of SEQ ID NO: 8, provided in Table 30 below. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 8.
[00057] In one embodiment, the cDNA encodes a hrFVIII lacking a B-domain of wild-type FVIII. In one embodiment, the cDNA encodes a hrFVIII comprising the amino acid modification Met2238Val (H3/H5). In one embodiment, the cDNA comprises the nucleic acid sequence of SEQ ID NO: 9 provided herewith wherein the gap in the sequence indicates the B-domain deleted sequence. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 9. In one embodiment, the cDNA encodes a hrFVIII comprising the amino acid modification Arg484His (H4/H8). In one embodiment, the cDNA comprises the nucleic acid sequence of SEQ ID NO: 10 provide herewith wherein the gap in the sequence indicates the B-domain deleted sequence. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 10. In one embodiment, the cDNA encodes a hrFVIII comprising the amino acid modification Gln334Pro (H7). In one embodiment, the cDNA comprises the amino acid sequence of SEQ ID NO: 11 provided herewith wherein the gap in the sequence indicates the B-domain deleted sequence. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 1 1. In one embodiment, the cDNA encodes a hrFVIII comprising the amino acid modifications Arg484His and Met2238Val (H3/H4). In one embodiment, the cDNA comprises the nucleic acid sequence of SEQ ID NO: 12 provided herewith wherein the gap in the sequence indicates the B-domain deleted sequence. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 12.
[00058] In one embodiment, the cDNA encoding the hrFVIII comprises the amino acid modifications Arg484His, Arg776Gly, Aspl241Glu, and Met2238Val. In one embodiment, the cDNA comprises the nucleic acid sequence of SEQ ID NO: 34 provided herewith. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 34. In one embodiment, the cDNA encodes a hrFVIII polypeptide comprising the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, and Met2238Val, the cDNA sequence of which is provided herewith in SEQ ID NO: 35. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 35. In one embodiment, the cDNA encodes a hrFVIII polypeptide comprising the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, Hisl919Asn, and Met2238Val, the cDNA sequence of which is provided herewith in SEQ ID NO: 36. In one embodiment, a hrFVIII is provided that is at least about 90%>, 91%>, 92%>, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 36.
[00059] In one embodiment, the cDNA encodes a low antigenicity hrFVIII polypeptide comprising the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Aspl241Glu, Argl260Lys, and Met2238Val, and the additional modifications Glul l3Asp, Ala387Thr, Argl l07Trp, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Pro2292Ser, the cDNA sequence of which is provided herewith in SEQ ID NO: 37. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 37.
[00060] In one embodiment, the cDNA encodes a low antigenicity universal donor hrFVIII polypeptide comprising the amino acid modifications Gln334Pro, Arg484His, Arg776Gly, Argl260Lys, and Met2238Val, and the additional modifications Glul l3Asp, Ala387Thr, Argl l07Trp, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Pro2292Ser, the cDNA sequence of which is provided herewith in SEQ ID NO: 38. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 38.
[00061] In one embodiment, the cDNA encoding hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, and Met2238Val, the cDNA sequence of which is provided herewith in SEQ ID NO: 39. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 39. In one embodiment, the cDNA encoding hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, His l919Asn, and Met2238Val, the cDNA sequence of which is provided herewith in SEQ ID NO: 40. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 40. In one embodiment, the cDNA encoding hrFVIII comprises the amino acid modifications Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser, the cDNA sequence of which is provided herewith in SEQ ID NO: 41. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 41.
[00062] Also provided herein are additional cDNA sequences encoding hrFVIII polypeptides comprising a FVIII polypeptide wherein at least a portion of the B -domain has been deleted, further comprising amino acid modifications at ns-SNP positions compared to the currently available BDD-FVIII products. In some embodiments, the linker region in the B-domain deleted constructs can be varied to include additional or fewer amino acids from the N-terminus and C-terminus of the B domain. In some embodiments, the linker comprises the linker cDNA sequence encoding the amino acid sequence SFSQNSRHPSQNPPVLK HQR, comprising ten amino acids from the N-terminus of the B- domain followed by eleven amino acids from the C-terminus of the B-domain. These constructs with the 21 amino acid B-domain linker are referred to as B-domain deleted 2 (BDD-2). In one embodiment, the hrFVIII comprises the amino acid modification Met2238Val (H3/H5). In one embodiment, the hrFVIII comprises the amino acid sequence of SEQ ID NO: 42 provided herewith. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 42. In one embodiment, the hrFVIII comprises the amino acid modification Arg484His (H4/H8). In one embodiment, the hrFVIII comprises the amino acid sequence of SEQ ID NO: 43, provided in Table 44 below. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 43. In one embodiment, the hrFVIII comprises the amino acid modifications Arg484His, Aspl241Glu, and Met2238Val (H3/H4). In one embodiment, the hrFVIII comprises the amino acid sequence of SEQ ID NO: 44 provided herewith. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 44. In one embodiment, the hrFVIII comprises the amino acid modification Gln334Pro (H7). In one embodiment, the hrFVIII comprises the amino acid sequence of SEQ ID NO: 45 provided herewith. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 45. In one embodiment, the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, and Met2238Val, the amino acid sequence of which is provided herewith in SEQ ID NO: 46. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 46. In one embodiment, the hrFVIII comprises the amino acid modifications Gln334Pro, Arg484His, Hisl919Asn, and Met2238Val, the amino acid sequence of which is provided herewith in SEQ ID NO: 47. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 47. In one embodiment, the hrFVIII comprises the amino acid modifications Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser, the amino acid sequence of which is provided herewith in SEQ ID NO: 48. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 48.
[00063] In one aspect, an isolated cDNA encoding Haplotype 9 polypeptide, is provided comprising the amino acid modifications Asp 1241 Glu and His l919Asn, the cDNA sequence of which is provided herewith in SEQ ID NO: 49. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 49. In one aspect, an isolated cDNA encoding a Haplotype 9 B- domain deleted (BDD) polypeptide, is provided comprising the amino acid modification Hisl919Asn, the cDNA sequence of which is provided herewith in SEQ ID NO: 50. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 50. In one aspect, an isolated cDNA encoding a Haplotype 9 B -domain deleted-2 (BDD-2) polypeptide, is provided comprising the amino acid modification Hisl919Asn, the cDNA sequence of which is provided herewith in SEQ ID NO: 51. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 51. In one aspect, an isolated Haplotype 9 B-domain deleted (BDD) polypeptide, is provided comprising the amino acid modification Hisl919Asn, the amino acid sequence of which is provided herewith in SEQ ID NO: 52. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 52. In one aspect, an isolated Haplotype 9 B-domain deleted-2 (BDD-2) polypeptide, is provided comprising the amino acid modification Hisl919Asn, the amino acid sequence of which is provided herewith in SEQ ID NO: 53. In one embodiment, a hrFVIII is provided that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NO: 53.
Additional Amino Acid Modifications
[00064] In addition to the naturally occurring ns-SNPs that may be combined to create hrFVIII polypeptides disclosed herein, additional amino modifications could also be included to lower antigenicity by even greater amounts. For example, further engineering of the lowest antigenicity constructs could proceed by engineering additional minimal substitutions. Thus, additional modifications in the A2- and C2-epitopes could be engineered. Software modeling programs can be used to help predict the effect of amino acid substitutions. In order to minimize the risk of creating new epitopes, insights are also emerging from rigorous studies of FVIII T-cell epitopes. A recent publication identified 32 peptide regions of FVIII presented on dendritic cells (via binding to MHC-class-II molecules) by HLA-typed healthy donors (van Haren et al. 2012). These same studies can be done among HA patients with inhibitors. Methods using an algorithm can be used which incorporates information concerning individual patient-specific HLA-class-II (HLA-II) repertoires and hemophilic F8 mutation types to generate an immunogenicity score that stratifies the risk for the development of inhibitors associated with common pharmacogenetically-relevant mutation types, e.g. the intron-22-inversion mutation and the recurrent subset of inhibitor-associated FVIII missense mutations, Arg593Cys, Tyr2105Cys, Arg2150His, Trp2229Cys or Pro2300Leu. These tools can provide additional engineering to create additional low antigenicity/low immunogenicity FVIII hybrid constructs. Additional modifications are described, for example, above and in Table 1.
Expression Vectors Containing Nucleic Acids Encoding hrFVIII Polypeptides
[00065] The expression vectors can be used to express the hrFVIIIs described herein in a eukaryotic host cell, for example a mammalian cell, wherein the hrFVIII can subsequently be isolated, purified, and processed into a form suitable for administration to a subject. In one embodiment, the expression vector is a viral vector. In one embodiment, the expression vector is a non-viral vector.
[00066] The nucleic acids that are delivered to cells typically contain expression controlling systems. For example, the inserted genes in viral and retroviral systems usually contain promoters, and/or enhancers to help control the expression of the desired gene product. A promoter is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site. A promoter contains core elements required for basic interaction of RNA polymerase and transcription factors, and may contain upstream elements and response elements.
[00067] Promoters controlling transcription from vectors in mammalian host cells may be obtained from various sources, for example, the genomes of viruses such as: polyoma, Simian Virus 40 (SV40), adenovirus, retroviruses, hepatitis-B virus and cytomegalovirus (CMV), or from heterologous mammalian promoters, e.g. beta actin promoter. The early and late promoters of the SV40 virus are conveniently obtained as an SV40 restriction fragment which also contains the SV40 viral origin of replication (Fiers et al, Nature, 273 : 1 13 (1978)). The immediate early promoter of the human cytomegalovirus is conveniently obtained as a Hindlll E restriction fragment (Greenway, P. J. et al, Gene 18: 355-360 (1982)). For instance, promoters from the host cell or related species also are useful herein.
[00068] Enhancer generally refers to a sequence of DNA that functions at no fixed distance from the transcription start site and can be either 5' (Laimins, L. et al, Proc. Natl. Acad. Sci. 78: 993 (1981)) or 3' (Lusky, M. L., et al, Mol. Cell Bio. 3: 1 108 (1983)) to the transcription unit. Furthermore, enhancers can be within an intron (Banerji, J. L. et al, Cell 33 : 729 (1983)) as well as within the coding sequence itself (Osborne, T. F., et al, Mol. Cell Bio. 4: 1293 (1984)). They are usually between 10 and 300 by in length, and they function in cis. Enhancers function to increase transcription from nearby promoters. Enhancers also often contain response elements that mediate the regulation of transcription. Promoters can also contain response elements that mediate the regulation of transcription. Enhancers often determine the regulation of expression of a gene. While many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, -fetoprotein and insulin), typically one will use an enhancer from a eukaryotic cell virus for general expression. Examples are the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
[00069] The promoter and/or enhancer may be specifically activated either by light or specific chemical events which trigger their function. Systems can be regulated by reagents such as tetracycline and dexamethasone. There are also ways to enhance viral vector gene expression by exposure to irradiation, such as gamma irradiation, or alkylating chemotherapy drugs.
[00070] In certain embodiments the promoter and/or enhancer region can act as a constitutive promoter and/or enhancer to maximize expression of the region of the transcription unit to be transcribed. In certain constructs the promoter and/or enhancer region are active in all eukaryotic cell types, even if it is only expressed in a particular type of cell at a particular time. A promoter of this type for example is the CMV promoter (650 bases). Other example promoters are SV40 promoters, cytomegalovirus (full length promoter), and retroviral vector LTR.
[00071] Expression vectors used in eukaryotic host cells (yeast, fungi, insect, plant, animal, human or nucleated cells) may also contain sequences necessary for the termination of transcription which may affect mRNA expression. These regions are transcribed as polyadenylated segments in the untranslated portion of the mRNA encoding tissue factor protein. The 3' untranslated regions also include transcription termination sites. In some embodiments, the transcription unit also contain a polyadenylation region. One benefit of this region is that it increases the likelihood that the transcribed unit will be processed and transported like mRNA. The identification and use of polyadenylation signals in expression constructs is well established. For instance, homologous polyadenylation signals can be used in the transgene constructs. In certain transcription units, the polyadenylation region is derived from the SV40 early polyadenylation signal and consists of about 400 bases. In one embodiment, the polyadenylation signal is derived from the human growth hormone poly-A signal (hGH-pA). The transcribed units can contain other standard sequences alone or in combination with the above sequences improve expression from, or stability of, the construct.
[00072] The expression vectors can include nucleic acid sequence encoding a marker product. This marker product is used to determine if the gene has been delivered to the cell and once delivered is being expressed. For example, the marker genes can be the E. Coli lacZ gene, which encodes β-galactosidase, and green fluorescent protein.
[00073] In some embodiments the marker may be a selectable marker.
Examples of suitable selectable markers for mammalian cells are dihydrofolate reductase (DHFR), thymidine kinase, neomycin, neomycin analog G418, hydromycin, and puromycin. When such selectable markers are successfully transferred into a mammalian host cell, the transformed mammalian host cell can survive if placed under selective pressure. There are two widely used distinct categories of selective regimes. The first category is based on a cell's metabolism and the use of a mutant cell line which lacks the ability to grow independent of a supplemented media. Two examples are: CHO DHFR -cells and mouse LT -cells. These cells lack the ability to grow without the addition of nutrients such as thymidine or hypoxanthine. Because these cells lack certain genes necessary for a complete nucleotide synthesis pathway, they cannot survive unless the missing nucleotides are provided in a supplemented media. An alternative to supplementing the media is to introduce an intact DHFR or TK gene into cells lacking the respective genes, thus altering their growth requirements. Individual cells which were not transformed with the DHFR or TK gene will not be capable of survival in non-supplemented media.
[00074] The second category is dominant selection which refers to a selection scheme used in any cell type and does not require the use of a mutant cell line. These schemes typically use a drug to arrest growth of a host cell. Those cells which have a novel gene would express a protein conveying drug resistance and would survive the selection. Examples of such dominant selection use the drugs neomycin, (Southern P. and Berg, P., J. Molec. Appl. Genet. 1 : 327 (1982)), mycophenolic acid, (Mulligan, R. C. and Berg, P. Science 209: 1422 (1980)) or hygromycin, (Sugden, B. et al, Mol. Cell. Biol. 5 : 410-413 (1985)). The three examples employ bacterial genes under eukaryotic control to convey resistance to the appropriate drug G418 or neomycin (geneticin), xgpt (mycophenolic acid) or hygromycin, respectively. Others include the neomycin analog G418 and puramycin. The disclosed vectors thus provide DNA molecules which are capable of integration into a mammalian chromosome without substantial toxicity.
[00075] The FVIII constructs disclosed herein are created using standard molecular cloning techniques (Sambrook, J. & Green, M. R. Molecular cloning: a laboratory manual, Cold Spring Harbor Laboratory Press, 2012). For instance, the starting material for cloning the constructs can consist of a cDNA construct that encodes for full-length H3 FVIII (FL-H3-FVIII), named HOW1 as shown in Figure 3. Several restriction endonuclease sites have been identified in the HOW1 cDNA construct to allow for digestion of the construct and subsequent ligation of replacement or insert construct into the construct. Referring to Figure 5, digestion of HOW1 with restriction endonucleases Kpnl and Xbal removes from the construct part of the A domain, all of the B domain, and the majority of the C domain. By ligation an insert construct entitled Fragment C-V can be inserted into HOW1 as shown in Figure 5 to create a H3 BDD-2 construct. This H3 BDD-2 construct encodes for a function B- domain-deleted FVIII in which the majority of the B domain has been deleted, with only a small linker sequence from the B domain remaining to connect the A and C domains. Similarly, when an insert construct entitled Fragment C-M is inserted into a HOW1 digested with Kpnl and Xbal as shown in Figure 6, a HI BDD-2 construct is created. The H3 BDD-2 construct can in turn be digested with Kpnl and Xbal followed by insertion of insert construct entitled Fragment A-H to create a H3/H4 BDD-2 construct as shown in Figure 7. Similarly, the HI BDD-2 construct can in turn be digested with Kpnl and Xbal followed by insertion of insert construct entitled Fragment A-H to create a H4 BDD-2 construct as shown in Figure 8. The FVIII constructs created can then be used to produce corresponding hrFVIII. For example the H3/H4 BDD-2 construct shown in Figure 7 comprises cDNA having a SEQ ID No: 44 can be used to create the hrFVIII having a SEQ ID NO: 28.
[00076] Using other insert constructs that have restriction endonuclease sites that are complementary to the sites in HOW1, a variety of combinations of modifications can be made to the FVIII constructs. These insert constructs can be synthesized to specifications in terms of sequence to form the cDNAs disclosed herein. In one embodiment, the insert construct is obtained through commercial sources. Although a cDNA construct that encodes for full-length H3 FVIII is used as an example, cDNA constructs that encodes other full length haplotype FVIIIs can also be used as the starting sequences. The digestion and subsequent insert construct ligation procedures outlined in Figures 4-8 can be used on these cDNA constructs that encodes other full length haplotype FVIIIs to produce the hrFVIII disclosed herein.
[00077] In one embodiment, provided is an expression vector comprising a nucleic acid encoding a hrFVIII described herein. In one embodiment, the expression vector comprises a complementary DNA (cDNA) encoding a hrFVIII comprising non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring ns-SNP. In one embodiment, the cDNA encodes a hrFVIII comprising non-naturally occurring combination comprising between 2 and 15 amino acid modifications selected from the group consisting of Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, and Met2238Val, and Pro2292Ser, as described above. In one embodiment, the cDNA encodes a hrFVIII lacking the B-domain of wild-type FVIII, as described above.
[00078] In one embodiment, the expression vector comprises a cDNA selected from the group consisting of SEQ ID NOs: 7-12, 14, and 34-51. In one embodiment, the cDNA is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% homologous to SEQ ID NOs. 7-12, 14, and 34-51.
[00079] In one embodiment, the expression vector further comprises a CMV promoter operably linked to the cDNA sequence. In one embodiment, the expression vector further comprises a human growth hormone poly -A signal 3' operably linked to the 3' end of the cDNA sequence. In one embodiment, the expression vector further comprises a neomycin resistance gene. An example expression vector capable of expressing the hrFVIII described herein is illustrated in Figure 3. Specifically, transient transfection of COS-7 cells validated the expression of the F8 cDNA encoding the full-length H3 haplotype FVIII and established the functionality of the: human growth hormone poly-A signal (hGH-pA); CMV promoter; and neomycin resistance cassette (Neo'). H3 has a "G" at 3591, coding Glu at translated residue 1260, which is residue 1241 in plasma FVIII and at 6940, coding Val at residue 2257, which is residue 2238 in plasma FVIII.
Cells Comprising Nucleic Acids Encoding hrFVIII Polypeptides
[00080] Further provided herein are cells capable of expressing the hrFVIII polypeptides described herein. In one embodiment, the cell comprises a nucleic acid encoding the hrFVIII polypeptides described herein. In one embodiment, the cell comprises a cDNAs encoding the hrFVIII polypeptides described herein. In one embodiment, the nucleic acid is contained within an expression construct.
[00081] Cells contemplated herein include eukaryotic cell lines suitable for recombinant protein production. For example, the cell is a mammalian cell that has the ability to synthesize proteins that are similar to those naturally occurring in humans with respect to molecular structures and biochemical properties. Contemplated cells include COS- 7, CHO, baby hamster kidney cells (BHK), mouse cells such as NSO (myeloma), Hek293, Per-C6, CAP (CEVEC's Aminocyte Production) cell lines, HKB-1 1, and HT-1080 cells. Suitable cell lines and recombinant protein production methods are known in the art and described in, for example, Swiech et al, Protein Expression and Purification 84 (2012); 147- 153; Zhu, Biotechnology Advances 30 (2012); 1 158-1 170; Hacker et al, Biotechnology Advances 27 (2009); 1023-1027.
[00082] The nucleic acids encoding the hrFVIIIs described herein can be delivered through a number of direct delivery systems such as, electroporation, lipofection, calcium phosphate precipitation, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, or via transfer of genetic material in cells or carriers such as cationic liposomes. Appropriate means for transfection, including viral vectors, chemical transfectants, or physico -mechanical methods such as electroporation and direct diffusion of DNA, are described by, for example, Wolff, J. A., et al, Science, 247, 1465 -1468, (1990); and Wolff, J. A. Nature, 352, 815-818, (1991). Such methods are well known in the art and readily adaptable for use with the compositions and methods described herein. In certain cases, the methods will be modified to specifically function with large DNA molecules. Transfer vectors can be any nucleotide construction used to deliver genes into cells (e.g., a plasmid), or as part of a general strategy to deliver genes, e.g., as part of recombinant retrovirus or adenovirus (Ram et al. Cancer Res. 53 :83-88, (1993)).
[00083] Nucleic acids that are delivered to cells which are to be integrated into the host cell genome, typically contain integration sequences. These sequences are often viral related sequences, particularly when viral based systems are used. These viral intergration systems can also be incorporated into nucleic acids which are to be delivered using a non-nucleic acid based system of deliver, such as a liposome, so that the nucleic acid contained in the delivery system can become integrated into the host genome.
[00084] Other general techniques for integration into the host genome include, for example, systems designed to promote homologous recombination with the host genome. These systems typically rely on sequence flanking the nucleic acid to be expressed that has enough homology with a target sequence within the host cell genome that recombination between the vector nucleic acid and the target nucleic acid takes place, causing the delivered nucleic acid to be integrated into the host genome. These systems and the methods necessary to promote homologous recombination are known to those of skill in the art.
Methods of Treating Subjects with Hemophilia A [00085] The hrFVIII polypeptides described herein are suitable for treating a patient suffering from Hemophilia A. Accordingly, provided herein is a method of treating a subject suffering from hemophilia A with a suitable amount of a hrFVIII polypeptide described herein.
[00086] In one embodiment, prior to administration of a hrFVIII polypeptide described herein, the level of inhibitors present in the subject is determined. If a significant level of inhibitors is present, for example, a Bethesda Unit titer of about 10 or greater, then a neutralization assay is performed on the hrFVIII polypeptide. If the subject's inhibitors do not significantly neutralize the ability of the hrFVIII polypeptide, then the polypeptide is administered to the patient. If the hrFVIII polypeptide is neutralized, then an alternative hrFVIII described herein is administered. Bethesda Unit neutralization assays are well known in the art, for example, as described further below and in US 2010/0256062.
[00087] Inhibitor to FVIII is screened for by mixing test plasma with a known amount of FVIII. After a 2 hour incubation period at 37° C, the residual FVIII activity is determined in a FVIII assay. By comparing the difference in the FVIII activity of the patient incubation mixture and a control mixture, the absence or presence of a FVIII inhibitor can be demonstrated. Some antibodies will only prolong the Protein Truncation Test (PTT) after incubation. The assay disclosed herein can utilize blood plasma that contains only one of the 6 wild type forms of FVIII protein.
[00088] FVIII inhibitors, IgG antibodies directed against FVIII, can occur in alloimmunized patients with congenital FVIII deficiency (Hemophilia A) or as autoantibodies. The latter are associated with pregnancy, autoimmune disease, or drugs but most often occur spontaneously, particularly among elderly persons.
[00089] General steps involved in a Bethesda assay for FVIII inhibitor include:
Serial subject plasma dilutions in citrated saline are prepared, from 1 :1 up to 1 :160 (or higher if necessary for high-titer factor inhibitors). The purpose of these dilutions is to dilute out the inhibitor. The patient plasma dilutions are then mixed with an equal volume of normal plasma containing a normal amount of coagulation factors. The mixed dilutions are usually incubated for up to 2 hours, because certain inhibitors show an inhibitory effect only after prolonged incubation (particularly factor V and FVIII inhibitors). FVIII assays are then performed on each mixed dilution. The dilution that inhibits 50% of FVIII in the assay defines the titer of the inhibitor. For example, if the 1 :40 dilution inhibits 50% of the FVIII in the assay, the patient is reported to have a titer of 40 BU of FVIII inhibitor.
[00090] The assay can be used to determine if the FVIII inhibitor cross-reacts with hrFVIII polypeptide. If there is little or no cross-reactivity, the hrFVIII can be used to treat bleeding due to a FVIII inhibitor.
[00091] Selecting hrFVIII that has the lowest immunogenicity risk for initiating replacement therapy in previously -untreated patients (PUPs) with hemophilia-A (HA) caused by pharmaco genetically relevant F8 mutation types (e.g., the intron-22 inversion, missense mutations, and the intron-1 inversion) can be personalized. For example, we recently discovered a new biomarker for the risk of immunogenicity with therapeutic FVIII proteins (tFVIIIs), which we refer to as a patient's "intracellular FVIII cross-reactive material" (I- FVIII-CRM) status, in distinction to their "plasma FVIII cross-reactive material" (P-FVIII- CRM) status. In addition, we discovered that the highly recurrent null-type intron-22- inversion (1221) mutation, which is by far the single most common cause of severe HA, underlying the disease in almost 50%> of all affected newborns, directs the expression of the entire primary amino acid sequence of a full-length FVIII protein, albeit within two non- secreted polypeptide chains. In other words, despite testing negative for circulating FVIII activity and antigen, and thus having a negative P-FVIII-CRM status, patients with the 1221 have a completely positive I-FVIII-CRM status. This FVIII expression characteristic no doubt contributes to the relatively low (-20%) overall risk of inhibitor development that has been associated with the 1221 (i.e., only about one in every five 1221 patients develops an inhibitor) and is likely associated with other HA-causing F8 gene abnormalities, including missense mutations, which considered together have an even lower immunogenicity risk (i.e., 5-10%). Because this biomarker identifies patients who may have a preexisting tolerance to tFVIIIs, we have coined the term pharmacogenetically-relevant mutation types to descriptively characterize this relatively large subgroup of null -type F8 gene abnormalities as defining the group of patients for whom pharmaco genomics may be most helpful.
[00092] As such, selecting the FVIII replacement product that has the lowest immunogenicity risk to initiate therapy in previously-untreated patients (PUPs) with severe HA involves first employing non-sequencing- and sequencing-based F8 mutation detection assays to identify and characterize the specific HA-causing abnormality as being either pharmacogenetically-relevant or -irrelevant. For those patients that are found to have pharmacogenetically-relevant abnormalities, e.g. the 1221, missense mutations and the intron- 1 (Il)-inversion, the remaining protein-encoding F8 exonic segments are sequenced to predict which amino acid residues are encoded by the specific alleles present at the multiple known (and any previously unknown) ns-SNP sites so as to guide the selection of the FVIII therapeutic that is most closely matched to the patient's endogenously expressed FVIII protein as it is believed to confer the lowest overall risk of triggering an allogeneic immune- response.
[00093] In some embodiments, selecting the hrFVIII product that has the lowest immunogenicity risk for initiating replacement therapy in previously -untreated patients (PUPs) with hemophilia-A (HA) caused by pharmacogenetically-irre levant F8 mutation types (e.g., large genomic deletions of multiple exons, nonsense mutations, and small frame-shift inducing INDELs arising in non-A-runs) can be personalized based on the following disclosure.
[00094] While pharmacogenomics may be less helpful in severe HA patients whose I-FVIII-CRM status is completely negative, which would obviously be the case for the rare individuals who have a complete F8 gene deletion from their genome — the pathognomonic gene abnormality for the class of mutations we refer to as being pharmacogenetically-irrelevant, as they underlie this severely deficient FVIII expression phenotype and preclude the development of pre-existing immunologic tolerance to tFVIIIs— the method of treatment detailed below is believed to help to select the FVIII replacement product that has the lowest immunogenicity risk to initiate therapy in such PUPs who have traditionally had rates of inhibitor development that are between 40-90%.
[00095] As for severe HA patients with pharmaco genetically -relevant mutation types, the method of treatment for patients whose I-FVIII-CRM status is completely negative also involves first employing non-sequencing- and sequencing-based F8 mutation detection assays to identify and characterize the specific HA-causing abnormality as being pharmacogenetically-irrelevant. For those patients found to have such abnormalities, which, as mentioned above, include, among other types, genomic deletions of multiple exons or large single exons (e.g., exon-14), nonsense mutations and small frame-shift inducing INDELs arising in non-A-runs, one of the BDD hrFVIII proteins disclosed in Tables IB, 1C and ID are believed to be associated with lower immunogenicity risk than the FL hrFVIII proteins disclosed in Tables 1A as they contain almost one-third less of the entire tFVIII protein, which is the source for one or more foreign peptides that might trigger an alloimmune response and lead to inhibitor development, and thus may have an approximately 33% reduced overall immunogenicity risk. Since a further reduction in inhibitor risk may be attainable by selecting a specific engineered BDD h-rFVIII product from within a family of such proteins (i.e., a patient with an in-frame deletion involving exon-14 that occurs on an H7 background haplotype) may have a lower risk of inhibitor development if he is treated with H7 BDD-1 h-rFVIII than if he is treated with the existing therapeutic in the class (i.e., Refacto®/Xyntha®). This is believed to be influenced by the individual repertoire of HLA- class-II (HLA-II) molecules that a given individual has as any person can only express at most 12 distinct of the literally lO's of thousands of different HLA-II isomers that exist at the population level.
[00096] Moreover, a given haplotype of one class of BDD h-rFVIII proteins such as the BDD-2 family may have a lower immunogenicity risk in a given patient than the same haplotype of another class such as the BDD-1 family. Specifically, for the patient described above, who has an in-frame deletion involving exon-14 that arose on the H7 background, the H7 BDD-2 h-rFVIII may have a lower immunogenicity risk than the H7 BDD-1 h-rFVIII, or vice versa, again depending on their specific highly -restricted and individually- limited HLA-II repertoire.
[00097] In some embodiments, selecting the hrFVIII product for initiating immune-tolerance induction therapy in previously-treated alloimmunized patients (PTPs) with severe HA caused by pharmacogenetically -re levant F8 mutation types, i.e., choosing the FVIII product with the greatest likelihood of successfully eradicating (or reducing the titer of) a neutralizing anti-FVIII antibody in a so called "inhibitor patient" is as follows.
[00098] As described above for selecting the hrFVIII product for preventing (or reducing the likelihood of) immunogenicity in the initial replacement therapy of PUPs, a pharmacogenomics-based strategy is also more likely to be successfully devised and implemented for selecting the optimal FVIII product for eradicating (or reducing the titer of) neutralizing anti-FVIII antibodies in PTPs who have already developed a clinically relevant inhibitor when the patients have pharmacogenetically-relevant F8 mutations. This is because it is easier to define which one (of the typically fewer than three) tFVIII-derived foreign peptides in any given therapeutic most likely triggered the alloimmune response to begin with and as such which should or should not be given back to minimize the risk of retriggering it during the trial of tolerance induction therapy. [00099] In some embodiments, selecting the FVIII product for initiating immune-tolerance induction therapy in previously-treated alloimmunized patients (PTPs) with severe HA caused by pharmacogenetically-irrelevant F8 mutation types, i.e., choosing the FVIII product with the greatest likelihood of successfully eradicating (or reducing the titer of) a neutralizing anti-FVIII antibody in an inhibitor patient:
[000100] While pharmacogenomics-guided immune-tolerance-induction (ΙΊΊ)- therapy may be more difficult to design and/or less likely to be successful when applied to PTPs with inhibitors and whose severe HA and completely negative I-FVIII-CRM status is caused by pharmacogenetically-irrelevant F8 mutation types— which again would obviously be the case for the rare individuals who have a complete F8 gene deletion from their genome, the pathognomonic gene abnormality for the class of mutations— the method of treatment, as detailed below, can help to select the optimal FVIII product to initiate ΙΉ -therapy in such PTPs who have traditionally had success rates of inhibitor eradication that are less than 30- 50%.
[000101] As for PTPs with clinically-significant inhibitors and severe HA caused by pharmacogenetically -relevant mutation types, the method of treatment for patients whose I-FVIII-CRM status is completely negative also involves first employing non- sequencing- and sequencing-based F8 mutation detection assays to identify and characterize the specific HA-causing abnormality as being pharmacogenetically-irrelevant. For those patients found to have such abnormalities, which, as mentioned above, include, among other types, genomic deletions of multiple exons or large single exons (e.g., exon-14), nonsense mutations and small frame-shift inducing INDELs arising in non-A-runs, one of the BDD hrFVIII proteins (see Tables IB, 1C and ID) may be associated with a higher success rate for ITI-therapy than the FL hrFVIII proteins (see Tables 1A) as they contain almost one -third less of the entire tFVIII protein, which would be a much less likely source for one or more additional foreign peptides that might trigger an alloimmune response and lead to ongoing stimulation of the alloimmune response and thus a reduced likelihood of successful inhibitor eradication. Since a further improvement in the chance of successful ITI-therapy may be attainable by selecting a specific engineered BDD hrFVIII product from within a family of such proteins (i.e., a patient with an in-frame deletion involving exon-14 that occurs on an H7 background haplotype) may have a greater chance of successful inhibitor eradication if he is treated with H7 BDD-1 hrFVIII than if he is treated with the existing therapeutic in the class (i.e., Refacto® Xyntha®). As described above for immunogenicity, this is likely going to be influenced by the highly -restricted individual repertoire of HLA-II molecules that any given patient can express on the surface of their antigen presenting cells.
[000102] Moreover, a given haplotype of one class of BDD h-rFVIII proteins (e.g., the BDD-2 family) may have a greater likelihood of successfully inducing immune- tolerance in a given patient than the same haplotype of another class (i.e., the BDD-1 family). Specifically, for the patient described above (i.e., who has an in-frame deletion involving exon-14 that arose on the H7 background), the H7 BDD-2 hrFVIII may have a greater chance of successfully inducing immune-tolerance and eradicating the inhibitor than the H7 BDD-1 hrFVIII, or vice versa, again depending on the nature of their specific highly-restricted and individually- limited HLA-II repertoire.
Pharmaceutical Carriers/Delivery of Pharmaceutical Products
[000103] The hybrid recombinant FVIII polypeptides described herein can be administered in a pharmaceutically acceptable carrier. By "pharmaceutically acceptable" is meant a material that is not biologically or otherwise undesirable, i.e., the material may be administered to a subject without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained. The carrier would naturally be selected to minimize any degradation of the active ingredient and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art.
[000104] The compositions may be administered in any suitable way, for example, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, or the like.
[000105] The exact amount of the compositions required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the disorder being treated, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein.
[000106] Parenteral administration of the composition, if used, is generally characterized by injection. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions. A more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, e.g., U.S. Pat. No. 3,610,795, which is incorporated by reference herein.
[000107] The hrFVIII polypeptide may be in solution or suspension (for example, incorporated into microp articles, liposomes, or cells).
[000108] Suitable carriers and their formulations are described in Remington: The Science and Practice of Pharmacy (19th ed.) ed. A. R. Gennaro, Mack Publishing Company, Easton, Pa. 1995. Typically, an appropriate amount of a pharmaceutically - acceptable salt is used in the formulation to render the formulation isotonic. Examples of the pharmaceutically-acceptable carrier include, but are not limited to, saline, Ringer's solution and dextrose solution. The pH of the solution is from about 5 to about 8, for example, from about 7 to about 7.5. It will be apparent to those persons skilled in the art that certain carriers may be more preferable depending upon, for instance, the route of administration and concentration of composition being administered.
[000109] Pharmaceutical carriers are known to those skilled in the art. These most typically would be standard carriers for administration of drugs to humans, including solutions such as sterile water, saline, and buffered solutions at physiological pH. Other compounds will be administered according to standard procedures used by those skilled in the art. Pharmaceutical compositions may include carriers, thickeners, diluents, buffers, preservatives, surface active agents and the like in addition to the molecule of choice. Pharmaceutical compositions may also include one or more active ingredients such as antimicrobial agents, anti-inflammatory agents, anesthetics, and the like. The pharmaceutical composition may be administered in a number of ways depending on whether local or systemic treatment is desired, and on the area to be treated. Preparations for parenteral administration include sterile aqueous or non -aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like. Methods of Making the Compositions
[000110] The hrFVIII polypeptides disclosed herein and the compositions necessary to perform the disclosed methods can be made using any method known to those of skill in the art for that particular reagent or compound unless otherwise specifically noted. Recombinant FVIII can be produced through the use of eukaryotic protein expression systems. In general, a eukaryotic cell line, which is deficient in a required gene, is transformed with a vector comprising the gene that it has a deficiency for, and the recombinant DNA which one wishes to express. Transformation can be accomplished by techniques such as electroporation or viral delivery. The cell line chosen to produce the polypeptide is selected to be compatible with the polypeptide of interest, capable of continuously expressing the polypeptide of interests, capable of growing on a medium which facilitates purification of the polypeptide of interest, along with other factors known to those skilled in the art. Examples of such techniques are disclosed in European Patent Application 0 302 968 A2 and U.S. Pat. No. 5,149,637 both of which are incorporated by reference in their entirety .u
EXAMPLES
Example 1
Creation of Hybrid Recombinant FVIII Polypeptides (hrFVIII)
[000111] An expression vector encoding a hrFVIII provided herein can be generated and validated. For example, a H3/4-rFVIIIFL expression vector can be generated and confirmed by sequence using an expression vector disclosed in Figure 3. All of the vector's sequences are confirmed by bi-directional DNA sequencing. The vectors are then transfected into a mammalian cell, for example CHO-cells, in order to generate research grade preparations of purified hrFVIII proteins. The expression vectors can be analyzed using standard Western blotting procedures to determine that the vector yields the human hrFVIII polypeptide disclosed herein in the conditioned medium of transiently transfected, for example, CHO cells.
Expression, purification, and characterization of the human hrFVIII Polypeptides
[000112] The monoclonal antibody FX008 or other similar FVIII antibodies can be used to purify the hrFVIII proteins expressed in CHO-cells. Additional in vitro analyses can be conducted to ensure that the proteins are of high-quality, including peptide -mapping by mass spectrometry. Assessment of the antigenicity of the human hrFVIII Polypeptides
[000113] The antigenicity of the human hrFVIII polypeptides disclosed herein can be analyzed. For example, the hrFVIII polypeptides can be analyzed using a haplotype- specific version of the Nijmegen-modified Bethesda assay, in accordance with the design outlined in Table 2, below.
Table 2
Figure imgf000046_0001
* Control antibody against FVIII heavy chain; ** Control antibody against FVIII light chain; PNP = pooled normal plasma. "Expected only if inhibitor plasma is comprised predominantly of anti-C2 antibodies. ^Expected only if inhibitor plasma is comprised predominantly of anti-A2 antibodies; zExpected only if inhibition is predominantly directed against A2 and C2 epitopes.
[000114] As indicated, the test antigens and controls can be evaluated for reactivity with domain-epitope-specific mouse antibodies. For example, these types of antibodies can be purchased from Green Mountain Antibodies, or additional FVIII domain specific antibodies. Sample plasmas can be obtained from inhibitor patients with congenital HA. For example, these plasmas are available from George King Biomedical, Inc. and are available with varying FVIII inhibitor titers.
[000115] The following inhibitory activities can be measured: (i) four monoclonal antibodies with specific reactivity against one of four different epitopes within the FVIII protein; and (ii) plasma from inhibitor patients against each of the FVIII test hybrid antigens. The inhibitor mAb responses in patients are against H I FVIII or H2 FVIII, since no other haplotypes are represented in the current commercially available rFVIII concentrates. Test plasmas containing hrFVIII described herein can be prepared by reconstituting human FVIII deficient plasma (FVIIIdp) to a concentration of 1 U/mL FVIII :C. Each site-specific anti-FVIII monoclonal antibody is reconstituted in FVIIIdp to a concentration determined to be between 5 and 10 BU/mL against the PNP used. Next, each hrFVIII can be mixed 1 :1 individually with each of the mAb -reconstituted inhibitor plasmas for 120 minutes at 37°C (Table 2). Each hrFVIII polypeptide is mixed 1 : 1 with patient plasma having the antibody titer indicated in Table 2. Each incubated mix is assayed for residual FVIILC, using the ACL Elite -Pro coagulation analyzer (Instrumentation Laboratory), or similar analyzers. The percent activity is recorded for each reaction mix and compared to FVIILC of pooled normal plasma (PNP) with no inhibitors. Results from antigenicity assessment of each construct against the individual mAB-reconstituted inhibitor plasmas reveals the extent to which the epitope specific substitution encoded by the ns-SNPs (e.g., A2, C2, both A2 and C2) that define the test antigens contributes to any reduced reactivity observed in the inhibitor patient plasma.
[000116] The anti-Al and anti-A3 reconstituted inhibitor plasmas serve primarily as controls. Many acquired HA patients frequently have a more targeted antibody response directed only to the A2- and/or C2-epitopes, and do not have a significant antibody response to the Al and A3 epitopes.
[000117] As the hrFVIII described herein are further characterized, they can be assessed to include pools of sample plasmas from inhibitor patients with congenital HA as well as with acquired HA. Stored plasma samples have been obtained from >700 patients with congenital HA (of which about half are either of Black African or White European descent and a few dozen each are either of Asian or Latino descent) and from 12 patients with the very rare acquired form of HA, who have racial/ethnic ancestries similar to the congenital HA samples. Genomic DNA, RNA, plasma and cell samples from these patients can be characterized at the genetic, molecular, biochemical and cellular level, in order to facilitate the use of these hybrid proteins in the context of the varying naturally occurring haplotypes.
Example 2
Design and Construction of Human FVIII B-Domain Deleted (BDD) Polypeptides
[000118] In B-domain-deleted proteins, a linker can be inserted in the place of the B domain in order to facilitate proper expression. In one example, the linker sequence can be SFSQNSRHPSQNPPVLKRHQR, consisting of 10 amino acids from the N-terminus of the B domain followed by 11 amino acids from the C- terminus of the B domain. {Haemophilia 16, 349-359 (2010)). These constructs containing the 21 amino acid linker are referred to as BDD-2. [000119] In one example, the design of the FVIII BDD-2 polypeptides can be constructed as highlighted in Figures 4 to 8. To verify that the correct linker sequence was obtained, the FVIII ORF from HOW 1 -BDD-2 (FVIII Haplotype 3 B-Domain Deleted-2) was translated. It was determined that its calculated mass is 161,381.73 Da, exactly the same as the expected BDD-2 protein. In order to construct the Human FVIII B-domain deleted BDD- 2 constructs, the FVIII Haplotype H3 full length cDNA was used as a starting sequence (Figure 5). Convenient restriction sites were identified, allowing insertion of the F8 BDD-2 gene into HOWl. The restriction sites that were identified were Aflll, Kpnl and Xbal. Next, the F8 gene sequence was examined to identify good restriction enzymes to allow swapping of V2238 for M2238 and R484 for H484. Based on examination of the F8 sequence, it was determined that there was a Kpnl enzyme cleavage site located fairly close to the middle of the gene. In order to change R484 to H484, Aflll, with a site located approximately 0.3 kb from the start codon, could be used in combination with Kpnl. In order to change V2238 to M2238, Xbal can be chosen on the 3' end, in combination with Kpnl site.
[000120] In one example, the FVIII BDD-2 constructs can be constructed through the use of four fragments that can be combined in different ways to produce the B- domain-deleted-2 constructs. For example, the FVIII Haplotype HI, H3, H4, and H3/H4 BDD-2 constructs can be constructed as depicted in Figures 4 though Figure 8. This method involves obtaining four DNA fragments to be combined into different constructs. In Figure 4, these four fragments are labeled A-R, A-H, C-V, and C-M. Fragments A-H (an Aflll-Kpnl fragment containing A1508 (to express the H484 protein)), C-V (a Kpnl-Xbal fragment with the B domain deleted and containing G6769 (to express the V2238 protein)), and C-M (a Kpnl-Xbal fragment with the B-domain deleted and containing A6769 (to express M2238 protein)) can all be synthesized. Fragment A-R (an Aflll-Kpnl fragment containing G1508 (to express R484)), does not need to be synthesized because it can be generated through the cleavage of the full length FVIII Haplotype H3 expression vector.
[000121] In one example, the Human FVIII H3 BDD-2 construct can be generated as depicted in Figure 5. In order to create the H3 BDD-2 construct, the Kpnl-Xbal fragment can be excised from the full length H3 Haplotype sequence and fragment C-V can be inserted. In one example, the HI BDD-2 construct can be generated as depicted in Figure 6. In order to create the Human FVIII HI BDD-2 construct, the Kpnl-Xbal fragment can be excised from the full length H3 sequence and fragment C-M can be inserted. In one example, the H3/H4 BDD-2 hybrid construct can be generated as depicted in Figure 7. In order to create the Human FVIII H3/H4 BDD-2 construct, the ΑβΙΪ-Κρηϊ fragment can be excised from the H3 BDD-2 construct and fragment A-H can be used to replace the Aflll-Kpnl fragment. In one example, the H4 BDD-2 hybrid construct can be generated as depicted in Figure 8. In order to create the Human FVIII H4 BDD-2 construct, the Aflll-Kpnl fragment from HI BDD-2 can be excised and fragment A-H can be used to replace the Aflll-Kpnl fragment. Human FVIII BDD-2 constructs for Haplotypes HI, H3, H4, and H3/H4 depicted in Figures 4-8 thus can all be obtained.
[000122] The embodiments above are intended to be illustrative and not limiting. Additional embodiments are within the claims. In addition, although the present disclosure has been described with reference to particular embodiments, those skilled in the art will recognize that changes can be made in form and detail without departing from the spirit and scope of the disclosure. Any incorporation by reference of documents above is limited such that no subject matter is incorporated that is contrary to the explicit disclosure herein.

Claims

We Claim,
1. A hybride recombinant factor VIII polypeptide (hrFVIII) having non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring nonsynonymous -single nucleotide polymorphisms.
2. The hrFVIII of claim 1 , wherein the hrFVIII have non-naturally occurring combinations of 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, or 15 amino acid modifications selected from the group consisting of: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser.
3. The hrFVIII of claim 1 or 2, wherein the hrFVIII comprises a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-6, 13, 15-33, 52, and 53.
4. A complementary DNA (cDNA) for the treatment of a subject having hemophilia A, encoding a hybride recombinant factor VIII polypeptide (hrFVIII) having non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring nonsynonymous -single nucleotide polymorphisms.
5. The cDNA of claim 4, wherein the hrFVIII has non-naturally occurring combinations of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, or 15 amino acid modifications selected from the group consisting of: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser.
6. The cDNA of claim 4 or 5 comprising a nucleic acid having a sequence selected from the group consisting of SEQ ID NOs: 7-12, 14, and 34-51.
7. An expression vector composition for the treatment of a subject having hemophilia A, comprising a complementary DNA (cDNA) encoding a hybride recombinant factor VIII polypeptide (hrFVIII) having non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring nonsynonymous -single nucleotide polymorphisms.
8. The expression vector of claim 7, wherein the hrFVIII has non-naturally occurring combinations of 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, or 15 amino acid modifications selected from the group consisting of: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser.
9. The expression vector of claim 7 or 8, wherein the cDNA comprises a nucleic acid having an sequence selected from the group consisting of SEQ ID NOs: 7-12, 14, and 34-51.
10. The expression vector of any one of claims 7-9, comprising a polyadenylated segments, a promoter, and an optional marker.
11. The expression vector of any one of claims 7-10, comprising human growth hormone poly-A signal (hGH-pA) and CMV promoter with an optional neomycin resistance cassette (Neo*).
12. A cell for the treatment of a subject having hemophilia A, comprising an expression vector having a complementary DNA (cDNA) encoding a hybride recombinant factor VIII polypeptide (hrFVIII) that has non-naturally occurring combinations of amino acid modifications, wherein the amino acid modifications occur at sites of naturally occurring nonsynonymous -single nucleotide polymorphisms.
13. The cell of claim 12, wherein the hrFVIII has non-naturally occurring combinations of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, or 15 amino acid modifications selected from the group consisting of: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, His l919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser.
14. The cell of claim 12 or 13, wherein the cDNA comprises a nucleic acid having an sequence selected from the group consisting of SEQ ID NOs: 7-12, 14, and 34-51.
15. The cell of any one of claims 12-14, wherein the cell is selected from the group consisting of COS-7, CHO, baby hamster kidney cells (BHK), mouse cells such as NSO (myeloma), Hek293, Per-C6, CAP (CEVEC's Aminocyte Production) cell lines, HKB-11 , and HT-1080 cells.
16. A method of making the hrFVIII of claims 1-3.
17. A method of making the cDNA of claims 4-6.
18. A method of making the expression vector of claims 7-11.
19. A method of making the cell of claims 12-15.
20. A method of making the hrFVIII of claim 1-3 from the cells of claims 12-15, wherein the cells comprises the expression vector of claims 7-11, which comprises the cDNA of claims 4-6.
21. A method of treating a subject having hemophilia A, comprising, administering an effective amount of a hybrid recombinant factor VIII polypeptide (hrFVIII) having non- naturally occurring combinations of amino acid modifications to the subject, wherein the amino acid modifications occur at sites of naturally occurring nonsynonymous -single nucleotide polymorphisms.
22. The method of claim 21, further comprising testing antigenicity of the hrFVIII in the subject.
23. The method of claim 21 or 22, further comprising matching the haplotype of the subject with the haplotype of the hrFVIII.
24. The method of claim 21, further comprising determining the level of inhibitors present in the subject.
25. The method of claim 24, further comprising performing a neutralization assay on the hrFVIII with the inhibitors present in the subject.
26. The method of any one of claims 21-25, wherein the hrFVIII have non-naturally occurring combinations of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 amino acid modifications selected from the group consisting of: Glul l3Asp, Gln334Pro, Ala387Thr, Arg484His, Arg776Gly, Argl l07Trp, Aspl241Glu, Argl260Lys, Leul462Pro, Ilel668Val, Hisl919Asn, Glu2004Lys, Val2223Met, Met2238Val, and Pro2292Ser.
27. The method of any one of claims 21-26, wherein the hrFVIII comprises a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-6, 13, 15-33, 52, and 53.
PCT/US2014/059787 2013-10-08 2014-10-08 Hybrid factor viii polypeptides for use to treat hemophilia a WO2015054439A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201361888373P 2013-10-08 2013-10-08
US61/888,373 2013-10-08

Publications (2)

Publication Number Publication Date
WO2015054439A2 true WO2015054439A2 (en) 2015-04-16
WO2015054439A3 WO2015054439A3 (en) 2015-06-04

Family

ID=52813741

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2014/059787 WO2015054439A2 (en) 2013-10-08 2014-10-08 Hybrid factor viii polypeptides for use to treat hemophilia a

Country Status (1)

Country Link
WO (1) WO2015054439A2 (en)

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3368560A4 (en) * 2015-10-30 2019-03-27 Spark Therapeutics, Inc. Cpg reduced factor viii variants, compositions and methods and uses for treatment of hemostasis disorders
US11083801B2 (en) 2012-12-07 2021-08-10 Haplomics, Inc. Factor VIII mutation repair and tolerance induction
US11185573B2 (en) 2004-12-06 2021-11-30 Haplomics, Inc. Allelic variants of human factor VIII
US11344608B2 (en) 2014-11-12 2022-05-31 Ucl Business Ltd Factor IX gene therapy

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100256062A1 (en) * 2004-12-06 2010-10-07 Howard Tommy E Allelic Variants of Human Factor VIII
WO2011046568A1 (en) * 2009-10-16 2011-04-21 Haplomics, Inc. Compositions and methods of treatment of black hemophiliac patients

Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11185573B2 (en) 2004-12-06 2021-11-30 Haplomics, Inc. Allelic variants of human factor VIII
US11083801B2 (en) 2012-12-07 2021-08-10 Haplomics, Inc. Factor VIII mutation repair and tolerance induction
US11344608B2 (en) 2014-11-12 2022-05-31 Ucl Business Ltd Factor IX gene therapy
EP3368560A4 (en) * 2015-10-30 2019-03-27 Spark Therapeutics, Inc. Cpg reduced factor viii variants, compositions and methods and uses for treatment of hemostasis disorders
US11168124B2 (en) 2015-10-30 2021-11-09 Spark Therapeutics, Inc. CpG reduced factor VIII variants, compositions and methods and uses for treatment of hemostasis disorders

Also Published As

Publication number Publication date
WO2015054439A3 (en) 2015-06-04

Similar Documents

Publication Publication Date Title
JP6868605B2 (en) Methods of reducing immunogenicity to factor VIII in individuals receiving factor VIII therapy
US9072722B2 (en) Recombinant factor VIII having increased stability
AU2017214378A1 (en) Optimized Factor VIII genes
JP2023179463A (en) Use of lentiviral vectors expressing factor VIII
JP2002501376A (en) New LDL-receptor
US20160038570A1 (en) Predicting and reducing alloimmunogenicity of protein therapeutics
WO2015054439A2 (en) Hybrid factor viii polypeptides for use to treat hemophilia a
KR20100087346A (en) Fviii peptides and their use in tolerising haemophiliacs
KR20200095462A (en) Adeno-associated virus composition for restoring HBB gene function and method of use thereof
TW201723180A (en) Viral vectors encoding recombinant FVIII variants with increased expression for gene therapy of hemophilia A
KR20230002681A (en) Integration of large adenovirus payloads
AU770018B2 (en) Human N-type calcium channel isoform and uses thereof
KR20200018690A (en) Modulation of FVIII Immunogenicity by Cleaved VWF
AU742598B2 (en) Method to diagnose and treat pathological conditions resulting from deficient ion transport such as pseudohypoaldosteronism type-1
US20100015654A1 (en) Negative regulation of NK cell functions by EAT-2, a sap-related adaptor expressed in innate immune cells
Famà et al. Identification and functional characterization of a novel splicing variant in the F8 coagulation gene causing severe hemophilia A
US6849399B1 (en) Methods and compositions for diagnosis and treatment of iron misregulation diseases
RU2803163C2 (en) Using of lentiviral vectors expressing factor viii
JP2010501160A (en) Promiscuous HER-2 / NeuCD4 T cell epitope
US20210046153A1 (en) Oca-b peptide conjugates and methods of treatment
EP1572870A2 (en) Molecular sequence of pig endogenous retrovirus receptors and methods of use
JP2006504407A (en) New therapeutic targets for the treatment of vascular disorders, dyslipidemia and related diseases
AU2002305190A1 (en) Molecular sequence of pig endogenous retrovirus receptors and methods of use

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 14851975

Country of ref document: EP

Kind code of ref document: A2

NENP Non-entry into the national phase in:

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 14851975

Country of ref document: EP

Kind code of ref document: A2