AU2009244633A1 - Modified Factor IX polypeptides and uses thereof - Google Patents

Description

WO 2009/137254 PCT/US2009/040813 MODIFIED FACTOR IX POLYPEPTIDES AND USES THEREOF [001] This application claims benefit of U.S. Provisional Application Serial No. 61/124,567; filed on April 16, 2008, and U.S. Provisional Application Serial No. 61/045,961; filed on April 17, 2008, the contents of which are incorporated herein by reference in their entirety. FIELD OF THE INVENTION [002] The invention relates to modified Factor IX polypeptides such as Factor IX polypeptides with one or more introduced glycosylation sites. The modified Factor IX polypeptides may exhibit increased in vitro or in vivo stability such as a longer plasma half-life. The invention also relates to methods of making modified Factor IX polypeptides, and methods of using modified Factor IX polypeptides, for example, to treat patients afflicted with hemophilia B. BACKGROUND OF THE INVENTION [003] Hemophilia B effects one out of 34,500 males and is caused by various genetic defects in the gene encoding coagulation Factor IX (FIX) that result in either low or undetectable FIX protein in the blood (Kurachi, et al., Hematol. Oncol. Clin. North Am. 6:991-997, 1992; Lillicrap, Haemophilia 4:350-357, 1998). Insufficient levels of FIX lead to defective coagulation and symptoms that result from uncontrolled bleeding. Hemophilia B is treated effectively by the intravenous infusion of either plasma-derived or recombinant FIX protein either to stop bleeds that have already initiated or to prevent bleeding from occurring (prophylaxis) (Dargaud, et al., Expert Opin. Biol. Ther. 7:651-663; Giangrande, Expert Opin. Pharmacother. 6:1517-1524, 2005). Effective prophylaxis requires maintaining a minimum trough level of FIX of about 1% of normal levels (Giangrande, Expert Opin. Pharmacother. 6:1517-1524, 2005). Because of the approximately 18 to 24 hour half-life of native FIX (either plasma-derived or recombinant), FIX levels drop to less than 1% of normal levels within 3 to 4 days following bolus injection which necessitates repeat injection on average every three days to achieve effective prophylaxsis (Giangrande, Expert Opin. Pharmacother. 6:1517-1524, 2005). Such frequent intravenous injection is problematic for patients and is a hurdle for achieving effective prophylaxsis (Petrini, Haemophilia 13 Suppl 2:16-22, 2007), especially in children. A FIX protein with a longer half-life would enable less frequent administration and thus, be of significant medical benefit. SUMMARY OF THE INVENTION [004] The application provides FIX polypeptides (also referred to as modified FIX polypeptides, FIX muteins, or FIX variants) comprising amino acid sequences that have been modified by introducing one or more glycosylation sites. In some embodiments, the one or more glycosylation WO 2009/137254 PCT/US2009/040813 sites may be N-linked glycosylation sites. In some embodiments, the polypeptides have coagulation activity. In some embodiments, the modified polypeptides may comprise at least one substitution such as, but not limited to R338A and V86A. In some embodiments, the modified polypeptides may comprise both the R338A and V86A substitutions. [005] The application also provides FIX polypeptides comprising amino acid sequences that have been modified by introducing one or more glycosylation sites. The FIX polypeptides may further comprise a carbohydrate chain attached to the one or more introduced glycosylation sites. In some embodiments, the carbohydrate chain may be an N-linked carbohydrate chain. In some embodiments, the carbohydrate chain may have a mammalian carbohydrate chain structure. In some embodiments, the carbohydrate chain may have a human carbohydrate chain structure. In some embodiments, the attachment of a carbohydrate chain at one or more of the introduced glycosylation sites may increase serum half-life of the polypeptide by, for example, at least 30% relative to the polypeptide lacking the introduced glycosylation sites. In some embodiments, the attachment of a carbohydrate chain at one or more of the introduced glycosylation sites does not reduce the amount of secreted polypeptide by, for example, more than 50% relative to the amount of the secreted polypeptide lacking the introduced glycosylation sites. In some embodiments, the attachment of a carbohydrate chain at one or more of the introduced glycosylation sites does not inhibit interaction of the polypeptide with at least one of Factor VIII (FVIII), Factor XI (FXI), or Factor X (FX) by, for example, more than 50% relative to interaction of the polypeptide lacking the carbohydrate chain at the introduced glycosylation sites with FVIII, FXI, or FX. In some embodiments, the modified polypeptide may have a specific activity of, for example, at least 100 units per mg of polypeptide. [006] The one or more glycosylation sites may be introduced via one or more amino acid substitutions. The substitutions may be at surface exposed residues and/or be limited to substitutions that do not introduce a mutation known to be associated with hemophilia B. Exemplary embodiments include FIX polypeptides comprising one or more substitutions such as, but not limited to: (a) G4T; E33N; E36T; E36N; R37N; F75N; F77T; E83T; D85N; V86A; K91T; A103T; V107T; K122N; K122T; S138N; A146N; T148N; F150T; P151N; T159N; A161T; A161N; T169N; Q170N; T172N; D177N; D177E; F178T; K201N; K201T; K214T; V223N; G226N; Y226T; K228N; K228T; E239N; E242N; 1251T; A262T; E294N; R338A; R338N; K341N; F353N; H354V; H3541; E355T; V370N; T371V; T3711; E372T; E374N; M391N; K392V; G393T; E41ON; K413N; L4141; (b) YIN and S3T; S3N and K5T; G4N and L6T; K5N and E7T; L6N and E8T; E7N and F9T; F9N and Q1 IT; VION and G12T; Q1 IN and N13T; G12N and L14T; N13 and E15T; L14N and RI6T; 2 WO 2009/137254 PCT/US2009/040813 E15N and E17T; M19N and E21T; E20N and K22T; S24N and E26T; F25N and E27T; E26N and A28T; E27N and R29T; A28N and E30T; R29N and V31T; E30N and F32T; V31N and E33T; F32N and N34T; T35N and R37T; T38N and E40T; T39N and F41T; E40N and W42T; F41N and K43T; W42N and Q44T; K43N and Y45T; Q44N and V46T; Y45N and D47T; V46N and G48T; E52N and N54T; S53N and P55T; G59N and S61T; K63N and D65T; 166N and S68T; S68N and E70T; G76N and E78T; E78N and K80T; E83N and D85T; L84N and V86T; 190N and N92T; KiON and S02T; S02N and D104T; Al03N and N105T; D04N and K106T; Kl06N and VI08T; RI 16N and Al 18T; El 19N and Ql21T; Ql21N and S123T; A127N and P129T; V135N and V137T; S136N and S138T; V137N and Q139T; Q139N and S141T; T140N and K142T; S141N and L143T; E147N and V149T; T148N and F150T; V149N and P151T; P151N and V153T; D152N and D154T; V153N and Y155T; D154N and V156T; Y155N and N157T; V156N and S158T; S158N and E160T; T159N and Al61T; E160N and E162T; E162N and 1164T; T163N and L165T; 164N and D166T; L165N and N167T; D166N and I168T; 168N and Q170T; T169N and S171T; S171N and Q173T; T172N and S174T; Q173N and F175T; S174N and N176T; G184N and D186T; El85N and Al87T; D186N and K188T; Al87N and P189T; P189N and Q191T; G200N and V202T; K201N and D203T; V202N and A204T; E224N and G226T; T225N and V227T; G226N and K228T; V227N and 1229T; H236N and 1238T; 1238N and E240T; E240N and E242T; T241N and H243T; H243N and E245T; K247N and N249T; V250N and R252T; 1251N and 1253T; 1253N and P255T; A261N and 1263T; A262N and N264T; D276N and P278T; V28ON and N282T; F302N and S304T; S304N and Y306T; R312N and F314T; V313N and H315T; F314N and K316T; H315N and G317T; K316N and R318T; G317N and S319T; S319N and L321T; A320N and V322T; R327N and P329T; P329N and V331T; D332N and A334T; L337N and S339T; S339N and K341T; T340N and F342T; T343N and Y345T; G352N and H354T; F353N and E355T; H354N and G356T; E355N and G357T; G356N and R358T; G357N and D359T; E372N and E374T; W385N and E387T; G386N and E388T; A390N and K392T; (c) D85N, K122T, and 1251T; D85N, K122T, and E242N; E125N, P126A, and A127T; P126N, V128T, and P129A; T148N, F150T, and P151A; F150N, P151A, and D152T; P151N, V153T, and A161N; P151N, V153T, and T172N; V153N, Y155T, and E294N; T172N, G226N, and K228T; F353N, H354V, and E355T; F353N, H3541, and E355T; V370N, T371V, and E372T; V370N, T3711, and E372T; M391N, K392V, and G393T; D85N, P151N, V153T, and K228N; D85N, P151N, V153T, and E242N; K122T, P151N, V153T, and K228N; K122T, P151N, V153T, and E242N; K122T, P151N, V153T, and 1251T; T148N, F150T, G226N, and K228T; P151N, V153T, T172N, and R338A; P151N, V153T, D177E, and F178T; P151N, V153T, G226N, and K228T; T172N, G226N, K228T, and R338A; D85N, K122T, P151N, V153T, and E242N; D85N, P151N, V153T, G226N, and K228T; K122T, P151N, V153T, G226N, and K228T; S138N, P151N, V153T, G226N, and K228T; T148N, F150T, G226N, K228T, and R338A; P151N, V153T, 3 WO 2009/137254 PCT/US2009/040813 T172N, G226N, and K228T; P151N, V153T, D177E, F178T, and R338A; P151N, V153T, G226N, K228T, and R338A; and P151N, V153T, T172N, G226N, K228T, and R338A; and any combination thereof. [007] The one or more glycosylation sites may be introduced into the catalytic domain of FIX or activation peptide. Exemplary embodiments include FIX polypeptides comprising one or more substitutions such as, but not limited to: R37N; D85N; K122T; S138N; A146N; A161N; Q170N; T172N; D177N; F178T; K201N; K228N; E239N; E242N; 1251T; A262T; E294N; E374N; and E410N. Other embodiments may comprise the following FIX polypeptides comprising one or more substitutions such as: G59N and S6 IT; K63N and D65T; G76N and E78T; S102N and D104T; A103N and N105T; D104N and K106T; E119N and Q121T; Q121N and S123T; S136N and S138T; Q139N and S141T; T140N and K142T; T148N and F150T; V149N and P151T; P151N and V153T; D152N and D154T; V153N and Y155T; D154N and V156T; V156N and S158T; S158N and E160T; E160N and E162T; E162N and I164T; T163N and L165T; I164N and D166T; D166N and I168T; I168N and Q170T; S171N and Q173T; T172N and S174T; Q173N and F175T; S174N and N176T; K201N and D203T; V202N and A204T; E224N and G226T; T225N and V227T; G226N and K228T; T241N and H243T; I251N and I253T; I253N and P255T; A262N and N264T; V28ON and N282T; T343N and Y345T; and E372N and E374T; F150N, P151A, and D152T. In some embodiments, the modified polypeptides may further comprise at least one substitution such as, for example, R338A and V86A. In some embodiments, the modified polypeptides may further comprise both the R338A and V86A substitutions. [008] The one or more glycosylation sites may be introduced by converting an O-linked glycosylation site to an N-linked glycosylation site. Exemplary embodiments include substitutions such as, but not limited to T169N; T172N; T148N and F150T; and T159N and A161T. In some embodiments, the substitutions may be T172N; T148N and F150T; and T159N and A161T. In some embodiments, the modified polypeptides may further comprise at least one substitution such as, but not limited to R338A and V86A. In some embodiments, the modified polypeptides may further comprise both the R338A and V86A substitutions. [009] The one or more glycosylation sites may be introduced by inserting between 1 and 12 amino acid residues between amino acid residues 160-164. The glycosylation sites may be introduced between amino acid residues 160-161, between amino acid residues 161-162, between amino acid residues 162-163, or between amino acid residues 163-164. In some embodiments, SEQ ID NO: 2 may be introduced between amino acid residues 160-161, between amino acid residues 161-162, between amino acid residues 162-163, or between amino acid residues 163-164. In other embodiments, glycosylation sites may be introduced by adding between 1 and 12 amino acid residues to the C-terminus of the FIX polypeptide. In some embodiments, SEQ ID NOs: 4, 5, 4 WO 2009/137254 PCT/US2009/040813 6, or 7 may be introduced to the to the C-terminus of the FIX polypeptide. In some embodiments, the polypeptide may further comprise amino acid substitutions D177E and F178T. In some embodiments, the polypeptide may further comprise amino acid substitutions P151N and V153T. In some embodiments, the polypeptide may further comprise amino acid substitution T172N. In some embodiments, the polypeptide may further comprise amino acid substitutions P15 IN, V153T, and T172N. In some embodiments, the polypeptide may further comprise amino acid substitutions T148N and F150T. In some embodiments, the polypeptide may further comprise amino acid substitutions G226N and K228T. In some embodiments, the modified polypeptides may further comprise at least one substitution such as R338A and V86A. In some embodiments, the modified polypeptides may further comprise both the R338A and V86A substitutions. [010] In exemplary embodiments, modified FIX polypeptides are provided comprising one or more substitutions such as: D85N; K122T; S138N; T172N; K201N; K228N; E239N; E242N; 1251T; A262T; E294N; G59N and S61T; G76N and E78T; S102N and D104T; A103N and N105T; D104N and K106T; E119N and Q121T; Q121N and S123T; S136N and S138T; Q139N and S141T; T140N and K142T; T148N and F150T; V149N and P151T; P151N and V153T; D152N and D154T; S158N and E160T; E162N and 1164T; T163N and L165T; T172N and S174T; Q173N and F175T; K201N and D203T; T225N and V227T; G226N and K228T; 1253N and P255T; A262N and N264T; V280N and N282T; E372N and E374T; F150N, P151A, and D152T; an insertion of SEQ ID NO:2 between A161 and E162; and G226N, K228T, and an insertion of SEQ ID NO:2 between A161 and E162. In some embodiments, the modified polypeptides may further comprise at least one substitution such as, for example, R338A and V86A. In some embodiments, the modified polypeptides may further comprise both the R33 8A and V86A substitutions. [011] The application also provides FIX polypeptides comprising an R338A substitution and a V86A substitution. In some embodiments, the polypeptide may have a specific activity of at least 700 units per mg of polypeptide. [012] The application also provides pharmaceutical preparations comprising modified FIX polypeptides and a pharmaceutically acceptable carrier. [013] The application also provides methods for treating hemophilia B comprising administering to a subject in need thereof a therapeutically effective amount of the pharmaceutical preparations described herein. [014] The application also provides DNA sequences encoding modified polypeptides, as well as eukaryotic host cells transfected with the DNA sequences. 5 WO 2009/137254 PCT/US2009/040813 [015] The application also provides methods for producing modified FIX polypeptides comprising (i) modifying the amino acid sequence of the polypeptide by introducing one or more glycosylation sites; (ii) expressing the polypeptide in a manner which allows glycosylation at the one or more glycosylation sites; and (iii) purifying the polypeptide. BRIEF DESCRIPTION OF THE DRAWINGS [016] Figure 1 depicts a multiple sequence alignment of FIX sequences within the activation peptide from eight species [017] Figure 2 depicts Western Blot analysis of media from HKB11 cells transfected with glycosylation site muteins of FIX. FIX protein was detected using an anti-FIX-HRP antibody. [018] Figure 3 depicts a table of expression and activity of FIX glycosylation site muteins in HKB1 1 cells. Expression was determined by ELISA and activity by aPTT assay. Specific activity is calculated as international units per mg of FIX protein. Values were converted to a percentage of FIX-R338A run in the same transfection experiment. (none): no change in mobility, (+): decreased mobility with the number of + indicating degree, (-): increased mobility. [019] Figure 4 depicts expression level, coagulation activity, and specific activity of FIX glycosylation site muteins in HKB11 cells. Values are expressed as a percentage of the FIX R338A mutein. Constructs are described in Figure 3. [020] Figure 5 depicts Western Blot analysis of media from HKB11 cells transfected with the G226N, K228T glycosylation site mutein of FIX. FIX protein was detected using an anti-FIX HRP antibody. DESCRIPTION OF THE INVENTION [021] The present application provides FIX polypeptides that include one or more 0- or N linked glycosylation sites. Increased glycosylation of therapeutic proteins may be used to achieve 1) reduced immunogenicity; 2) less frequent administration of the protein; 3) increased protein stability such as increased serum half-life; and 4) reduction in adverse side effects such as inflammation. [022] The application provides variants of human FIX with one or more additional glycosylation sites. The modified FIX polypeptides may also have an increased plasma half-life that would provide, for example, an extended time of protection against bleeding in hemophilia B patients. The modified FIX polypeptides would enable hemophilia B patients to achieve protection against 6 WO 2009/137254 PCT/US2009/040813 bleeding with fewer injections of FIX than is possible with the currently available therapy of wild type FIX protein. [023] The application provides a number of exemplary variants of FIX in which functional glycosylation sites were created in both the catalytic domain and in the activation peptide. Moreover, the application demonstrates that these variants may be expressed in mammalian cells, have increased apparent molecular weight indicative of increased glycosylation, and maintain between 50% and 100% activity in a coagulation assay. Finally, these modification sites may be combined with alterations that enhance the specific activity of FIX, including but not limited to the R338A substitution and/or the V86A substitution (Chang, et al., J. Biol. Chem. 273:12089-12094, 1998 and Chang, et al., J. Biol. Chem. 277:25393-25399, 2002). The combination with one or both of the R338A and V86A substitutions compensates for any reduction in activity resulting from the addition of glycosylation sites such that the specific activity of the modified polypeptides may be similar to or higher than that of wild type FIX. [024] Once expressed, wild type FIX is a single chain glycoprotein of about 55,000 Daltons. It can structurally be considered as having four domains: the Gla or gamma carboxyglutamate-rich domain; the EGF-like regions; the activation peptide; and the catalytic domain containing the active site (Thomson, Blood 67:565-572, 1986). FIX is synthesized in the liver as a single chain polypeptide of 461 amino acids and undergoes extensive posttranslational modification during passage through the golgi and endoplasmic reticulum (Nemerson, et al., CRC Crit. Rev. Biochem. 9:45-48, 1980; Stenflo, et al., Annu. Rev. Biochem. 46:157-172, 1977). Both the signal sequence and the propeptide are removed resulting in a mature protein of 415 amino acids (SEQ ID NO: 1) (Choo, et al., Nature 299:178-180, 1982; Kurachi, et al., Proc. Natl. Acad. Sci. USA 79:6461 6464, 1982). Efficient gamma carboxylation is essential for the coagulation activity of FIX and in humans 12 Gla residues are generated within the N terminal Gla domain, although gamma carboxylation on Gla36 and Gla40 are not required for function (DiScipio, et al., Biochemistry 18:899-904, 1979; Gillis, et al., Protein Sci. 6:185-196, 1997). In addition, FIX contains two N linked glycosylation sites (N157, N167), six O-linked glycosylation sites (S53, S61, T159, T169, T172, T179), and one site each for Ser phosphorylation (S158), tyrosine sulfation (Y155) and B hydroxylation (D64) (McMullen, et al., Biochem. Biophys. Res. Comm. 115:8-14, 1983). [025] Activated Factor VII (FVII) initiates the normal hemostatic process by forming a complex with tissue factor (TF), exposed as a result of injury to the vessel wall. The complex subsequently activates FIX; the active form referred to as FIXa. The activation peptide of FIX is removed by proteolytic cleavage at two sites by either Factor XIa (FXIa) or the tissue factor (TF)/Factor VIIa complex to generate the catalytically active molecule, Factor IXa (FIXa). FIXa and Factor VIIIa 7 WO 2009/137254 PCT/US2009/040813 (FVIIIa) convert FX to Factor Xa (FXa), which in turn converts prothrombin to thrombin. Thrombin then converts fibrinogen to fibrin resulting in formation of a fibrin clot. [026] As wild-type FIX has numerous post-translational modifications some of which have been suggested to play a role in the in vivo pharmacokinetic profile, an ectopic glycosylation site may be introduced at a position that does not affect these other modifications. Once produced, FIX should retain enzymatic activity and interact with FVIII, FXI, and FX in order to be an effective treatment for hemophilia B. The introduced glycosylation site should not perturb these interactions and function. The application provides, in part, modifications to FIX which are likely to result in an increased number of glycosylation sites with minimal perturbation of function and thus have utility for increasing the bioavailability of FIX. Finally, these modification sites may be combined with alterations that enhance the specific activity of FIX, including but not limited to the R338A substitution and/or the V86A substitution. Alterations that enhance the specific activity of FIX may compensate for potential loss of coagulation activity and also potentially prolong the efficacy of modified molecules by conferring efficacy at lower levels of protein. Modified FIX Polypeptides [027] The application provides FIX polypeptides comprising one or more introduced glycosylation sites, that is, modified FIX polypeptides. "Factor IX" as used herein refers to a human plasma FIX glycoprotein that is a member of the intrinsic coagulation pathway and is essential to blood coagulation. It is to be understood that this definition includes native as well as recombinant forms of the human plasma FIX glycoprotein. Unless otherwise specified or indicated, as used herein FIX means any functional human FIX protein molecule in its normal role in coagulation, including any fragment, analogue, variant, and derivative thereof. The terms "fragment," "derivative," "analogue," "mutein," and "variant," when referring to the polypeptides of the application, means fragments, derivatives, analogues, muteins, and variants of the polypeptides which retain substantially the same biological function or activity. [028] Non-limiting examples of FIX polypeptides include FIX, FIXa, and truncated versions of FIX having FIX activity. Biologically active fragments, deletion variants, substitution variants, or addition variants of any of the foregoing that maintain at least some degree of FIX activity can also serve as a FIX polypeptide. In some embodiments, the FIX polypeptides may comprise an amino acid sequence at least about 70, 80, 90, or 95% identical to SEQ ID NO: 1. In some embodiments, the modified FIX polypeptides are biologically active. Biological activity can be determined, for example, by coagulation assays described herein. [029] Modified FIX polypeptides may also contain conservative substitutions of amino acids. A conservative substitution is recognized in the art as a substitution of one amino acid for another 8 WO 2009/137254 PCT/US2009/040813 amino acid that has similar properties and include, for example, the changes of alanine to serine; arginine to lysine; asparagine to glutamine or histidine; aspartate to glutamate; cysteine to serine; glutamine to asparagine; glutamate to aspartate; glycine to proline; histidine to asparagine or glutamine; isoleucine to leucine or valine; leucine to valine or isoleucine; lysine to arginine; methionine to leucine or isoleucine; phenylalanine to tyrosine, leucine or methionine; serine to threonine; threonine to serine; tryptophan to tyrosine; tyrosine to tryptophan or phenylalanine; and valine to isoleucine or leucine. In some embodiments, the FIX polypeptides of SEQ ID NO: 1 comprise from 1-30, from 1-20, or from 1-10 conservative amino acid substitutions in addition to the introduction of one or more glycosylation sites. [030] The single letter abbreviation for a particular amino acid, its corresponding amino acid, and three letter abbreviation are as follows: A, alanine (Ala); C, cysteine (Cys); D, aspartic acid (Asp); E, glutamic acid (Glu); F, phenylalanine (Phe); G, glycine (Gly); H, histidine (His); I, isoleucine (Ile); K, lysine (Lys); L, leucine (Leu); M, methionine (Met); N, asparagine (Asn); P, proline (Pro); Q, glutamine (Gln); R, arginine (Arg); S, serine (Ser); T, threonine (Thr); V, valine (Val); W, tryptophan (Trp); Y, tyrosine (Tyr); and norleucine (Nle). [031] Glycosylation of polypeptides is typically either N-linked or O-linked. N-linked refers to the attachment of a carbohydrate moiety to the side chain of an asparagine residue. The tripeptide sequences Asn-X-Ser and Asn-X-Thr, where X is any amino acid except proline, are the recognition sequences for enzymatic attachment of the carbohydrate moiety to the Asn side chain. Thus, the presence of either of these tripeptide sequences in a polypeptide creates a potential N linked glycosylation site. An exemplary N-linked glycosylation site useful for the invention may also be represented as follows X1-Asn-X2-X3-X4; where X1 is optionally Asp, Val, Glu, Gly, or Ile; X2 is any amino acid except Pro; X3 is Ser or Thr; and X4 is optionally Val, Glu, Gly, Gln, or Ile. In some embodiments, X1 is optionally Asp; X2 is Ser; X3 is Thr; and X4 is Gln. In some embodiments, X1 is Asp; X2 is Ile; X3 is Thr; and X4 is Gln. Addition of N-linked glycosylation sites to a FIX polypeptide is accomplished by altering the amino acid sequence such that one or more of the above-described tripeptide sequences is introduced. [032] O-linked glycosylation refers to the attachment of one of the sugars N aceytlgalactosamine, galactose, or xylose to a hydroxyamino acid, most commonly to seine or threonine, although attachment to 5-hydroxyproline or 5-hydroxylysine is also possible. Addition of O-linked glycosylation sites to a FIX polypeptide may be accomplished by altering the amino acid sequence such that one or more Ser or Thr residues are introduced. [033] Glycosylation sites may be introduced, for example, by deleting one or more amino acid residues, substituting one or more endogenous FIX amino acid residues with another amino acid(s), or adding one or more amino acid residues. The addition of an amino acid residue may be 9 WO 2009/137254 PCT/US2009/040813 either between two existing amino acid residues or at the N- or C-terminal end of the native FIX molecule. [034] The terminology for amino acid substitutions used is as follows. The first letter represents the amino acid residue naturally present at a position of human FIX. The following number represents the position in the mature human FIX amino acid sequence (SEQ ID NO:1). The second letter represent the different amino acid substituting for (replacing/substituting) the natural amino acid. As an example, R338A denotes that the Arg residue at position 338 of SEQ ID NO: 1 has been replaced with an Ala residue. With respect to SEQ ID NO: 26 which includes an additional 5' amino acid sequence (46 amino acids) of human FIX polypeptide, position 338 of SEQ ID NO: 1 corresponds to position 384 of SEQ ID NO: 26. [035] The FIX residue number system used herein refers to that of the mature human FIX protein in which residue 1 represents the first amino acid of the mature FIX polypeptide following removal of both the signal sequence and the propeptide. Native or wild type FIX is the full length mature human FIX molecule as shown in SEQ ID NO: 1. [036] In some embodiments, the glycosylation sites are engineered in FIX at locations that will not abolish the function of the protein or its expression in cells. In order to design FIX polypeptides comprising one or more introduced glycosylation sites, several criteria may be applied. In some embodiments, the introduced glycosylation site is surface exposed. Surface exposure can be determined based on the solvent accessible surface area as determined in Autin, et al., (J. Thromb. Haemost. 3:2044-56, 2005). In some embodiments, the introduced glycosylation site does not introduce a mutation known to be associated with hemophilia B. Known mutations can be found on the world wide web at kcl.ac.uk/ip/petergreen/haemBdatabase.html and in Table 1. 10 WO 2009/137254 PCT/US2009/040813 TABLE 1 Residue Mutation Residue Mutation Residue Mutation No. No. No. 2 N-D 43 K-*E 82 C-*R 3 S-*P 45 Y-*N 88 C-*R 4 G-S 46 V-A 90 I-*T 5 K-*E 47 D-*N 92 N-*H 6 L-*S 48 G-R 96 E-*K 7 E-*K 49 D-*Y 97 Q-*K 8 E-*K 51 C-*S 99 C-*R 9 F-*I 55 P-*T 108 V-*A 11 Q-*E 56 C-*S 109 C-*Y 12 G-*R 58 N-*K 110 S-*P 14 L-*P 59 G-S 111 C-*R 17 E-*K 60 G-S 114 G-*E 18 C-*R 62 C-*Y 115 Y-*C 20 E-*K 64 D-*N 117 L-*F 21 E-*K 66 I-*N 118 A-*V 23 C-*R 67 N-*K 120 N-*Y 25 F-*S 69 Y-*N 121 Q-*H 26 E-*Q 71 C-*S 123 S-*P 27 E-*K 72 W-*R 124 C-*F 30 E-*K 73 C-R 127 A-*P 32 F-*S 76 G-R 128 V-*M 33 E-*K 77 F-*S 131 P-*S 38 T-*A 78 E-*K 132 C-*R 41 F-V 79 G-*R 133 G-*R 11 WO 2009/137254 PCT/US2009/040813 Residue Mutation Residue Mutation Residue Mutation No. No. No. 145 R-*S 217 V-*E 268 H-*R 146 A-*P 218 T-*I 269 D-*N 178 F-L 219 A-T 270 I-*F 180 R-*G 220 A-T 271 A-*D 181 V-F 221 H-*Y 272 L-*F 182 V-L 222 C-*S 273 L-*P 183 G-S 226 G-*N 274 E-*G V-*I, G, 184 G-*R 227 E 275 L-*Q 187 A-*D 228 K-*T 276 D-*Y 190 G-*C 231 V-F 277 E-*K 191 Q-*K 233 V-T 278 P-*H 192 F-V 234 G-S 279 L-*V 193 P-*S 236 H-R 282 N-*I 194 W-*R 237 N-D 284 Y-*C 195 Q-*K 238 I-*N 287 P-*T 198 L-*S 245 E-*K 288 I-*T 204 A-*V 246 Q-*K 289 C-*R 206 C-*R 248 R-*G 290 I-*H 207 G-*R 250 V-M 291 A-*T 208 G-S 251 I-*N 293 K-*E 210 I-*T 256 H-R 295 Y-*C 211 V-F 257 H-*Y 296 T-*A 212 N-*K 259 Y-*N 298 I--N 215 W-*R 260 N-S 299 F-*V 216 I-*F 264 N-*Y 300 L-*F 12 WO 2009/137254 PCT/US2009/040813 Residue Mutation Residue Mutation Residue Mutation No. No. No. 301 K-*I 337 L-*I 366 G-*W 303 G-*E 339 S-*P 367 G-*R 305 G-*D 340 T-R 368 P-*T 307 V-L 341 K-*E 369 H-*I 308 S-*R 344 I-*F 370 V-*N T-V, E, 309 G-*S 345 Y-*C 371 G, I 310 W-*R 346 N-D 372 E-*T 311 G-*R 347 N-*I 373 V-*E 312 R-G 348 M-*V 376 T-*N 313 V-*G 349 F-L 378 F-*L 314 F-*I 350 C-R 379 L-*F 316 K-*E 351 A-P 380 T-*P 317 G-*R 352 G-S 381 G-*R 320 A-*P 353 F-*N 382 I-*F H-V, E, 323 L-*F 354 G, I 384 S-*C 324 Q-*E 355 E-*T 385 W-*R 325 Y-S 356 G-R 386 G-*S 328 V-*I 357 G-*C 387 E-*K 329 P-T 358 R-*T 388 E-*G 330 L-*P 359 D-*N 389 C-*G 331 V-F 360 S-*L 390 A-*T 332 D-*Y 361 C-*S 391 M-*N K-V, E, 333 R-G 363 G-R 392 G, I 334 A-*T 364 D-*N 393 G-*T 336 C-*R 365 S-*G 394 K-*E 13 WO 2009/137254 PCT/US2009/040813 Residue Mutation Residue Mutation Residue Mutation No. No. No. 395 Y-H 400 K--N 407 W-*R 396 G-*R 402 S-*Y 408 I--N 397 I-*L 403 R-W 412 T-*K 398 Y-S 404 Y-H 413 K--N L-V, E, 399 T-*N 405 V-F 414 G, I [037] It may be desirable to compare the properties of the modified FIX polypeptides having one or more introduced glycosylation sites to a control polypeptide. Properties for comparison include, for example, solubility, activity, plasma half-life, glycosylation state, and binding properties. In some embodiments, the modified FIX polypeptides may be glycosylated. It is within the purview of one skilled in the art to select the most appropriate control polypeptide for comparison. In some embodiments, the control polypeptide may be identical to the modified polypeptide except for the one or more introduced glycosylation sites. Exemplary polypeptides include wild-type FIX polypeptide and FIX polypeptides comprising one or more activating substitutions, such as R338A and/or V86A. [038] One aspect of the application provides modified FIX polypeptides having increased in vitro or in vivo stability over a control polypeptide. Enhanced serum half-life and in vivo stability may be desirable to reduce the frequency of dosing that is required to achieve therapeutic effectiveness. Accordingly, in certain embodiments, the glycosylated FIX polypeptides have a serum half-life increased by about 20, 30, 40, 60, 80, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, or 1000% relative to a control protein. In some embodiments, the modified FIX polypeptides may have a serum half-life of at least one, at least two, at least three, at least four, at least five, at least ten, or at least twenty days or more. [039] The term "half-life," as used herein in the context of administering a polypeptide drug to a patient, is defined as the time required for plasma concentration of a drug in a patient to be reduced by one half. Methods for pharmacokinetic analysis and determination of half-life and in vivo stability will be familiar to those skilled in the art. Details may be found in Kenneth, et al., Chemical Stability of Pharmaceuticals: A Handbook for Pharmacists and in Peters, et al., Pharmacokinetc analysis: A Practical Approach (1996). Reference is also made to "Pharmacokinetics," M Gibaldi & D Perron, published by Marcel Dekker, 2nd Rev. edition (1982), which describes pharmacokinetic parameters such as t-alpha and t-beta half lives and area under the curve (AUC). 14 WO 2009/137254 PCT/US2009/040813 [040] The activity of modified FIX polypeptides may be described either as an absolute value, such as in units, or as a percentage of the activity of a control polypeptide. In some embodiments, the modified FIX polypeptides may have a specific activity that is not reduced more than about 10, 20, 30, 40, 50, 60, 70, or 80% relative to a control protein. For example, a modified FIX polypeptide may have a specific activity that is not reduced more than about 80% relative to a control FIX polypeptide, if the modified polypeptide maintains at least about 20% of the specific activity as compared to the specific activity of the control. FIX specific activity may be defined as the ability to function in the coagulation cascade, induce the formation of FXa via interaction with FVIIIa on an activated platelet, or support the formation of a blood clot. The activity may be assessed in vitro by techniques such as clot analysis, as described in, for example, McCarthy, et al., (Thromb. Haemost. 87:824-830,2002), and other techniques known to those skilled in the art. The activity may also be assessed in vivo using one of the several animal lines that have been intentionally bred with a genetic mutation for hemophilia B such that an animal produced from such a line is deficient for FIX. Such lines are available from a variety of sources such as, without limitation, the Division of Laboratories and Research, New York Department of Public Health, Albany, N.Y. and the Department of Pathology, University of North Carolina, Chapel Hill, N.C. Both of these sources, for example, provide canines suffering from canine hemophilia B. Alternatively, mice deficient in FIX are also available (Sabatino, et al., Blood 104:2767-2774, 2005). In order to test for FIX activity, a test polypeptide is injected into the diseased animal, a small cut made and bleeding time compared to a healthy control. [041] Human wild-type FIX has a specific activity of around 200 units per mg. One unit of FIX has been defined as the amount of FIX present in one millilitre of normal (pooled) human plasma (corresponding to a FIX level of 100%). In some embodiments, the modified FIX polypeptides may have a specific activity of at least about 100 units per mg of FIX polypeptide. In some embodiments, the modified FIX polypeptides may have a specific activity of at least about 120, 140, 160, 180, 200, 220, 240, 260 units, or more per mg of FIX polypeptide. In some embodiments, the specific activity of FIX may be measured using the APTT or activated partial thromboplastin time assay (described by, e.g., Proctor, et al., Am. J. Clin. Pathol. 36:212, 1961 and see Examples). [042] When expressed in cells, such as liver or kidney cells, FIX polypeptide may be synthesized by the cellular machinery, undergoes posttranslational modification, and is then secreted by the cells into the extracellular milieu. The amount of FIX polypeptide secreted from cells is therefore dependent on both processes of protein translation and extracellular secretion. In some embodiments, the modified FIX polypeptides may be secreted in an amount that is not reduced more than about 10, 20, 30, 40, 50, 60, 70, or 80% relative to the amount secreted of a control protein. For example, a modified FIX polypeptide may be secreted in an amount that is not 15 WO 2009/137254 PCT/US2009/040813 reduced more than about 80% relative to a control FIX polypeptide, if the modified polypeptide is secreted in an amount of at least about 20% as compared to the control. The amount of FIX polypeptide secreted may be measured, for example, by determining the protein levels in the extracellular medium using any art-known method. Traditional methodologies for protein quantification include 2-D gel electrophoresis, mass spectrometry, and antibody binding. Exemplary methods for assaying protein levels in a biological sample include antibody-based techniques, such as immunoblotting (western blotting), immunohistological assay, enzyme linked immunosorbent assay (ELISA), or radioimmunoassay (RIA). [043] In some embodiments, the modified FIX polypeptides interact with at least one of FVIII, FXI, or FX at a level not reduced more than about 40, 50, 60, 70, or 80% relative to the interaction of a control protein with at least one of FVIII, FXI, or FX. For example, a modified FIX polypeptide may interact with at least one of FVIII, FXI, or FX at a level not reduced more than about 80% relative to a control FIX polypeptide, if the modified polypeptide interacts with at least one of FVIII, FXI, or FX at a level of at least about 20% as compared to the control. The binding of FIX to other members of the coagulation cascade can be determined by any method known to one skilled in the art, including for example, the methods described in Chang, et al., (J. Biol. Chem. 273:12089-12094, 1998). [044] As previously described, FIX is composed of four structural domains with different biological functions. One aspect of the invention is to provide FIX polypeptides that are modified in particular domains, such as in the activation peptide and in the catalytic domain. The application provides, in part, FIX polypeptides comprising one more glycosylation sites introduced into the activation peptide of FIX. The natural glycosylation sites in FIX are located in the EGF1 domain (two 0-linked sites on Ser53 and Ser61) and in the activation peptide (four O-linked sites at Thr159, Thr169, Thr172, and Thr179 and 2 N-linked sites at Asn157 and Asn 167). Thus, six of the eight natural glycosylation sites are located in the activation peptide. Introduced glycosylation sites may have less of a negative impact on activity or expression when introduced into regions of FIX that have natural glycosylation sites, such as the activation peptide. In addition, the activation peptide is cleaved when FIX is activated and so is not required for the catalytic activity of FIXa. However, the activation peptide is present in the zymogen, making the activation peptide an attractive region to introduce glycosylation sites to improve the circulating half-life of the zymogen. [045] The application also provides, in part, FIX polypeptides comprising one or more glycosylation sites. In some embodiments, FIX polypeptides are provided comprising one or more substitutions selected from G4T; E33N; E36T; E36N; R37N; F75N; F77T; E83T; D85N; V86A; K91T; A103T; V107T; K122N; K122T; S138N; A146N; T148N; F150T; P151N; T159N; A161T; 16 WO 2009/137254 PCT/US2009/040813 A161N; T169N; Q170N; T172N; D177N; D177E; F178T; K201N; K201T; K214T; V223N; G226N; Y226T; K228N; K228T; E239N; E242N; 1251T; A262T; E294N; R338A; R338N; K341N; F353N; H354V; H3541; E355T; V370N; T371V; T3711; E372T; E374N; M391N; K392V; G393T; E41ON; K413N; L4141; or any combination thereof. [046] In some embodiments, FIX polypeptides are provided comprising one or more substitutions selected from YIN and S3T; S3N and K5T; G4N and L6T; K5N and E7T; L6N and E8T; E7N and F9T; F9N and Q1IT; VION and G12T; Q11N and N13T; G12N and L14T; N13 and E15T; L14N and R16T; E15N and E17T; M19N and E21T; E20N and K22T; S24N and E26T; F25N and E27T; E26N and A28T; E27N and R29T; A28N and E30T; R29N and V3 IT; E30N and F32T; V3 IN and E33T; F32N and N34T; T35N and R37T; T38N and E40T; T39N and F41T; E40N and W42T; F41N and K43T; W42N and Q44T; K43N and Y45T; Q44N and V46T; Y45N and D47T; V46N and G48T; E52N and N54T; S53N and P55T; G59N and S61T; K63N and D65T; 166N and S68T; S68N and E70T; G76N and E78T; E78N and K80T; E83N and D85T; L84N and V86T; 190N and N92T; KiON and S102T; S102N and D104T; A103N and N105T; D104N and K106T; K106N and V108T; R116N and A118T; E119N and Q121T; Q121N and S123T; A127N and P129T; V135N and V137T; S136N and S138T; V137N and Q139T; Q139N andS141T; T14ONandK142T; S141N and L143T; E147N and V149T; T148N and F150T; V149N and P151T; P151N and V153T; D152N and D154T; V153N and Y155T; D154N and V156T; Y155N and N157T; V156N and S158T; S158N and E160T; T159N and A161T; E160N and E162T; E162N and 1164T; T163N and L165T; I164N and D166T; L165N and N167T; D166N and 1168T; 1168N and Q170T; T169N and S171T; S171N and Q173T; T172N and S174T; Q173N and F175T; S174N and N176T; G184N and D186T; E185N and A187T; D186N and K188T; A187N and P189T; P189N and Q191T; G200N and V202T; K201N and D203T; V202N and A204T; E224N and G226T; T225N and V227T; G226N and K228T; V227N and 1229T; H236N and 1238T; 1238N and E240T; E240N and E242T; T241N and H243T; H243N and E245T; K247N and N249T; V250N and R252T; 125 IN and 1253T; 1253N and P255T; A261N and 1263T; A262N and N264T; D276N and P278T; V28ON and N282T; F302N and S304T; S304N and Y306T; R312N and F314T; V313N and H315T; F314N and K316T; H315N and G317T; K316N and R318T; G317N and S319T; S319N and L321T; A320N and V322T; R327N and P329T; P329N and V33 IT; D332N and A334T; L337N and S339T; S339N and K341T; T340N and F342T; T343N and Y345T; G352N and H354T; F353N and E355T; H354N and G356T; E355N and G357T; G356N and R358T; G357N and D359T; E372N and E374T; W385N and E387T; G386N and E388T; A390N and K392T; or any combination thereof [047] In some embodiments, FIX polypeptides are provided comprising one or more substitutions selected from D85N, K122T, and 1251T; D85N, K122T, and E242N; E125N, P126A, and A127T; P126N, V128T, and P129A; T148N, F150T, and P151A; F150N, P151A, and D152T; 17 WO 2009/137254 PCT/US2009/040813 P151N, V153T, and A161N; P151N, V153T, and T172N; V153N, Y155T, and E294N; T172N, G226N, and K228T; F353N, H354V, and E355T; F353N, H3541, and E355T; V370N, T371V, and E372T; V370N, T3711, and E372T; M391N, K392V, and G393T; D85N, P151N, V153T, and K228N; D85N, P151N, V153T, and E242N; K122T, P151N, V153T, and K228N; K122T, P151N, V153T, and E242N; K122T, P151N, V153T, and 1251T; T148N, F150T, G226N, and K228T; P151N, V153T, T172N, and R338A; P151N, V153T, D177E, and F178T; P151N, V153T, G226N, and K228T; T172N, G226N, K228T, and R338A; D85N, K122T, P151N, V153T, and E242N; D85N, P151N, V153T, G226N, and K228T; K122T, P151N, V153T, G226N, and K228T; S138N, P151N, V153T, G226N, and K228T; T148N, F150T, G226N, K228T, and R338A; P151N, V153T, T172N, G226N, and K228T; P151N, V153T, D177E, F178T, and R338A; P151N, V153T, G226N, K228T, and R338A; and P151N, V153T, T172N, G226N, K228T, and R338A; or any combination thereof [048] In some embodiments, FIX polypeptides are provided comprising one or more substitutions selected from (a) G4T; E33N; E36T; E36N; R37N; F75N; F77T; E83T; D85N; V86A; K91T; A103T; V107T; K122N; K122T; S138N; A146N; T148N; F150T; P151N; T159N; A161T; A161N; T169N; Q170N; T172N; D177N; D177E; F178T; K201N; K20iT; K214T; V223N; G226N; Y226T; K228N; K228T; E239N; E242N; 1251T; A262T; E294N; R338A; R338N; K341N; F353N; H354V; H3541; E355T; V370N; T371V; T3711; E372T; E374N; M391N; K392V; G393T; E41ON; K413N; L4141; (b) YIN and S3T; S3N and K5T; G4N and L6T; K5N and E7T; L6N and E8T; E7N and F9T; F9N and Q1 IT; VION and G12T; Q1 IN and N13T; G12N and L14T; N13 and E15T; L14N and R16T; E15N and E17T; M19N and E21T; E20N and K22T; S24N and E26T; F25N and E27T; E26N and A28T; E27N and R29T; A28N and E30T; R29N and V31T; E30N and F32T; V31N and E33T; F32N and N34T; T35N and R37T; T38N and E40T; T39N and F41T; E40N and W42T; F41N and K43T; W42N and Q44T; K43N and Y45T; Q44N and V46T; Y45N and D47T; V46N and G48T; E52N and N54T; S53N and P55T; G59N and S61T; K63N and D65T; 166N and S68T; S68N and E70T; G76N and E78T; E78N and K80T; E83N and D85T; L84N and V86T; 190N and N92T; KiON and S102T; S102N and DI04T; A103N and N105T; D104N and Ki06T; Ki06N and VI08T; RI 16N and Al 18T; El 19N and Q121T; Q121N and S123T; A127N and P129T; V135N and V137T; S136N and S138T; V137N and Q139T; Q139N and S141T; T140N and K142T; S141N and L143T; E147N and V149T; T148N and F150T; V149N and P151T; P15IN and V153T; D152N and D154T; V153N and Y155T; D154N and V156T; Y155N and N157T; V156N and S158T; S158N and E160T; T159N and A161T; E160N and E162T; E162N and 1164T; T163N and L165T; 164N and D166T; L165N and N167T; D166N and I168T; 168N and Q170T; T169N 18 WO 2009/137254 PCT/US2009/040813 and S171T; S171N and Q173T; T172N and S174T; Q173N and F175T; S174N and N176T; G184N and D186T; E185N and A187T; D186N and K188T; A187N and P189T; P189N and Q19 1T; G200N and V202T; K201N and D203T; V202N and A204T; E224N and G226T; T225N and V227T; G226N and K228T; V227N and 1229T; H236N and 1238T; 1238N and E240T; E240N and E242T; T241N and H243T; H243N and E245T; K247N and N249T; V250N and R252T; 1251N and 1253T; 1253N and P255T; A261N and 1263T; A262N and N264T; D276N and P278T; V28ON and N282T; F302N and S304T; S304N and Y306T; R312N and F314T; V313N and H315T; F314N and K316T; H315N and G317T; K316N and R318T; G317N and S319T; S319N and L321T; A320N and V322T; R327N and P329T; P329N and V331T; D332N and A334T; L337N and S339T; S339N and K341T; T340N and F342T; T343N and Y345T; G352N and H354T; F353N and E355T; H354N and G356T; E355N and G357T; G356N and R358T; G357N and D359T; E372N and E374T; W385N and E387T; G386N and E388T; A390N and K392T; (c) D85N, K122T, and 1251T; D85N, K122T, and E242N; E125N, P126A, and A127T; P126N, V128T, and P129A; T148N, F150T, and P151A; F150N, P151A, and D152T; P151N, V153T, and A161N; P151N, V153T, and T172N; V153N, Y155T, and E294N; T172N, G226N, and K228T; F353N, H354V, and E355T; F353N, H3541, and E355T; V370N, T371V, and E372T; V370N, T3711, and E372T; M391N, K392V, and G393T; D85N, P151N, V153T, and K228N; D85N, P151N, V153T, and E242N; K122T, P151N, V153T, and K228N; K122T, P151N, V153T, and E242N; K122T, P151N, V153T, and 1251T; T148N, F150T, G226N, and K228T; P151N, V153T, T172N, and R338A; P151N, V153T, D177E, and F178T; P151N, V153T, G226N, and K228T; T172N, G226N, K228T, and R338A; D85N, K122T, P151N, V153T, and E242N; D85N, P151N, V153T, G226N, and K228T; K122T, P151N, V153T, G226N, and K228T; S138N, P151N, V153T, G226N, and K228T; T148N, F150T, G226N, K228T, and R338A; P151N, V153T, T172N, G226N, and K228T; P151N, V153T, D177E, F178T, and R338A; P151N, V153T, G226N, K228T, and R338A; and P151N, V153T, T172N, G226N, K228T, and R338A; and any combination thereof. [049] The application provides, in part, FIX polypeptides comprising one more glycosylation sites introduced by converting an endogenous O-linked glycosylation site to an N-linked glycosylation site. It has been reported that N-linked glycosylation sites are more likely to be sialylated than O-linked glycosylation sites and there is evidence that higher sialic acid content confers increased protein half-life. It is generally believed that the increased sialic acid content provided by additional N-linked glycosylation may be responsible for the increased half-life in blood (White, et al., Thromb. Haemost. 78:261-265, 1997). Exemplary embodiments of such modified FIX polypeptides are as follows. In some embodiments, FIX polypeptides are provided comprising a T169N substitution. In some embodiments, FIX polypeptides are provided comprising a T172N substitution. In some embodiments, FIX polypeptides are provided 19 WO 2009/137254 PCT/US2009/040813 comprising a T148N substitution and an F150T substitution. In some embodiments, FIX polypeptides are provided comprising a T159N substitution and an A161T substitution. [050] Another aspect of the invention provides for the insertion of amino acids into the activation peptide in order to generate one or more glycosylation sites. The application provides, in part, FIX polypeptides comprising one more glycosylation sites introduced between amino acid residues 160 to 164 of human FIX. In some embodiments, the amino acid residues introduced include a glycosylation site. In some embodiments, the amino acid residues introduced form a glycosylation site in combination with wild-type FIX amino acid residues. The multiple sequence alignment of the FIX sequence from 8 species demonstrated that the mouse, rat, and guinea pig sequences all have additional amino acids (between 7 and 10 residues) in the activation peptide that are not found in other species (human, rhesus, dog, rabbit, pig) (Figure 1). These additional sequences are located between E160 and E162 of human FIX. This suggests that insertion of at least 10 amino acid residues is tolerated in the FIX structure at this site. This region was targeted for the introduction of additional amino acids and was found to be a good location as activity was not significantly reduced. In some embodiments, up to 30, 25, 20, 18, 16, 14, or 12 amino acid residues may be inserted between amino acid residues 160 to 164 of human FIX. In some embodiments, up to 10 amino acids may be inserted. In some embodiments, up to 9 amino acid may be inserted. [051] Depending upon the criteria used to perform the multiple sequence alignment between FIX from the eight species, the apparent site at which the additional amino acids in rat, mouse, and guinea pig are found can vary such that the site can be either between E160 and A161, between A161 and E162, between E162 and T163, or between T163 and 1164 of human FIX. In some embodiments, the amino acid sequence inserted between E160 and A161 may be SEQ ID NO: 2. In some embodiments, the amino acid sequence inserted between A161 and E162 may be SEQ ID NO: 2. In some embodiments, the amino acid sequence inserted between E162 and T163 may be SEQ ID NO: 2. In some embodiments, the amino acid sequence inserted between T163 and 1164 may be SEQ ID NO: 2. In some embodiments, one or more amino acids may be inserted between E160 and A161 and one or more amino acids may be inserted between A161 and E162. In some embodiments, one or more amino acids may be inserted between E160 and A161 and one or more amino acids may be inserted between E162 and T163. In some embodiments, one or more amino acids may be inserted between A161 and E162 and one or more amino acids may be inserted between E162 and T163. In some of the above described embodiments, one or more amino acids maybe inserted between T163 and 1164. In some embodiments, up to about 30, 25, 20, 18, 16, 14, or 12 total amino acid residues may be inserted between amino acid residues 160 to 164 of human FIX. In some embodiments, up to about 10 total amino acids may be inserted between amino acid residues 160 to 164 of human FIX. In some embodiments, up to about 9 total amino acids may be 20 WO 2009/137254 PCT/US2009/040813 inserted between amino acid residues 160 to 164 of human FIX. In some embodiments, one, two, three, or four glycosylation sites may be introduced. [052] The application further provides modified FIX polypeptides comprising more than one of the introduced glycosylation sites disclosed herein. FIX polypeptides are provided that comprise at least one introduced glycosylation site in the catalytic domain and at least one introduced glycosylation site in the activation peptide. FIX polypeptides are provided that comprise at least two introduced glycosylation sites in the catalytic domain. FIX polypeptides are provided that comprise at least two introduced glycosylation sites in the activation peptide. In some embodiments, the FIX polypeptides may comprise one or more of the following substitutions: R37N; D85N; K122T; S138N; A146N; A161N; Q170N; T172N; D177N; F178T; K201N; K228N; E239N; E242N; 1251T; A262T; E294N; E374N; and E410N. Other embodiments may comprise one or more of the following substitutions: G59N and S6 IT; K63N and D65T; G76N and E78T; S102N and D104T; A103N and N105T; D104N and K106T; E119N and Q121T; Q121N and S123T; S136N and S138T; Q139N and S141T; T140N and K142T; T148N and F150T; V149N and P151T; P151N and V153T; D152N and D154T; V153N and Y155T; D154N and V156T; V156N and S158T; S158N and E160T; E160N and E162T; E162N and 1164T; T163N and L165T; I164N and D166T; D166N and I168T; I168N and Q170T; S171N and Q173T; T172N and S174T; Q173N and F175T; S174N andN176T; K201N and D203T; V202N and A204T; E224N and G226T; T225N and V227T; G226N and K228T; T241N and H243T; 125 IN and 1253T; 1253N and P255T; A262N and N264T; V28ON and N282T; T343N and Y345T; E372N and E374T; F150N, P151A, and D152T; and insertion of SEQ ID NO:2 between A161 and E162. In some embodiments, the modified polypeptides may further comprise at least one substitution such as, for example, R338A and V86A. In some embodiments, the modified polypeptides may further comprise both the R338A and V86A substitutions. [053] The application further provides modified FIX polypeptides that comprise at least one introduced glycosylation site at the C-terminus of the FIX polypeptide (i.e., following amino acid residue 415 of the FIX polypeptide). FIX polypeptides are provided that comprise at least two, at least three, at least four, or more glycosylation sites at the C-terminus of the FIX polypeptide. In some embodiments, the FIX polypeptide may comprise the addition of the amino acid sequence of SEQ ID NO: 4 at the C-terminus of the FIX polypeptide. In some embodiments, the FIX polypeptide may comprise the addition of the amino acid sequence of SEQ ID NO: 5 at the C terminus of the FIX polypeptide. In some embodiments, the FIX polypeptide may comprise the addition of the amino acid sequence of SEQ ID NO: 6 at the C-terminus of the FIX polypeptide. In some embodiments, the FIX polypeptide may comprise the addition of the amino acid sequence of SEQ ID NO: 7 at the C-terminus of the FIX polypeptide. 21 WO 2009/137254 PCT/US2009/040813 [054] One aspect of the application provides modified FIX polypeptides comprising at least one or more glycosylation sites and one or more substitutions that increase the activity of FIX. Examples of activating substitutions include the R338A and the V86A substitutions. In some embodiments, modified FIX polypeptides may comprise the R338A substitution. In some embodiments, modified FIX polypeptides may comprise the V86A substitution. In some embodiments, modified FIX polypeptides may comprise both the R338A and the V86A substitution. [055] A further aspect of the application provides FIX polypeptides with increased specific activity. In some embodiments, FIX polypeptides may comprise an R338A substitution and a V86A substitution. In some embodiments, the polypeptides may have a specific activity of at least about 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1400, 1600, 1800, or 2000 units per mg of polypeptide. The specific activity can be determined as previously described, such as, for example, using the APTT assay. These polypeptides are useful as therapeutic agents, particularly in patients afflicted with hemophilia B. These polypeptides may comprise further substitutions or modifications, such as the glycosylation sites described herein. [056] One aspect of the application provides modified Factor IX polypeptides comprising the following amino acid sequence: YNSGKLEEFVQGNLERECMEEKCSFEEAREVFENTERTTEFWKQYVDGDQCESNPC LNGGSCKDDINSYECWCPFGFEGKNCELXssXs 6 TCNIKNGRCEQFCKNSAXio 4 NKVV

CSCTEGYRLAENX

121

KSCEPAVPFPCGRVSVX

1 3

QTSKLTRAEX

14 sVXisOXi 1 Xi 2

X

1 s 3 D

YVNSX

15 9 EZiX 16 i 1

Z

2

EZ

3

TZ

4

ILDNIX

169

QSX

172

QX

174

FNX

1 77

X

1 7 TRVVGGEDAKPGQFPW

QVVLNGKVDAFCGGSIVNEKWIVTAAHCVETX

22 6

VX

228 ITVVAGEHNIEETEHTEQK RNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGY

VSGWGRVFHKGRSALVLQYLRVPLVDRATCLX

33

STKFTIYNNMFCAGX

353

X

35 4

X

3 55

GGRDSCQGDSGGPHX

37

X

37 1

X

372

VEGTSFLTGIISWGEECAX

39

X

392

X

393 KYGIYTKVS RYVNWIKE KTX 4 13

X

4 14 T (SEQ ID NO: 3); wherein X 85 is selected from D and E; wherein X 86 is selected from A, E, P, S, and V; wherein X 104 is selected from D, N, and T; wherein X 12 1 is selected from N, Q, and T; wherein X 138 is selected from N, S, and T; wherein X 148 and X 150 are selected from: (i) X 14 8 is T and X 15 o is F; 22 WO 2009/137254 PCT/US2009/040813 (ii) X 14 8 is N and Xi 50 is T; and (iii) X 14 S is N and Xi 50 is S; wherein X 151 is selected from A, P, and T; wherein X 151 and X 153 are selected from: (i) X 151 is P and X 153 is V; (ii) X 151 is N and X 15 3 is T; and (iii) X 151 is N and X 15 3 is S; wherein Zi, Z 2 , Z 3 , and Z 4 are independently selected from (i) zero to twelve amino acid residues and (ii) SEQ ID NO: 2; wherein X 152 is selected from D, N, and T; wherein X 159 and X 16 are selected from: (i) X 159 is T and X 1 61 is A; (ii) X 159 is N and X 161 is T; and (iii) X 159 is N and X 161 is S; wherein X 169 is selected from T and N; wherein X 172 is selected from T and N; wherein X 174 is selected from S and T; wherein X 177 and X 1 7 s are selected from: (i) X 177 is D and X 1 78 is F; (ii) X 177 is E and X 1 78 is T; and (iii) X 1 77 is E orD and X 1 7 S is S; wherein X 22 6 and X 228 are selected from: (i) X 226 is G and X 228 is K; (ii) X 226 is N and X 228 is T; and (iii) X 226 is N and X 228 is S; wherein X 338 is selected from R and A; wherein X 353 , X 354 , and X355 are selected from: (i) X 353 is F, X 354 is H, X 355 is E; (ii) X 353 is N, X 354 is V, X 3 55 is T; (iii) X 353 is N, X 354 is I, X 3 55 is T; and (iv) X 353 is N, X 354 is H, V, or I, X 3 55 is S; 23 WO 2009/137254 PCT/US2009/040813 wherein X 370 , X 37 1 , and X 37 2 are selected from: (i) X 370 is V, X 371 is T, X 372 is E; (ii) X 370 is N, X 371 is V, X 372 is T; (iii) X 370 is N, X 371 is I, X 372 is T; and (iv) X 370 is N, X 37 1 is T, V, or I, X 372 is S; wherein X 39 1 , X 392 , and X 39 3 are selected from: (i) X 391 is M, X 392 is K, X 393 is G; (ii) X 39 1 is N, X 39 2 is K, X 393 is T; (iii) X 391 is N, X 392 is V, X 393 is T; and (iv) X391 is N, X392 is V or K, X393 is S; wherein X 4 13 and X 4 1 4 are selected from: (i) X 41 3 is K and X 41 4 is L; (ii) X 4 1 3 is N and X 4 1 4 is L; and (iii) X 4 1 3 is N and X 4 1 4 is I; and wherein the FIX polypeptide comprises at least one introduced glycosylation site as compared to the FIX polypeptide having SEQ ID NO: 1. [057] The introduction of at least one glycosylation site is the result of a substitution at least one of the X positions or an insertion in at least one of the Z positions. In some embodiments, the modified polypeptide additionally comprises between about 1-30, 1-20, or 1-10 conservative amino acid changes and maintains FIX activity. In some embodiments, the modified polypeptide is at least about 80, 85, 90, 95, or 99% identical to SEQ ID NO: 1 and maintains FIX activity. Production of Modified FIX Polypeptides [058] Amino acid residues may be inserted, deleted, or substituted in order to introduce a non native glycosylation site. For example, glycosylation sites may be introduced by altering the amino acid sequence of FIX. Amino acid sequence alteration may be accomplished by a variety of techniques, such as, for example, by modifying the corresponding nucleic acid sequence by site specific mutagenesis. Techniques for site-specific mutagenesis are well known in the art and are described in, for example, Zoller et al., (DNA 3:479-488, 1984) or Horton, et al., (Gene 77:61-68, 1989, pp. 61-68). Thus, using the nucleotide and amino acid sequences of FIX, one may introduce the alteration(s) of choice. Likewise, procedures for preparing a DNA construct using polymerase chain reaction using specific primers are well known to persons skilled in the art (see, e.g., PCR Protocols, 1990, Academic Press, San Diego, California, USA). [059] The nucleic acid construct encoding the FIX polypeptide may also be prepared synthetically by established standard methods, for example, the phosphoramidite method described 24 WO 2009/137254 PCT/US2009/040813 by Beaucage, et al., (Gene Amplif. Anal. 3:1-26, 1983). According to the phosphoamidite method, oligonucleotides are synthesized, for example, in an automatic DNA synthesizer, purified, annealed, ligated, and cloned in suitable vectors. The DNA sequences encoding the human FIX polypeptides may also be prepared by polymerase chain reaction using specific primers, for example, as described in US Patent No. 4,683,202; or Saiki, et al., (Science 239:487-491, 1988). Furthermore, the nucleic acid construct may be of mixed synthetic and genomic, mixed synthetic and cDNA, or mixed genomic and cDNA origin prepared by ligating fragments of synthetic, genomic, or cDNA origin (as appropriate), corresponding to various parts of the entire nucleic acid construct, in accordance with standard techniques. [060] The DNA sequences encoding the FIX polypeptides may be inserted into a recombinant vector using recombinant DNA procedures. The choice of vector will often depend on the host cell into which the vector is to be introduced. The vector may be an autonomously replicating vector or an integrating vector. An autonomously replicating vector exists as an extrachromosomal entity and its replication is independent of chromosomal replication, for example, a plasmid. An integrating vector is a vector that integrates into the host cell genome and replicates together with the chromosome(s) into which it has been integrated. [061] The vector may be an expression vector in which the DNA sequence encoding the modified FIX is operably linked to additional segments required for transcription, translation, or processing of the DNA, such as promoters, terminators, and polyadenylation sites. In general, the expression vector may be derived from plasmid or viral DNA, or may contain elements of both. The term "operably linked" indicates that the segments are arranged so that they function in concert for their intended purposes, for example, transcription initiates in a promoter and proceeds through the DNA sequence coding for the polypeptide. [062] Expression vectors for use in expressing FIX polypeptides may comprise a promoter capable of directing the transcription of a cloned gene or cDNA. The promoter may be any DNA sequence that shows transcriptional activity in the host cell of choice and may be derived from genes encoding proteins either homologous or heterologous to the host cell. [063] Examples of suitable promoters for directing the transcription of the DNA encoding the FIX polypeptides in mammalian cells are, for example, the SV40 promoter (Subramani, et al., Mol. Cell Biol. 1:854-864, 1981), the MT-I (metallothionein gene) promoter (Palmiter, et al., Science 222:809-814, 1983), the CMV promoter (Boshart, et al., Cell 41:521-530, 1985), or the adenovirus 2 major late promoter (Kaufiman et al.,, Mol. Cell Biol, 2:1304-1319, 1982). [064] The DNA sequences encoding the FIX polypeptide may also, if necessary, be operably connected to a suitable terminator, such as the human growth hormone terminator (Palmiter, et al., Science 222:809-814, 1983) or TPIl (Alber et al., J. Mol. Appl. Gen. 1:419-434, 1982) or ADH3 25 WO 2009/137254 PCT/US2009/040813 (McKnight, et al., EMBO J. 4:2093-2099, 1985) terminators. The expression vectors may also contain a polyadenylation signal located downstream of the insertion site. Polyadenylation signals include the early or late polyadenylation signal from SV40, the polyadenylation signal from the adenovirus 5 EIb region, the human growth hormone gene terminator (DeNoto, et al., Nucl. Acids Res. 9:3719-3730, 1981), or the polyadenylation signal from the human FIX gene. The expression vectors may also include enhancer sequences, such as the SV40 enhancer. [065] To direct the FIX polypeptides of the present invention into the secretory pathway of the host cells, the native FIX secretory signal sequence may be used. Alternatively, a secretory signal sequence (also known as a leader sequence, prepro sequence, or pre sequence) may be provided in the recombinant vector. The secretory signal sequence may be joined to the DNA sequences encoding the FIX analogues in the correct reading frame. Secretory signal sequences are commonly positioned 5' to the DNA sequence encoding the peptide. Exemplary signal sequences include, for example, the MPIF-1 signal sequence and the stanniocalcin signal sequence. [066] The procedures used to ligate the DNA sequences coding for the FIX polypeptides, the promoter, and optionally the terminator and/or secretory signal sequence and to insert them into suitable vectors containing the information necessary for replication, are well known to persons skilled in the art (see, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, New York, 1989). [067] Methods of transfecting mammalian cells and expressing DNA sequences introduced into the cells are described in, for example, Kaufiman, et al., (J. Mol. Biol. 159:601-621, 1982); Southern, et al., (J. Mol. Appl. Genet. 1:327-341, 1982); Loyter, et al., (Proc. Natl. Acad. Sci. USA 79:422-426, 1982); Wigler, et al., (Cell 14:725-731, 1978); Corsaro, et al., (Somatic Cell Genetics 7:603-616, 1981), Graham, et al., (Virology 52:456-467, 1973); and Neumann, et al., (EMBO J. 1:841-845, 1982). Cloned DNA sequences may be introduced into cultured mammalian cells by, for example, lipofection, DEAE-dextran-mediated transfection, microinj ection, protoplast fusion, calcium phosphate precipitation, retroviral delivery, electroporation, sonoporation, laser irradiation, magnetofection, natural transformation, and biolistic transformation (see, e.g., Mehier Humbert, et al., Adv. Drug Deliv. Rev. 57:733-753, 2005). To identify and select cells that express the exogenous DNA, a gene that confers a selectable phenotype (a selectable marker) is generally introduced into cells along with the gene or cDNA of interest. Selectable markers include, for example, genes that confer resistance to drugs such as neomycin, puromycin, hygromycin, and methotrexate. The selectable marker may be an amplifiable selectable marker, which permits the amplification of the marker and the exogenous DNA when the sequences are linked. Exemplary amplifiable selectable markers include dihydrofolate reductase (DHFR) and 26 WO 2009/137254 PCT/US2009/040813 adenosine deaminase. It is within the purview of one skilled in the art to choose suitable selectable markers (see, e.g., US Patent No. 5,238,820). [068] After cells have been transfected with DNA, they are grown in an appropriate growth medium to express the gene of interest. As used herein the term "appropriate growth medium" means a medium containing nutrients and other components required for the growth of cells and the expression of the active FIX polypeptides. [069] Media generally include, for example, a carbon source, a nitrogen source, essential amino acids, essential sugars, vitamins, salts, phospholipids, protein, and growth factors, and in the case of vitamin K dependent proteins such as FIX, vitamin K may also be provided. Drug selection is then applied to select for the growth of cells that are expressing the selectable marker in a stable fashion. For cells that have been transfected with an amplifiable selectable marker the drug concentration may be increased to select for an increased copy number of the cloned sequences, thereby increasing expression levels. Clones of stably transfected cells are then screened for expression of the FIX polypeptide. [070] Examples of mammalian cell lines for use in the present invention are the COS-1 (ATCC CRL 1650), baby hamster kidney (BHK), HKB1 1 cells (Cho, et al., J. Biomed. Sci, 9:631-638, 2002), and HEK-293 (ATCC CRL 1573; Graham, et al., J. Gen. Virol. 36:59-72, 1977) cell lines. In addition, a number of other cell lines may be used within the present invention, including rat Hep I (rat hepatoma; ATCC CRL 1600), rat Hep II (rat hepatoma; ATCC CRL 1548), TCMK-1 (ATCC CCL 139), Hep-G2 (ATCC HB 8065), NCTC 1469 (ATCC CCL 9.1), CHO-KI (ATCC CCL 61), and CHO-DUKX cells (Urlaub and Chasm, Proc. Natl. Acad. Sci. USA 77:4216-4220, 1980). [071] FIX polypeptides may be recovered from cell culture medium and may then be purified by a variety of procedures known in the art including, but not limited to, chromatography (e.g., ion exchange, affinity, hydrophobic, chromatofocusing, and size exclusion), electrophoretic procedures (e.g., preparative isoelectric focusing (IEF), differential solubility (e.g., ammonium sulfate precipitation)), extraction (see, e.g., Protein Purification, Janson and Lars Ryden, editors, VCH Publishers, New York, 1989), or various combinations thereof. In an exemplary embodiment, the polypeptides may be purified by affinity chromatography on an anti-FIX antibody column. Additional purification may be achieved by conventional chemical purification means, such as high performance liquid chromatography. Other methods of purification are known in the art, and may be applied to the purification of the modified FIX polypeptides (see, e.g., Scopes, R., Protein Purification, Springer-Verlag, N.Y., 1982). [072] Generally, "purified" shall refer to a protein or peptide composition that has been subjected to fractionation to remove various other components, and which substantially retains its 27 WO 2009/137254 PCT/US2009/040813 expressed biological activity. Where the term "substantially purified" is used, this designation shall refer to a composition in which the protein or peptide forms the major component of the composition, such as constituting about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, or more of the proteins in the composition. [073] Various methods for quantifying the degree of purification of the polypeptide are known to those of skill in the art. These include, for example, determining the specific activity of an active fraction, or assessing the amount of polypeptides within a fraction by SDS/PAGE analysis. An exemplary method for assessing the purity of a fraction is to calculate the specific activity of the fraction, compare the activity to the specific activity of the initial extract, and to thus calculate the degree of purity, herein assessed by a "-fold purification number." The actual units used to represent the amount of activity will, of course, be dependent upon the particular assay technique. [074] In some embodiments, FIX polypeptides are recombinantly expressed in tissue culture cells and glycosylation is the result of the normal post-translational cell functioning of the host cell, such as a mammalian cell. [075] Alternatively, glycosylation may be achieved through chemical or enzymatic modification. FIX polypeptides may be glycosylated by using, for example, an enzyme that adds alpha-(2,6) linked sialic acid to protein. For example, dihydrofolate reductase (DHFR) deficient CHO cells are commonly used host cells for recombinant glycoprotein production. CHO cells do not endogenously express the enzyme beta-galactoside alpha-2,6 sialyltransferase, which is used to add sialic acid in the 2,6 linkage to galactose on the mannose alpha-1,3 branch. To add sialic acid at this linkage to a protein produced in CHO cells, the CHO cells may be transfected with a functional beta-galactosidase alpha-2,6 sialyltransferase gene to allow for incorporation of sialic acid in the 2,6 linkage to galactose as desired (see, e.g., Lee, et al., J. Biol. Chem. 264:13848 13855, 1989). [076] Similarly, a bisecting N-acetylglucosamine (GlcNAc) may be added to FIX by transfecting a host cell that does not endogenously produce this oligosaccharide linkage with the functional gene for the enzyme N-acetylglucosaminyltransferase, which has been reported to catalyze formation of a bisecting GlcNAc structure. Systems have also been established to express proteins in plant cells that produce proteins with mammalian glycosylation patterns (see, e.g., bryophyte cells, WO 2004/057002). [077] For N-linked glycosylation, the final structures of the N-glycans are typically dependent upon the organism in which the polypeptide is produced. Generally, polypeptides produced in bacteria are completely unglycosylated. Polypeptides expressed in insect cells contain high mannose and pauci-mannose N-linked oligosaccharide chains, among others. Polypeptides produced in mammalian cell culture are usually glycosylated differently depending upon, for 28 WO 2009/137254 PCT/US2009/040813 example, the species and cell culture conditions. Further, polypeptides produced in plant cells comprise glycan structures that differ significantly from those produced in animal cells. The goal in the art of the production of recombinant polypeptides, particularly when the polypeptides are to be used as therapeutic agents, is to be able to generate polypeptides that are correctly glycosylated, that is, to be able to generate a polypeptide having a glycan structure that resembles, or is identical to that present on the naturally occurring form of the polypeptide. [078] A variety of methods have been proposed in the art to customize the glycosylation pattern of a polypeptide (see, e.g., WO 99/22764; WO 98/58964; WO 99/54342; US Publication No. 2008/0050772; and US Patent No. 5,047,335). Essentially, many of the enzymes required for the in vitro glycosylation of polypeptides have been cloned and sequenced. In some instances, these enzymes have been used in vitro to add specific sugars to an incomplete glycan molecule on a polypeptide. In other instances, cells have been genetically engineered to express a combination of enzymes and desired polypeptides such that addition of a desired sugar moiety to an expressed polypeptide occurs within the cell. [079] For O-linked glycosylation, 0-glycans are linked primarily to seine and threonine residues and are formed by the stepwise addition of sugars from nucleotide sugars (Tanner, et al., Biochim. Biophys. Acta. 906:81-99, 1987); Hounsell, et al., Glycoconj. J. 13:19-26, 1996). Polypeptide function can be affected by the structure of the O-linked glycans present. For a review of O-linked glycan structures, see, for example, Schachter and Brockhausen, The Biosynthesis of Branched O-Linked Glycans, 1989, Society for Experimental Biology, pp. 1-26 (Great Britain). [080] Whether a FIX polypeptide has N-linked and/or O-linked glycosylation may be determined using standard techniques (see, e.g., Techniques in Glycobiology, R. Townsend and A. Hotchkiss, eds. (1997) Marcel Dekker; and Glycoanalysis Protocols (Methods in Molecular Biology, Vol. 76), E. Hounsell, ed. (1998) Humana Press). The change in electrophoretic mobility of a protein before and after treatment with chemical or enzymatic deglycosylation (e.g., using endoglycosidases and/or exoglycosidases) is routinely used to determine the glycosylation status of a protein. Enzymatic deglycosylation may be carried out using any of a variety of enzymes, including, but not limited to, peptide-N4-(N-acetyl-beta-D-glycosaminyl) asparagine amidase (PNGase F), endoglycosidase F1, endoglycosidase F2, endoglycosidase F3, and the like. For example, sodium docecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the protein, either pre-treated with PNGaseF or untreated with PNGaseF, may be conducted. A marked decrease in band width and change in migration position after treatment with PNGaseF may be considered diagnostic of N-linked glycosylation. The carbohydrate content of a glycosylated protein also can be detected using lectin analysis of protein blots (e.g., proteins 29 WO 2009/137254 PCT/US2009/040813 separated by SDS-PAGE and transferred to a support, such as a nylon membrane). Lectins, carbohydrate binding proteins from various plant tissues, have both high affinity and narrow specificity for a wide range of defined sugar epitopes found on glycoprotein glycans (Cummings, Methods Enzymol. 230:66-86, 1994). Lectins may be labeled (either directly or indirectly) allowing detection of binding of lectins to carbohydrates on glycosylated proteins. For example, when conjugated with biotin or digoxigenin, a lectin bound to a glycosylated protein can be easily identified on membrane blots through a reaction utilizing avidin or anti-digoxigenin antibodies conjugated with an enzyme such as alkaline phosphatase, beta-galactosidase, luciferase, or horse radish peroxidase, to yield a detectable product. Screening with a panel of lectins with well defined specificity provides considerable information about a glycoprotein's carbohydrate complement. The electrophoretic mobility of the modified FIX polypeptide may also be compared to the mobility of a reference protein. [081] The application provides, in part, FIX polypeptides with introduced glycosylation sites, wherein the carbohydrate chain attached to the glycosylation site may have a mammalian carbohydrate chain structure, that is, a mammalian glycosylation pattern. In some embodiments, the carbohydrate chain has a human glycosylation pattern. As used herein, a pattern of glycosylation refers to the representation of particular oligosaccharide structures within a given population of FIX polypeptides. Non-limiting examples of such patterns include the relative proportion of oligosaccharide chains that (i) have at least one sialic acid residue; (ii) lack any sialic acid residues (i.e., are neutral in charge); (iii) have at least one terminal galactose residue; (iv) have at least one terminal N-acetylgalactosamine residue; (v) have at least one "uncapped" antenna, that is, have at least one terminal galactose or N-acetylgalactosamine residue; or (vi) have at least one fucose linked alphal->3 to an antennary N-acetylglucosamine residue. [082] The pattern of glycosylation may be determined using any method known in the art, including, without limitation: high-performance liquid chromatography (HPLC); capillary electrophoresis (CE); nuclear magnetic resonance (NMR); mass spectrometry (MS) using ionization techniques such as fast-atom bombardment, electrospray, or matrix-assisted laser desorption (MALDI); gas chromatography (GC); and treatment with exoglycosidases in conjunction with anion-exchange (AIE)-HPLC, size-exclusion chromatography (SEC), or MS (see, e.g., Weber, et al., Anal. Biochem. 225:135-142, 1995; Klausen, et al., J. Chromatog. 718:195-202, 1995; Morris, et al., in Mass Spectrometry of Biological Materials, McEwen et al., eds., Marcel Dekker, (1990), pp 137-167; Conboy et al., Biol. Mass Spectrom. 21:397-407, 1992; Hellerqvist, Meth. Enzymol. 193:554-573, 1990; Sutton, et al., Anal. Biochem. 218:34-46, 1994; Harvey, et al., Organic Mass Spectrometry 29:753-766, 1994). 30 WO 2009/137254 PCT/US2009/040813 Pharmaceutical Compositions [083] Based on well known assays used to determine the efficacy for treatment of conditions identified above in mammals, and by comparison of these results with the results of known medicaments that are used to treat these conditions, the effective dosage of the polypeptides of this invention may readily be determined for treatment of each desired indication. The amount of the active ingredient to be administered in the treatment of one of these conditions can vary widely according to such considerations as the particular polypeptide and dosage unit employed, the mode of administration, the period of treatment, the age and sex of the patient treated, and the nature and extent of the condition treated. [084] The application provides, in part, compositions comprising FIX polypeptides with one or more introduced glycosylation sites as described herein. The compositions may be suitable for in vivo administration and are pyrogen free. The compositions may also comprise a pharmaceutically acceptable carrier. The phrase "pharmaceutically or pharmacologically acceptable" refers to molecular entities and compositions that do not produce adverse, allergic, or other untoward reactions when administered to an animal or a human. As used herein, "pharmaceutically acceptable carrier" includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like. The use of such media and agents for pharmaceutically active substances is well known in the art. Supplementary active ingredients also may be incorporated into the compositions. [085] The compositions of the present invention include classic pharmaceutical preparations. Administration of these compositions according to the present invention may be via any common route. The pharmaceutical compositions may be introduced into the subject by any conventional method, for example, by intravenous, intradermal, intramuscular, subcutaneous, intramammary, intraperitoneal, intrathecal, retrobulbar, intrapulmonary, oral, sublingual, nasal, anal, vaginal, or transdermal delivery, or by surgical implantation at a particular site. The treatment may consist of a single dose or a plurality of doses over a period of time. [086] The active compounds may be prepared for administration as solutions of free base or pharmacologically acceptable salts in water, suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions also may be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof, and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms. [087] The pharmaceutical forms, suitable for injectable use, include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. The form should be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and should be 31 WO 2009/137254 PCT/US2009/040813 preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier may be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like) sucrose, L-histidine, polysorbate 80, or suitable mixtures thereof, and vegetable oils. The proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion, and by the use of surfactants. The prevention of the action of microorganisms may be brought about by various antibacterial an antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. The injectable compositions may include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions may be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin. [088] Sterile injectable solutions may be prepared by incorporating the active compounds (e.g., FIX polypeptides) in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. [089] Generally, dispersions may be prepared by incorporating the various sterilized active ingredients into a sterile vehicle that contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, methods of preparation include, for example, vacuum-drying and freeze-drying techniques that yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. [090] Upon formulation, solutions may be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective. "Therapeutically effective amount" is used herein to refer to the amount of a polypeptide that is needed to provide a desired level of the polypeptide in the bloodstream or in the target tissue. The precise amount will depend upon numerous factors, for example, the particular FIX polypeptide, the components and physical characteristics of the therapeutic composition, intended patient population, mode of delivery, individual patient considerations, and the like, and can readily be determined by one skilled in the art, based upon the information provided herein. [091] The formulations may be easily administered in a variety of dosage forms, such as injectable solutions, and the like. For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered, if necessary, and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. [092] Dosages of FIX are normally expressed in units. One unit of FIX per kg of body weight may raise plasma levels by 0.01 U/ml, that is, 1%. Otherwise healthy patients have one unit of 32 WO 2009/137254 PCT/US2009/040813 FIX per ml of plasma, that is, 100%. Mild cases of hemophilia B are defined by FIX plasma concentrations between 6

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6 0 %, moderate cases between 1-5%, and severe cases, which account for about half of the hemophilia B cases, have less than 1% FIX. Prophylactic treatment or treatment of minor hemorrhaging usually requires raising FIX levels to between 15-300%. Treatment of moderate hemorrhaging usually requires raising levels to between 30-50%, while treatment of major trauma may require raising levels from 50 to 100%. The total number of units needed to raise a patient's blood level can be determined as follows: 1.0 unit/kg x body weight (kg) x desired percentage increase (% of normal). Parenteral administration may be carried out with an initial bolus followed by continuous infusion to maintain therapeutic circulating levels of drug product. In some embodiments, between 15 to 150 units/kg of FIX polypeptide may be administered. Those of ordinary skill in the art will readily optimize effective dosages and administration regimens as determined by good medical practice and the clinical condition of the individual patient. [093] The frequency of dosing will depend on the pharmacokinetic parameters of the agents and the routes of administration. The optimal pharmaceutical formulation may be determined by one of skill in the art depending on the route of administration and the desired dosage (see, e.g., Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 2 0 th edition, 2000, incorporated herein by reference). Such formulations may influence the physical state, stability, rate of in vivo release, and rate of in vivo clearance of the administered agents. Depending on the route of administration, a suitable dose may be calculated according to body weight, body surface area, or organ size. Further refinement of the calculations necessary to determine the appropriate treatment dose is routinely made by those of ordinary skill in the art without undue experimentation, especially in light of the dosage information and assays disclosed herein, as well as the pharmacokinetic data observed in animals or human clinical trials. Exemplary dosing schedules include, without limitation, administration five times a day, four times a day, three times a day, twice daily, once daily, three times weekly, twice weekly, once weekly, twice monthly, once monthly, and any combination thereof. [094] Appropriate dosages may be ascertained through the use of established assays for determining blood clotting levels in conjunction with relevant dose response data. The final dosage regimen may be determined by the attending physician, considering factors that modify the action of drugs, for example, the drug's specific activity, severity of the damage, and the responsiveness of the patient, the age, condition, body weight, sex and diet of the patient, the severity of any infection, time of administration, and other clinical factors. [095] The composition may also include an antimicrobial agent for preventing or deterring microbial growth. Non-limiting examples of antimicrobial agents suitable for the present 33 WO 2009/137254 PCT/US2009/040813 invention include benzalkonium chloride, benzethonium chloride, benzyl alcohol, cetylpyridinium chloride, chlorobutanol, phenol, phenylethyl alcohol, phenylmercuric nitrate, thimersol, and combinations thereof. [096] An antioxidant may be present in the composition as well. Antioxidants may be used to prevent oxidation, thereby preventing the deterioration of the preparation. Suitable antioxidants for use in the present invention include, for example, ascorbyl palmitate, butylated hydroxyanisole, butylated hydroxytoluene, hypophosphorous acid, monothioglycerol, propyl gallate, sodium bisulfite, sodium formaldehyde sulfoxylate, sodium metabisulfite, and combinations thereof. [097] A surfactant may be present as an excipient. Exemplary surfactants include: polysorbates such as Tween@-20 (polyoxyethylenesorbitan monolaurate) and Tween@-80 (polyoxyethylenesorbitan monooleate) and pluronics such as F68 and F88 (both of which are available from BASF, Mount Olive, N.J.); sorbitan esters; lipids such as phospholipids such as lecithin and other phosphatidylcholines, phosphatidylethanolamines, fatty acids and fatty esters; steroids such as cholesterol; and chelating agents such as EDTA, zinc and other such suitable cations. [098] Acids or bases may be present as an excipient in the composition. Non-limiting examples of acids that may be used include hydrochloric acid, acetic acid, phosphoric acid, citric acid, malic acid, lactic acid, formic acid, trichloroacetic acid, nitric acid, perchloric acid, phosphoric acid, sulfuric acid, fumaric acid, and combinations thereof. Examples of suitable bases include, without limitation, sodium hydroxide, sodium acetate, ammonium hydroxide, potassium hydroxide, ammonium acetate, potassium acetate, sodium phosphate, potassium phosphate, sodium citrate, sodium formate, sodium sulfate, potassium sulfate, potassium fumerate, and combinations thereof. [099] The amount of any individual excipient in the composition may vary depending on the activity of the excipient and particular needs of the composition. Typically, the optimal amount of any individual excipient may be determined through routine experimentation, that is, by preparing compositions containing varying amounts of the excipient (ranging from low to high), examining the stability and other parameters, and then determining the range at which optimal performance is attained with no significant adverse effects. Generally, the excipient may be present in the composition in an amount of about 1% to about 99% by weight, from about 5% to about 98% by weight, from about 15 to about 95% by weight of the excipient, with concentrations less than 30% by weight. These foregoing pharmaceutical excipients along with other excipients are described in "Remington: The Science & Practice of Pharmacy," 19 ed., Williams & Williams, (1995); the "Physician's Desk Reference," 52 ed., Medical Economics, Montvale, N.J. (1998); and Kibbe, A. H., Handbook of Pharmaceutical Excipients, 3 Edition, American Pharmaceutical Association, Washington, D.C., 2000. 34 WO 2009/137254 PCT/US2009/040813 Exemplary Uses [100] The compositions described herein may be used to treat any bleeding disorder associated with functional defects of FIX or deficiencies of FIX such as a shortened in vivo half-life of FIX, altered binding properties of FIX, genetic defects of FIX, and a reduced plasma concentration of FIX. Genetic defects of FIX comprise, for example, deletions, additions, and/or substitution of bases in the nucleotide sequence encoding FIX. In one embodiment, the bleeding disorder may be hemophilia B. Symptoms of such bleeding disorders include, for example, severe epistaxis, oral mucosal bleeding, hemarthrosis, hematoma, persistent hematuria, gastrointestinal bleeding, retroperitoneal bleeding, tongue/retropharyngeal bleeding, intracranial bleeding, and trauma associated bleeding. [101] The compositions of the present invention may be used for prophylactic applications. In some embodiments, modified FIX polypeptides may be administered to a subject susceptible to or otherwise at risk of a disease state or injury to enhance the subject's own coagulative capability. Such an amount may be defined to be a "prophylactically effective dose." Administration of the modified FIX polypeptides for prophylaxis includes situations where a patient suffering from hemophilia B is about to undergo surgery and the polypeptide is administered between one to four hours prior to surgery. In addition, the polypeptides are suited for use as a prophylactic against uncontrolled bleeding, optionally in patients not suffering from hemophilia. Thus, for example, the polypeptide may be administered to a patient at risk for uncontrolled bleeding prior to surgery. [102] The polypeptides, materials, compositions, and methods described herein are intended to be representative examples of the invention, and it will be understood that the scope of the invention is not limited by the scope of the examples. Those skilled in the art will recognize that the invention may be practiced with variations on the disclosed polypeptides, materials, compositions and methods, and such variations are regarded as within the ambit of the invention. [103] The following examples are presented to illustrate the invention described herein, but should not be construed as limiting the scope of the invention in any way. 35 WO 2009/137254 PCT/US2009/040813 EXAMPLES [104] In order that this invention may be better understood, the following examples are set forth. These examples are for the purpose of illustration only, and are not to be construed as limiting the scope of the invention in any manner. All publications mentioned herein are incorporated by reference in their entirety. Example 1: In Silico Analysis [105] An in silico analysis of the FIX sequence for solvent accessibility, known secondary structure, location of known hemophilia B mutations, proximity to predicted sites of interaction with both FVIII and FX, and predicted effect of a given mutation upon FIX protein stability was performed in order to identify potential sites for the addition of new N-glycosylation site consensus sequences. [106] Based upon this analysis, five sites were identified within the catalytic domain for creation of new N-linked glycosylation sites. The selected sites and the altered amino acid sequences that were designed are shown in Table 2. TABLE 2 Mutein name Native Sequence Mutated sequence G226N, K228T Gly226-Val227-Lys228 Asn226-Val227-Thr228 F353N, H354V, E355T Phe353-His354-Glu355 Asn353-Val354-Thr355 F353N, H3541, E355T Asn353-Ile354-Thr355 V370N, T371V, E372T Val370-Thr371-Glu372 Asn370-Val371-Thr372 V370N, T3711, E372T Asn370-Ile371-Thr372 M391N, G393T Met391-Lys392-Gly393 Asn391- Lys392- Thr393 M391N, K392V, G393T Asn391- Val392- Thr393 K413N Lys413-Leu414-Thr415 Asn413-Leu414-Thr415 K413N, L4141 Asn413-Ile414-Thr415 Example 2: Sequence Alignment of Activation Peptide [107] Conserved and non-conserved residues in the activation peptide were identified by a multiple species sequence alignment as shown in Figure 1. [108] The consensus sequence of N-linked glycosylation sites is Asn-X-Ser/Thr (where X is any amino acid except proline or perhaps aspartic acid which is also not favorable). To design new N linked glycosylation sites in the activation peptide of FIX, the amino acids within the activation peptide that are conserved between species was avoided as well as and consensus sequences for 36 WO 2009/137254 PCT/US2009/040813 other N-linked sites and the consensus sequence for tyrosine sulfation so as not to disrupt these posttranslational modifications since these could be important for the pharmacokinetics of FIX. Using these criteria, three sites for adding new N-linked glycosylation sites within the activation peptide were identified as shown in Table 3. TABLE 3 Designation Mutein Native sequence Glycosylation site created HG1 A161N A161-E162-T163 N161-E162-T163 HG2 D177E plus F178T D177-F178-T179 N176-E177-T178 HG3 P151N plus V153T P151-D152-V153 N151-D152-T153 Example 3: Insertion ofAmino Acids to Generate N-linked Glycosylation Sites [109] The multiple sequence alignment (Figure 1) also revealed that mouse, rat, and guinea pig have additional amino acids between residues A 161 and E162 relative to human, rhesus monkey, pig, dog, and rabbit FIX. These additional amino acids vary in size from 7 to 10 between the three species and contain an over representation of Asp and to some extent Ile residues. This observation demonstrates that between 7 and 10 additional residues are tolerated at this site in rat, mouse, and guinea pig without significant effects on FIX activity. Depending upon the criteria used to perform the multiple sequence alignment between FIX from the eight species, the apparent site at which the additional amino acids in rat, mouse, and guinea pig are found can vary such that the site can be either between E160 and A161, between A161 and E162, between E162 and T163, or between T163 and 1164 of human FIX. [110] Nine extra amino acids with the sequence N-S-T-Q-D-N-I-T-Q (SEQ ID NO: 2) were inserted in the activation peptide between A161 and E162. The sequences " N-S-T" and "N-I-T" are the N-linked consensus sequences from the natural FIX activation peptide. In both cases, these are followed by a glutamine (Q) and preceded by an aspartic acid (D) in the natural FIX sequence. Therefore, a glutamine as well as an aspartic acid were included in an attempt to emulate the natural site. It is envisioned that additional sequences containing between 1 and 3 consensus sequences for N-glycosylation site (N-X-S/T) may also be inserted between A161 and E162. [111] Additional examples of modified FIX polypeptides are described in Tables 4a, 4b, and 4c. 37 WO 2009/137254 PCT/US2009/040813 TABLE 4a Construct Substitution Description Specific Activity (% of Control) HG10 D85N Creates 1 new N-linked site in EGF1 99 HG1 1 K122T Creates 1 new N-linked site in EGF2 137 HG12 S138N Creates 1 new N-linked site in EGF2- 75 AP linker region HG13 K228N Creates 1 new N-linked site in 67 catalytic domain HG14 E242N Creates 1 new N-linked site in 183 catalytic domain HG15 K201T Creates 1 new N-linked site in 21 catalytic domain HG16 E41ON Creates 1 new N-linked consensus in 1040 catalytic domain HG17 K413N Creates 1 new N-linked consensus in 388 catalytic domain HG1 8 E83T Creates 1 new N-linked consensus in NT EGF 1 domain HG19 K214T Creates 1 new N-linked consensus in NT catalytic domain HG20 V223N Creates 1 new N-linked consensus in NT catalytic domain HG21 Y266T Creates 1 new N-linked consensus in NT catalytic domain HG22 F353N-H354V- Creates 1 new N-linked consensus in NT E355T catalytic domain HG23 V370N-T371V- Creates 1 new N-linked consensus in NT E372T catalytic domain HG24 M391N-K392V- Creates 1 new N-linked consensus in NT G393T catalytic domain HG25 415 - T-N-S-T-T Adds 1 new N-linked consensus 57 (SEQ ID NO: 4) sequence to C terminus HG26 415 - T-N-S-T- Adds 2 new N-linked consensus 42 Q-N-I-T-T sequences to C terminus (SEQ ID NO: 5) HG27 415 - T-N-S-T- Adds 3 new N-linked consensus NT Q-N-I-T-G-N-D- sequences to C terminus T-E-K-T (SEQ ID NO: 6) HG28 415 - T-N-S-T- Adds 4 new N-linked consensus 45 Q-N-I-T-G-N-D- sequences to C terminus T-E-N-G-T-K-T (SEQ ID NO: 7) Specific activity was calculated by dividing the activity measured in the cell culture supernatant by the FIX antigen concentration in the same supernatant and is expressed as a percentage of the control FIX molecule lacking the new glycosylation sites. NT: not tested. 38 WO 2009/137254 PCT/US2009/040813 TABLE 4b Construct Residue Substitution Specific Activity Specific Activity (% of WT) (% of Control) HG3/9 P151N, V153T, G226N, 270 40 K228T HG5/9 T172N, G226N, K228T 300 47 HG8/9 Insertion of SEQ ID NO: 350 55 2 between A161 and E162, G226N, K228T HG3/9/12 S138N, P151N, V153T, 200 26 G226N, K228T HG3/5/9 P151N, V153T, T172N, 190 38 G226N, K228T HG3/9/10 D85N, P151N, V153T, 200 26 G226N, K228T HG3/10/13 D85N, P151N, V153T, 200 20 K228N HG3/11/13 K122T, P151N, V153T, 400 40 K228N HG3/10/14 D85N, P151N, V153T, 210 21 E242N HG3/11/14 K122T, P151N, V153T, 800 80 E242N HG10/11/14 D85N, K122T, E242N 650 65 HG3/11/1251T K122T, P151N, V153T, 540 47 1251T HG1O/11/1251T D85N, K122T, 1251T 570 50 HG3/10/11/14 D85N, K122T, P151N, 400 40 V153T, E242N 39 WO 2009/137254 PCT/US2009/040813 TABLE 4c Expression Activity Construct Substitution (relative to control)* (relative to control)* Cl YIN, S3T 4 1 C2 G4T 5 1 C3 S3N, K5T 4 1 C4 G4N, L6T 4 1 C5 K5N, E7T 4 1 C6 L6N, E8T 4 1 C7 E7N, F9T 4 1 C8 E8N, V1OT 2 1 C9 F9N, Q11T 3 1 C1O V1ON, G12T 3 1 C1l Q11N, N13T 3 1 C12 G12N, L14T 4 1 C13 N13, E15T 4 2 C14 L14N, R16T 4 1 C15 E15N, E17T 5 1 C16 M19N, E21T 5 1 C17 E20N, K22T 4 1 C18 S24N,E26T 4 1 C19 F25N,E27T 4 1 C20 E26N, A28T 4 1 C21 E27N,R29T 3 1 C22 A28N,E30T 3 1 C23 R29N, V31T 3 1 C24 E30N,F32T 5 1 C25 V31N,E33T 4 1 C26 F32N, N34T 4 1 C27 E33N 4 1 C28 E36T 4 1 C29 T35N,R37T 4 1 C30 E36N 4 1 C31 R37N 4 2 C32 T38N,E40T 4 1 40 WO 2009/137254 PCT/US2009/040813 C33 T39N, F41T 4 1 C34 E40N, W42T 4 1 C35 F41N, K43T 3 1 C36 W42N, Q44T 4 1 C37 K43N, Y45T 3 1 C38 Q44N, V46T 4 2 C39 Y45N, D47T 3 1 C40 V46N, G48T 2 1 C41 D47N, D49T 1 1 C42 G48N, Q50T 2 1 C43 E52N, N54T 1 2 C44 S53N, P55T 1 2 C45 L57N, G59T 1 1 C46 G60T 1 1 C47 G59N,S61T 4 4 C48 K63N, D65T 3 2 C49 D64N, 166T 2 1 C50 D65N, N67T 3 1 C51 166N, S68T 2 1 C52 Y69T 1 1 C53 S68N, E70T 4 1 C54 P74N, G76T 1 1 C55 F75N, F77T 1 2 C56 G76N,E78T 2 4 C57 F77N, G79T 1 1 C58 E78N, K80T 2 1 C59 G79N, N81T 1 1 C60 E83N, D85T 2 2 C61 L84N, V86T 2 1 C62 D85N 3 4 C63 K91T 2 2 C64 190N, N92T 1 1 C65 K91N, G93T 1 1 C66 R94T 1 1 C67 K100N,S102T 2 3 41 WO 2009/137254 PCT/US2009/040813 C68 A103T 2 2 C69 S102N, D104T 3 4 C70 A103N, N105T 2 4 C71 D104N, K106T 3 4 C72 V107T 2 3 C73 K106N, V108T 3 3 C74 R116N, A118T 1 3 C75 L117N, E119T 1 1 C76 A118N, N120T 1 2 C77 E119N, Q121T 2 3 C78 K122T 1 4 C79 Q121N, S123T 3 4 E125N, P126A, C80 A127T 2 4 P126N, V128T, C81 P129A 2 4 C82 A127N,P129T 2 4 V128N, P129A, C83 F130T,P131A 1 1 C84 P129N, P131T 1 1 C85 R134N,S136T 1 1 C86 V135N, V137T 1 1 C87 S136N, S138T 2 4 C88 V137N, Q139T 2 4 C89 S138N 4 3 C90 Q139N,S141T 3 3 C91 T140N, K142T 2 3 C92 S141N, L143T 3 2 C93 A146N 4 3 C94 E147N, V149T 4 1 T148N, F150T, C95 P151A 4 2 C96 V149N,P151T 3 3 F150N, P151A, C97 D152T 3 3 42 WO 2009/137254 PCT/US2009/040813 C98 P151N, V153T 4 4 C99 D152N, D154T 3 4 ClOG V153N, Y155T 4 4 ClOl D154N, V156T 3 4 C102 Y1 55N, NI57T 3 4 C103 V156N,S158T 3 4 C104 N157 3 4 C105 S158N, E160T 3 4 C106 T159N, A161T 3 4 C107 E16ON,E162T 3 3 C108 A161N 5 4 C109 E162N,1164T 6 4 Clio T163N, L165T 5 4 Cili 1164N, D166T 5 4 C112 L165N, N167T 5 4 C113 D166N, 1168T 5 4 C114 N167 5 4 C115 1168N, Q170T 6 4 C116 T169N,S171T 5 3 C117 Q17ON 5 3 C118 S171N, Q173T 5 3 C119 T172N,S174T 5 3 C120 Q173N,F175T 5 3 C 121 S174N, N176T 4 3 C 122 F175N, D177T 4 1 C123 F178T 5 1 C 124 D177N 5 3 C125 G184N, D186T 4 1 C126 E185N, A187T 1 2 C127 D186N, K188T 2 2 C128 A187N, P189T 1 1 K188N, P189A, C129 G190T 1 1 C130 P189N, Q191T 1 1 C131 L198N, G200T 1 1 43 WO 2009/137254 PCT/US2009/040813 C132 K201T 2 2 C133 G200N, V202T 2 1 C134 K2O1N, D203T 3 3 C135 V202N, A204T 3 2 C136 1210ON, N212T 1 1 C137 V211IN, E213T 1 1 C138 K214T 1 1 C139 E213N, W215T 1 1 C140 V223N 1 1 C 141 E224N, G226T 4 2 C142 T225N, V227T 3 3 C143 G226N, K228T 2 2 C 144 V227N, 1229T 1 3 C145 K228N 3 3 C146 H236N, 1238T 1 1 C147 E239T 2 3 C148 1238N, E240T 1 1 C149 E239N 3 3 C150 E240N, E242T 1 1 C151 T241N, H243T 2 3 C152 E242N 1 2 C153 H243N,E245T 2 2 C154 T244N, Q246T 1 1 C155 E245N, K247T 1 1 C156 Q246N,R248T 1 1 C157 K247N, N249T 2 2 C158 R248N, V250T 1 1 C159 1251T 3 4 C160 V250N, R252T 1 1 C161 1251N,1253T 1 3 R252N, 1254T, C162 P255A 1 2 C163 1253N, P255T 2 3 1254N, P255A, C164 H256T 1 1 44 WO 2009/137254 PCT/US2009/040813 C165 P255N, H257T 1 2 C166 H256N, N258T 1 1 C167 H257N, Y259T 1 1 C168 N260T 1 1 C169 Y259N, A261IT 1 1 C170 A262T 4 3 C171 A261N, 1263T 2 3 C172 A262N, N264T 3 3 C173 1263N, K265T 1 1 C174 Y266T 1 1 C175 K265N, N267T 1 1 C176 Y266N, H268T 1 1 C177 E274N, D276T 1 1 L275N, E277T, C178 P278A 1 1 C179 D276N,P278T 1 2 E277N, P278A, C180 L279T 1 1 C181 P278N, V280T 1 3 C182 L279N, L281IT 1 1 C183 V280N, N282T 2 3 C184 L281N,S283T 1 1 C185 Y284T 1 1 C186 S283N, V285T 1 3 C187 E294N 2 2 C188 Y295N, N297T 1 1 C189 T296N,1298T 1 1 C190 F299T 1 1 C191 1298N, L300T 1 1 C192 F299N, K301T 1 1 C193 L300N,F302T 1 1 C194 K3O1N, G303T 1 1 C195 F302N, S304T 5 1 C196 G303N, G305T 1 1 C197 S304N, Y306T 5 1 45 WO 2009/137254 PCT/US2009/040813 C198 R312N,F314T 5 1 C199 V313N, H315T 5 1 C200 F314N, K316T 4 1 C201 H315N, G317T 5 1 C202 K316N, R318T 4 1 C203 G317N,S319T 4 1 C204 R318N, A320T 3 1 C205 S319N, L321T 5 1 C206 A320N, V322T 4 1 L326N, V328T, C207 P329A 1 1 C208 R327N, P329T 4 1 V328N, P329A, C209 L330T 1 1 C210 P329N, V331T 3 1 C211 L330N, D332T 1 1 C212 V331N,R333T 1 1 C213 D332N, A334T 3 1 C214 R333N 1 1 C215 L337N,S339T 2 1 C216 R338N 4 1 C217 S339N, K341T 4 1 C218 T340N,F342T 2 1 C219 K341N 5 1 C220 F342N,1344T 1 1 C221 T343N, Y345T 5 1 C222 1344N, N346T 1 1 C223 Y345N, N347T 2 1 C224 A351N,F353T 1 1 C225 G352N, H354T 1 1 C226 F353N, E355T 2 1 C227 H354N, G356T 4 1 C228 E355N, G357T 4 1 C229 G356N,R358T 4 1 C230 G357N, D359T 5 1 46 WO 2009/137254 PCT/US2009/040813 C231 T371N, V373T 1 1 C232 E372N, E374T 2 3 C233 V373N, G375T 1 1 C234 E374N 5 2 C235 W385N, E387T 3 1 C236 G386N,E388T 3 1 C237 A390N, K392T 3 1 C238 M391N, G393T 3 1 C239 K392N, K394T 4 1 C240 G393N, Y395T 1 1 C241 R403N, V405T 2 1 C242 Y404N, N406T 1 1 C243 V405N, W407T 1 1 C244 1408T 1 1 C245 W407N, K409T 1 1 C246 1408N, E410T 1 1 C247 K409N, K411T 1 1 C248 E41ON 2 4 C249 K411N, K413T 1 1 C250 T412N, L414T 1 1 C251 K413N, T415 2 1 Expression and activity relative to the wild type control are expressed on a scale of I to 5 where 1 = <10%; 2 = 10-50%; 3 = 50-100%; 4 = 100-200%; 5 = >200%. Example 4: Substitutions to Convert 0-linked to N-linked Glycosylation Sites [112] Table 5 shows the substitutions that were designed to convert O-linked glycosylation sites to N-linked glycosylation sites. TABLE 5 Designation Mutein Native Sequence N-linked Glycosylation site (0-linked site underlined) created HG4 T169N T169-Q170-S171 N169-Q170-S171 HG5 T172N T172-Q173-S174 N172-Q173-S174 HG6 T148N plus T148-V149-F150 N148-V149-T150 F150T HG7 T159N plusA161T T159-E160-A161 N159-E160-T161 47 WO 2009/137254 PCT/US2009/040813 Example 5: Expression of FIX Variants in HKB11 Cells [113] In order to determine if the FIX genes with altered protein sequences could be expressed and secreted from mammalian cells and to determine the effect of these substitutions upon FIX coagulation activity, expression plasmids encoding these FIX variants were transfected into HKB1 1 cells. HKB1 1 is a human cell line generated by the fusion of HEK293 cells and a B cell lymphoma. In this example, each of the glycosylation site substitutions were combined with a second substitution, R338A, as shown for HG1 through HG8 in Figure 3. The R338A substitution increases the specific activity of FIX by 3- to 4-fold as measured by the aPTT assay. Additional combinations of two glycosylation site muteins and R338A were also created and tested (Figure 3). [114] Three days after transfection, the media from the cells was collected and analyzed for FIX expression by Western blot using an antibody specific to FIX. The results demonstrated that the FIX muteins tested were expressed and secreted into the media at levels similar to that of wild type FIX or FIX with only the R338A substitution (Figure 2). [115] The activity of the FIX muteins was also tested using the aPPT assay. The results demonstrated that the Factor IX muteins have activity similar to or increased compared to that of wild type FIX (Figures 3 and 4). Compared to R338A, the activity of the muteins varied between 14% and 109%. In particular, muteins HG1, HG3, HG4, HG5, HG6, HG7, HG8, and HG3 plus HG8 had coagulation activity that was at least 55% of that of R338A, and at least 300% of wild type FIX. Example 6: Glycosylation of Factor IX variants in HKBJ1 cells [116] An initial analysis of muteins HG1 through HG8 (Figure 3) and HG9 (Figure 5) demonstrated that HG2, HG3, HG5, HG6, HG8, and HG9 had increased glycosylation as evidenced by an increase in apparent molecular weight on SDS-PAGE gels. Additional FIX polypeptides were created containing various combinations of the substitutions present in HG2, HG3, HG5, HG6, and HG8. For example, the following combinations were created: HG2/HG3, HG8/HG2, HG8/HG3, HG8/HG2/HG3. Other possible combinations include, for example, HG3/HG5, HG5/HG8, HG3/HG5/HG8. HG3/HG6, HG5/HG6, HG8/HG6, HG3/HG5/HG6, HG3/HG6/HG8, HG5/HG6/HG8, and HG3/HG5/HG6/HG8. Combinations with HG9 may also be generated. [117] Glycosylation increases the molecular weight of a protein and this can be visualized as reduced mobility in SDS-PAGE gels. As demonstrated in Figures 2 and 3, the substitutions made in HG2, HG3, HG5, HG6, HG8, and HG9 resulted in reduced mobility on a SDS-PAGE gel. Among these eight single muteins, HG8 which has two additional N-linked consensus sequences 48 WO 2009/137254 PCT/US2009/040813 inserted between A161 and E162, exhibited the greatest increase in apparent molecular weight suggesting that both N-linked sites were functional. Of the four muteins in which an O-linked site was mutated to an N-linked site (HG4 to HG7), HG4 exhibited increased mobility on the gel demonstrating that this substitution destroyed the O-linked site (thus reducing the molecular weight of the FIX protein), but failed to create a functional N-linked site. In contrast, HG5 and HG6 exhibited reduced mobility on the gel demonstrating that the substitutions in these clones did create functional N-linked glycosylation sites. Mutein HG7 which also has an O-linked site mutated to an N-linked site exhibited no change in mobility on the gel compared to wild-type FIX or FIX-R338A. Given the fact that the substitution in HG7 would be expected to eliminate an 0 linked site and thus increase the mobility on the gel, the finding that there was no change in mobility suggests that the introduced N-linked site may be functional. [118] The combinations of substitutions present in HG2/HG3, HG8/HG2, HG8/HG3, and HG8/HG2/HG3 resulted in more significant reductions in mobility compared to the individual muteins, indicating that the various new glycosylation sites present in these combinations were functional when combined in a single FIX molecule. The HG8/HG2/HG3 mutein that contains a total of 4 new N-linked sites exhibited the largest decrease in mobility. Example 7: Combination of R338A and V86A Substitutions [119] Amino acid V86 of FIX was changed to alanine by site directed mutagenesis either in the context of wild type FIX (WT-FIX) or FIX-R338A. Expression vectors containing these constructs were transfected into HKB 11 cells and media was collected 3 days later and assayed for FIX protein level by ELISA and for FIX coagulation activity by aPTT assay. Both muteins were expressed at similar levels to WT-FIX and FIX-R338A. The data from a single experiment is summarized in Table 6a. Table 6b summarizes the average of three experiments. TABLE 6a Sample FIX Activity ELISA Specific Activity (mU/mL) (pg/mL) (IU/mg) pAGE16-V86A 255 0.97 263 pAGE16-R338A 383 0.73 527 pAGE-R338A-V86A 1237 1.03 1198 pAGE16-FIX 88 0.89 99 49 WO 2009/137254 PCT/US2009/040813 TABLE 6b Factor IX construct FIX activity FIX expression FIX specific activity (% of WT-FIX) (% of WT-FIX) (% of WT-FIX) WT-Factor IX 100 100 100 V86A 210 120 180 R338A 390 90 450 R338A-V86A 950 105 810 [120] The results demonstrate that the V86A substitution alone results in about a 1.8-fold increase in specific activity, while R338A alone resulted in a 4.5-fold increase in specific activity. The combination of R338A and V86A resulted in a 8.1-fold increase in specific activity as compared to wild type FIX. These results show that the positive effects of the R338A and V86A substitutions are additive and result in a Factor IX mutein with an 8-fold increased specific activity compared to WT-FIX. The R338A-V86A mutein would have improved therapeutic benefit for hemophilia B patients as it would allow a 8-fold lower dose of protein to achieve the same therapeutic effect as the currently available recombinant WT-IX. In addition, the increased specific activity of R338A-V86A is beneficial when creating glycosylated forms of FIX in which a reduction in activity may result from glycosylation. Example 8: Cloning of Human FIX cDNA [121] A pair of PCR primers complementary to sequences at the 5' and 3' ends of the coding region of the human FIX cDNA were designed from the published cDNA sequence (NM_000133). The 5' primer (FIXF1; ATCATAAGCTTGCCACCATGCAGCGCGTGAACATG (SEQ ID NO: 8), start codon of FIX is in bold text) contained the first 18 nucleotides of the FIX coding region including the ATG start codon preceded by a consensus Kozak sequence (underlined) and a HindIlI restriction site. The 3' primer (FIXR3, ATCATAAGCTTGATTAGTTAGTGAGA GGCCCTG) (SEQ ID NO: 9) contained 22 nucleotides of FIX sequence that lies 45 nucleotides 3' of the end of the FIX coding region preceded by a HindIll site. Amplification of first strand cDNA from normal human liver (Stratagene, San Diego CA) using these primers and high fidelity proofreading polymerase (Invitrogen, Carlsbad, CA) resulted in a single band of the expected size for human FIX cDNA (1464 bp). After digestion with HindIII, the PCR product was gel purified and then cloned into the HindIll site of the plasmid pAGE16. Clones in which the FIX cDNA was inserted in the forward orientation relative to the CMV promoter in the vector were identified by restriction digest. Double stranded DNA sequencing was performed for the insert of several clones and alignment of the derived sequence to the published FIX sequence demonstrated that the cDNA encodes human FIX with threonine at amino acid 148 of the mature protein. This plasmid was designated as pAGE 16-Factor IX (pAGE 16-FIX). 50 WO 2009/137254 PCT/US2009/040813 Example 9: Generation of Modified FIX Polypeptides [122] To change various amino acids within the human FIX sequence, a pair of primers were designed using the QuickchangeTM primer design program available from Stratagene. These primers were used to generate mutations in the pAGE 1 6-FIX plasmid employing the QuickchangeTM II XL site directed mutagenesis kit (Stratagene, San Diego, CA) according to the manufacturer's instructions. Clones containing the desired substitution were identified by DNA sequencing of the entire FIX coding region. Table 7 below shows the sequence of the sense strand oligonucleotide used to create the substitutions. TABLE 7 Substitution Sense Strand Oligonucleotide Sequence G226N/K228T CTGCTGCCCACTGTGTTGAAACTAACGTTACCATTACA GTTGTCGCAGGTGAAC (SEQ ID NO: 10) F353N/H354V/E355T CACCATCTATAACAACATGTTCTGTGCTGGCAACGTGA CCGGAGGTAGAGATTCATGTCAAGGAGATAGTG (SEQ ID NO: 11) V370N/T371V/E372T GATTCATGTCAAGGAGATAGTGGGGGACCCCATAACG TGACCGTGGAAGGGACCAGTTTCTTAACTGGAATTA (SEQ ID NO: 12) M391N/K392V/G393T GGAATTATTAGCTGGGGTGAAGAGTGTGCAAACGTGA CCAAATATGGAATATATACCAAGGTATCCCGG (SEQ ID NO: 13) K413N TCAACTGGATTAAGGAAAAAACAAACCTCACTTAATG AAAGATGGATTTC (SEQ ID NO: 14) A161N CTGATGTGGACTATGTAAATTCTACTGAAAATGAAACC ATTTTGGATAACATCAC (SEQ ID NO: 15) D177E/F178T ACTCAAAGCACCCAATCATTTAATGAGACCACTCGGGT TGTTGGTGG (SEQ ID NO: 16) P151N/V153T ACTTCTAAGCTCACCCGTGCTGAGACTGTTTTTAATGA TACGGACTATGTAAATTCTACTG (SEQ ID NO: 17) T169N GAAGCTGAAACCATTTTGGATAACATCAATCAAAGCA CCCAATC (SEQ ID NO: 18) T172N ATTTTGGATAACATCACTCAAAGCAACCAATCATTTAA TGACTTCAC (SEQ ID NO: 19) T148N/F150T ACTTCTAAGCTCACCCGTGCTGAGAATGTTACTCCTGA 51 WO 2009/137254 PCT/US2009/040813 TGTGGAC (SEQ ID NO: 20) T159N/A161T GTTTTTCCTGATGTGGACTATGTAAATTCTAATGAAAC TGAAACCATTTTGGATAAC (SEQ ID NO: 21) The underlined residues are those that were changed relative to wild type FIX to create a consensus sequence for N-linked glycosylation. [123] In addition to the substitutions described above, a sequence of nine amino acids containing 2 consensus sequences for N-glycosylation was inserted into the activation peptide between residues A161 and E162. To generate this variant of FIX, unique restriction sites for SnaB1 and XbaI at Y155 and 1164 were created without altering the amino acid sequence by site directed mutagenesis with primers t8216cg8218a and t8188c (Table 8). The resulting plasmid was digested with SnaB1 and XbaI to remove the 27 bp fragment corresponding to residues VI 56 to 1164 and then ligated to a double stranded fragment created by annealing of oligonucleotides 2PrimerF and 2PrimerR (Table 8). The sequence of the resulting plasmid was determined by double strand DNA sequencing to have an insertion of 27 bp encoding nine amino acids with the sequence NSTQDNITQ (SEQ ID NO: 2) that contains two consensus sequences for N-linked glycosylation (NXT). TABLE 8 Primer name Primer sequence (5' to 3') T8216cg821 TTCTACTGAAGCTGAAACCATTCTAGATAACATCACTCAAAGCACCC 2a (SEQ ID NO: 22) T8188c CTGTTTTTCCTGATGTGGACTACGTAAATTCTACTGAAGCTGAAA (SEQ ID NO: 23) 2PrimerF GTAAATTCTACTGAAGCTAACTCCACACAGGATAATATCACACAAG AAACCATT (SEQ ID NO: 24) 2PrimerR CTAGAATGGTTTCTTGTGTGATATTATCCTGTGTGGAGTTAGCTTCA GTAGAATTTAC (SEQ ID NO: 25) The bold/underline residues are those that were changed relative to wild type Factor IX to create either a new restriction site or the insertion of nine additional amino acids encoding two consensus sequences for N-linker glycosylation. Example 10: Cell Culture and Transient Transfection [124] HKBi11 cells (a hybrid of HEK293 and a Burkitt B cell lymphoma line, 2B8) were grown in suspension culture on an orbital shaker (100-125 rpm) in a CO 2 (5%) incubator at 37'C in serum free media (RF#277) supplemented with 10 ng/mL soluble vitamin K 3 (Sigma-Aldrich, St. Louis, MO) and maintained at a density between 0.25 and 1.5 x 106 cells/mL. [125] Cells for transfection were collected by centrifugation at 1000 rpm for 5 minutes then resuspended in FreeStyleTM 293 Expression Medium (Invitrogen, Carlsbad, CA) at 1.1 x 106 52 WO 2009/137254 PCT/US2009/040813 cells/mL. The cells were seeded in 6 well plates (4.6 mL/well) and incubated on an orbital rotator (125 rpm) in a 37 0 C CO 2 incubator. For each well, 5 pg plasmid DNA was mixed with 0.2 mL Opti-MEM@ I medium (Invitrogen). For each well, 7 pL 293fectin T M reagent (Invitrogen) was mixed gently with 0.2 mL Opti-MEM@ I medium and incubated at room temperature for 5 minutes. The diluted 293fectinTM was added to the diluted DNA solution, mixed gently, incubated at room temperature for 20-30 minutes and then added to each well that had been seeded with 5 x 106 (4.6 mL) HKB11 cells. The cells were then incubated on an orbital rotator (125 rpm) in a CO 2 incubator at 37 0 C for 3 days after which the cells were pelleted by centrifugation at 1000 rpm for 5 minutes, and the supernatant was collected and stored at 4 0 C. [126] In some instances, HEK293 cells were transfected with expression constructs for FIX variants in 384 well plates using standard lipofection protocols and commercial reagents. The cells were cultivated for 72 hours post-transfection at which time the supernatant was harvested for further analyses. Example 11: Western Blot for FIX. [127] Cell culture supernatant (50 pL) was mixed with 20 pL 4x SDS-PAGE loading dye, heated at 95 0 C for 5 minutes, loaded on NuPAGE@ 4-12% SDS PAGE gels and then transferred to nitrocellulose membranes. After blocking with 5% milk powder for 30 minutes, the membranes were incubated with a HRP-labeled goat polyclonal antibody against human FIX (US Biological, Swaampscoit, Massachusetts, Catalog No. F0017-07B) for 60 minutes at room temperature. After washing with phosphate-buffered saline with 0.l1% Tween@-20 buffer, the signal from HRP was detected using SuperSignal® Pico (Pierce, Rockford, IL) and exposure to x-ray film. Example 12: FIX ELISA [128] FIX antigen levels in cell culture supernatants were determined using a FIX ELISA kit (Hyphen Biomed/Aniara, Mason, OH). Cell culture supernatant was diluted in sample diluent buffer (supplied in the kit) to achieve a signal within the range of the standard curve. FIX protein purified from human plasma (Hyphen Biomed/Aniara, Catalog No. RK032A, specific activity 196 U/mg) diluted in sample diluent was used as to create a standard curve from 100 ng/mL to 0.2 ng/mL. Diluted samples and the standards were added to the ELISA plate that is pre-coated with a polyclonal anti-FIX capture antibody. After adding the polyclonal detection antibody, the plate was incubated at room temperature for 1 hour, washed extensively, then developed using TMB substrate (3,3',5,5'-tetramethylbenzidine) as described by the kit manufacturer and the signal is measured at 450 nM using a SpectraMax® plate reader (Molecular Devices, Sunnyvale, CA). The standard curve was fitted to a 2-component plot and the values of the unknowns extrapolated from the curve. 53 WO 2009/137254 PCT/US2009/040813 [129] FIX expression levels were also quantitated using commercially available FIX ELISA reagents (Haemochrom Diagnostica GmbH, Essen, Germany) according to the manufacturer's instructions. Wheat germ agglutinin (Sigma-Aldrich, St. Louis, MO) was coated on 384 well MaxiSorpTM plates (Nunc

TM

, Rochester, NY). The wells were blocked, washed, and then supernatant was added. After further washing, detection was carried out using HRP-coupled polyclonal anti-FIX antibody (Haemochrom Diagnostica GmbH, Essen, Germany). Example 13: FIX Coagulation Assay [130] FIX coagulation activity was determined using an aPTT assay in FIX deficient human plasma run on a ElectraTM 1800C automatic coagulation analyzer (Beckman Coulter, Fullerton, CA). Briefly, three dilutions of supernatant samples in coagulation diluent were created by the instrument, and 100 pL was then mixed with 100 pL FIX deficient plasma (Aniara, Mason, OH) and 100 pL automated aPTT reagent (rabbit brain phospholipid and micronized silica (bioM6rieux, Inc., Durham, NC). After the addition of 100 pL 25 mM CaCl 2 solution, the time to clot formation was recorded. A standard curve was generated for each run using serial dilutions of the same purified human FIX (Hyphen Biomed/Aniara) used as the standard in the ELISA assay. The standard curve was routinely a straight line with a correlation coefficient of 0.95 or better and was used to determine the FIX activity of the unknown samples. Example 14: Measurement of Circulating FIX [131] The circulating half-life of FIX polypeptides is measured using an in vitro assay. This assay is based on the ability of FIX in vivo and in vitro to mediate the accumulation of adenovirus (Ad) in hepatocytes. Briefly, it has been shown that FIX can bind the Ad fiber knob domain and provide a bridge for virus uptake through cell surface heparin sulfate proteoglycans (HSPG) (Shayakhmetov, et al., J. Virol 79:7478-7491, 2005). An Adenovirus vector mutant, Ad5mut, which contains mutations in the fiber knob domain, does not bind to FIX. Ad5mut has significantly reduced ability to infect liver cells and liver toxicity in vivo, demonstrating that FIX plays a major role in targeting Ad vectors to hepatic cells (Shayakhmetov, et al., 2005). The ability of FIX to target Ad vector to hepatic cells can be blocked by inhibitors of protein-HSPG interactions (Shayakhmetov, et al., 2005). [132] Furthermore, HSPG-mediated uptake of FIX contributes significantly to FIX clearance and consequently, interfering with the HSPG interaction is expected to increase the half-life of FIX. Therefore, in vitro uptake of FIX and/or FIX variants in hepatocytes is measured, and variants with reduced uptake are expected to have increased half-life in vivo. [133] To measure FIX half-life in vitro, mammalian cells are incubated with adenovirus in the presence or absence of FIX or FIX variants. Viral uptake is mediated by wild-type FIX and 54 WO 2009/137254 PCT/US2009/040813 measured by expression of the reporter gene encoded in viral genome, for example, green fluorescent protein (GFP) or luciferase expression. Reduced uptake of adenovirus in the presence of FIX variants are measured as reduced reporter gene expression, for example, reduced GFP fluorescence or reduced luciferase enzymatic activity as compared to wild-type FIX. [134] FIX circulating half-life is measured in vivo using standard techniques well-known to those of ordinary skill in the art. Briefly, the respective dose of FIX or FIX variant is administered to a subject by intravenous injection. Blood samples are taken at a number of time points after injection and the FIX concentration is determined by an appropriate assay (e.g.. ELISA). To determine the half-life, that is the time at which the concentration of FIX is half of the concentration of FIX immediately after dosing, the FIX concentration at the various time points is compared to the FIX concentration expected or measured immediately after administering the dose of FIX. A correlation between reduced cellular uptake in the in vitro assay and increased half-life in the in vivo assay is expected. [135] All publications and patents mentioned in the above specification are incorporated herein by reference. Various modifications and variations of the described methods of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. [136] Although the invention has been described in connection with specific embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the above-described modes for carrying out the invention which are obvious to those skilled in the field of biochemistry or related fields are intended to be within the scope of the following claims. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims. 55

Claims (23)

1. A Factor IX polypeptide comprising an amino acid sequence that has been modified by introducing one or more amino acid substitutions or insertions.

2. The polypeptide according to claim 1, wherein the amino acid sequence has been modified by introducing one or more glycosylation sites.

3. The polypeptide according to claim 2, wherein the one or more glycosylation sites are selected from N-linked glycosylation sites and O-linked glycosylation sites.

4. The polypeptide according to claims 2 and 3, further comprising a carbohydrate chain attached to the one or more introduced glycosylation sites.

5. The polypeptide according to any one of claims 1 to 4, wherein the one or more amino acid substitutions are selected from G4T; E33N; E36T; E36N; R37N; F75N; F77T; E83T; D85N; V86A; K91T; A103T; V107T; K122N; K122T; S138N; A146N; T148N; F150T; P151N; T159N; A161T; A161N; T169N; Q170N; T172N; D177N; D177E; F178T; K201N; K201T; K214T; V223N; G226N; Y226T; K228N; K228T; E239N; E242N; 1251T; A262T; E294N; R338A; R338N; K341N; F353N; H354V; H3541; E355T; V370N; T371V; T3711; E372T; E374N; M391N; K392V; G393T; E41ON; K413N; L4141; YIN and S3T; S3N and K5T; G4N and L6T; K5N and E7T; L6N and E8T; E7N and F9T; F9N and Q1IT; ViON and G12T; Q1 IN and N13T; G12N and L14T; N13 and E15T; L14N and R16T; E15N and E17T; M19N and E21T; E20N and K22T; S24N and E26T; F25N and E27T; E26N and A28T; E27N and R29T; A28N and E30T; R29N and V3 IT; E30N and F32T; V3IN and E33T; F32N and N34T; T35N and R37T; T38N and E40T; T39N and F41T; E40N and W42T; F4IN and K43T; W42N and Q44T; K43N and Y45T; Q44N and V46T; Y45N and D47T; V46N and G48T; E52N and N54T; S53N and P55T; G59N and S61T; K63N and D65T; 166N and S68T; S68N and E70T; G76N and E78T; E78N and K80T; E83N and D85T; L84N and V86T; 190N and N92T; KiON and S102T; S102N and D104T; A103N and N105T; D104N and K106T; K106N and V108T; RI 16N and Al 18T; El 19N and Q121T; Q121N and S123T; A127N and P129T; V135N and V137T; S136N and S138T; V137N and Q139T; Q139N and S141T; T140N and K142T; S141N and L143T; E147N and V149T; T148N and F150T; V149N and P151T; P151N and V153T; D152N and D154T; V153N and Y155T; D154N and V156T; Y155N and N157T; V156N and S158T; S158N and E160T; T159N and A161T; E160N and E162T; E162N and 1164T; T163N and L165T; 1164N and D166T; L165N and N167T; D166N and 1168T; 1168N and Q170T; T169N and S171T; S171N and Q173T; T172N and S174T; Q173N and F175T; S174N and N176T; GI84N and DI86T; E185N and A187T; DI86N and K188T; A187N and PI89T; P189N and Q191T; G200N and V202T; K201N and 56 WO 2009/137254 PCT/US2009/040813 D203T; V202N and A204T; E224N and G226T; T225N and V227T; G226N and K228T; V227N and 1229T; H236N and 1238T; 1238N and E240T; E240N and E242T; T241N and H243T; H243N and E245T; K247N and N249T; V250N and R252T; 125 IN and 1253T; 1253N and P255T; A261N and 1263T; A262N and N264T; D276N and P278T; V28ON and N282T; F302N and S304T; S304N and Y306T; R312N and F314T; V313N and H315T; F314N and K316T; H315N and G317T; K316N and R318T; G317N and S319T; S319N and L321T; A320N and V322T; R327N and P329T; P329N and V33 IT; D332N and A334T; L337N and S339T; S339N and K341T; T340N and F342T; T343N and Y345T; G352N and H354T; F353N and E355T; H354N and G356T; E355N and G357T; G356N and R358T; G357N and D359T; E372N and E374T; W385N and E387T; G386N and E388T; A390N and K392T; D85N, K122T, and 1251T; D85N, K122T, and E242N; E125N, P126A, and A127T; P126N, V128T, and P129A; T148N, F150T, and P151A; F150N, P151A, and D152T; P151N, V153T, and A161N; P151N, V153T, and T172N; V153N, Y155T, and E294N; T172N, G226N, and K228T; F353N, H354V, and E355T; F353N, H3541, and E355T; V370N, T371V, and E372T; V370N, T3711, and E372T; M391N, K392V, and G393T; D85N, P151N, V153T, and K228N; D85N, P151N, V153T, and E242N; K122T, P151N, V153T, and K228N; K122T, P151N, V153T, and E242N; K122T, P151N, V153T, and 1251T; T148N, F150T, G226N, and K228T; P151N, V153T, T172N, and R338A; P151N, V153T, D177E, and F178T; P151N, V153T, G226N, and K228T; T172N, G226N, K228T, and R338A; D85N, K122T, P151N, V153T, and E242N; D85N, P151N, V153T, G226N, and K228T; K122T, P151N, V153T, G226N, and K228T; S138N, P151N, V153T, G226N, and K228T; T148N, F150T, G226N, K228T, and R338A; P151N, V153T, T172N, G226N, and K228T; P151N, V153T, D177E, F178T, and R338A; P151N, V153T, G226N, K228T, and R338A; and P151N, V153T, T172N, G226N, K228T, and R338A; and any combination thereof.

6. The polypeptide according to any one of claims 1 to 4, wherein the one or more amino acid substitutions are selected from R37N; D85N; K122T; S138N; A146N; A161N; Q170N; T172N; D177N; F178T; K201N; K228N; E239N; E242N; 1251T; A262T; E294N; E374N; E41ON; G59N and S61T; K63N and D65T; G76N and E78T; S102N and Di04T; A103N and N105T; D104N and K106T; El 19N and Q121T; Q121N and S123T; S136N and S138T; Q139N and S141T; T140N and K142T; T148N and F150T; V149N and P151T; P151N and V153T; D152N and D154T; V153N and Y155T; D154N and V156T; V156N and S158T; S158N and E160T; E160N and E162T; E162N and 1164T; T163N and L165T; 1164N and D166T; D166N and 1168T; 1168N and Q170T; S171N and Q173T; T172N and S174T; Q173N and F175T; S174N and N176T; K201N and D203T; V202N and A204T; E224N and G226T; T225N and V227T; G226N and K228T; T241N 57 WO 2009/137254 PCT/US2009/040813 and H243T; 125 IN and 1253T; 1253N and P255T; A262N and N264T; V28ON and N282T; T343N and Y345T; E372N and E374T; D85N, K122T, and E242N; D85N, K122T, and 1251T; F150N, P151A, and D152T; T172N, G226N, and K228T; D85N, P151N, V153T, and K228N; D85N, P151N, V153T, and E242N; K122T, P151N, V153T, and K228N; K122T, P151N, V153T, and E242N; K122T, P151N, V153T, and 1251T; P151, V153T, G226N, and K228T; D85N, K122T, P151N, V153T, and E242N; D85N, P151N, V153T, G226N, and K228T; S138N, P151N, V153T, G226N, and K228T; P151N, V153T, T172N, G226N, and K228T.

7. The polypeptide according to any one of claims 1 to 4, wherein the one or more amino acid substitutions are selected from D85N; K122T; S138N; T172N; K201N; K228N; E239N; E242N; 1251T; A262T; E294N; G59N and S61T; G76N and E78T; S102N and D104T; A103N and N105T; D104N and K106T; El 19N and Q121T; Q121N and S123T; S136N and S138T; Q139N and S141T; T140N and K142T; T148N and F150T; V149N and P151T; P151N and V153T; D152N and D154T; S158N and E160T; E162N and 1164T; T163N and L165T; T172N and S174T; Q173N and F175T; K201N and D203T; T225N and V227T; G226N and K228T; 1253N and P255T; A262N and N264T; V28ON and N282T; E372N and E374T; and D85N, K122T, and E242N; D85N, K122T, and 1251T; F150N, P151A, and D152T; T172N, G226N, and K228T; D85N, P151N, V153T, and K228N; D85N, P151N, V153T, and E242N; K122T, P151N, V153T, and K228N; K122T, P151N, V153T, and E242N; K122T, P151N, V153T, and 1251T; P151, V153T, G226N, and K228T; D85N, K122T, P151N, V153T, and E242N; D85N, P151N, V153T, G226N, and K228T; S138N, P151N, V153T, G226N, and K228T; P151N, V153T, T172N, G226N, and K228T.

8. A Factor IX polypeptide comprising the amino acid sequence YNSGKLEEFVQGNLERECMEEKCSFEEAREVFENTERTTEFWKQYVDGDQCE SNPCLNGGSCKDDINSYECWCPFGFEGKNCELXXs 6 TCNIKNGRCEQFCKNSA X i o 4 NKVVCSCTEGYRLAENX 1 21 KSCEPAVPFPCGRVSVX 138 QTSKLTRAEX 1 48 V X 150 Xi 51 Xi 2 Xi 3 DYVNSX 159 EZiX 16 i 1 Z 2 EZ 3 TZ 4 1LDNIX 169 QSX 172 QX 174 FNX 1 77 X 178 TR VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETX 22 VX 22 ITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNS YVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATC LX 338 STKFTIYNNMFCAGX 353 X 354 X 3 55 GGRDSCQGDSGGPHX 3 7OX 3 7 1 X 3 7 2 VEGTSF LTGIISWGEECAX 391 X 392 X 393 KYGIYTKVSRYVNWIKE KTX 4 13 X 4 14 T (SEQ ID NO: 3); 58 WO 2009/137254 PCT/US2009/040813 wherein X 85 is selected from D and E; wherein X 86 is selected from A, E, P, S, and V; wherein X 104 is selected from D, N, and T; wherein X 121 is selected from N, Q, and T; wherein X 138 is selected from N, S, and T; wherein X 1 48 and X 150 are selected from: (i) X 14 8 is T and X 15 o is F; (ii) X 14 8 is N and Xi 50 is T; and (iii) X 14 S is N and Xi 50 is S; wherein X 151 is selected from A, P, and T; wherein X 151 and X 153 are selected from: (i) X 151 is P and X 15 3 is V; (ii) X 151 is N and X 1 53 is T; and (iii) X 15 is N and Xi 53 is S; wherein Zi, Z 2 , Z 3 , and Z 4 are independently selected from (i) zero to twelve amino acid residues and (ii) SEQ ID NO: 2; wherein X 152 is selected from D, N, and T; wherein X 159 and X 16 are selected from: (i) X 159 is T and X 161 is A; (ii) X 159 is N and Xi 61 is T; and (iii) X 159 isNandXi 6 i is S; wherein X 169 is selected from T and N; wherein X 172 is selected from T and N; wherein X 174 is selected from S and T; wherein X 177 and X 17 s are selected from: (i) X 177 is D and X 1 78 is F; (ii) X 177 is E and X 1 78 is T; and (iii) X 1 77 is E orD and X 17 S is S; wherein X 2 2 6 and X 22 8 are selected from: (i) X 22 6 is G and X 228 is K; 59 WO 2009/137254 PCT/US2009/040813 (ii) X 22 6 is N and X 22 8 is T; and (iii) X 22 6 is N and X 228 is S; wherein X 3 38 is selected from R and A; wherein X 3 53 , X 354 , and X355 are selected from: (i) X 353 is F, X 354 is H, X 3 55 is E; (ii) X 353 is N, X 354 is V, X 3 55 is T; (iii) X 353 is N, X 354 is I, X 3 55 is T; and (iv) X 353 is N, X 354 is H, V, or I, X 3 55 is S; wherein X 3 70 , X 37 1 , and X 372 are selected from: (i) X 370 is V, X 371 is T, X 372 is E; (ii) X 370 is N, X 371 is V, X 372 is T; (iii) X 370 is N, X 371 is I, X 372 is T; and (iv) X 370 is N, X 37 1 is T, V, or I, X 372 is S; wherein X 3 91 , X 392 , and X 393 are selected from: (i) X 391 is M, X 392 is K, X 39 3 is G; (ii) X 39 1 is N, X 392 is K, X 393 is T; (iii) X 391 is N, X 392 is V, X 393 is T; and (iv) X391 is N, X392 is V or K, X393 is S; wherein X 4 13 and X 4 1 4 are selected from: (i) X 413 is K and X 41 4 is L; (ii) X 4 13 is N and X 4 1 4 is L; and (iii) X 4 13 is N and X 4 1 4 is I; and wherein the FIX polypeptide comprises at least one introduced glycosylation site as compared to the FIX polypeptide having SEQ ID NO: 1.

9. The polypeptide according to claims 6 or 7, further comprising amino acid substitutions selected from R338A and V86A.

10. The polypeptide according to any one of claims 1-9, wherein the amino acid sequence has been modified by introducing between 1 and 10 amino acid residues between amino acid residues 160-164 of human Factor IX resulting in the introduction of one or more glycosylation sites.

11. The polypeptide according to claim 10, wherein the amino acid residues are inserted between amino acid residues 160-161, between amino acid residues 161-162, between amino acid residues 162-163, or between amino acid residues 163-164. 60 WO 2009/137254 PCT/US2009/040813

12. The polypeptide according to claim 11, wherein a polypeptide comprising the amino acid sequence of SEQ ID NO: 2 is introduced between amino acid residues 160-161, between amino acid residues 161-162, between amino acid residues 162-163, or between amino acid residues 163-164.

13. The polypeptide according to claim 11 or 12 further comprising amino acid substitutions selected from V86A; R338A; V86A and R338A; T148N and F150T; D177E and F178T; P151N and V153T; P151N, V153T, and T172N; G226N and K228T.

14. The polypeptide according to any one of claims 1-7, wherein the amino acid sequence has been modified by introducing between 1 and 10 amino acid residues at the C-terminus of Factor IX polypeptide resulting in the introduction of one or more glycosylation sites.

15. The polypeptide according to claim 14, wherein a polypeptide comprising the amino acid sequence selected from SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, and SEQ ID NO: 7 is introduced at the C-terminus of Factor IX polypeptide.

16. A Factor IX polypeptide comprising an R338A substitution and a V86A substitution.

17. The polypeptide according to any one of claims I to 15, wherein attachment of a carbohydrate chain at one or more of the introduced glycosylation sites increases serum half-life of the polypeptide by at least 30% relative to the polypeptide lacking the introduced glycosylation sites.

18. The polypeptide according to any one of claims I to 17, wherein the polypeptide has a specific activity of at least 100 units per mg of polypeptide.

19. A pharmaceutical preparation comprising the Factor IX polypeptide of any one of claims 1-18 and a pharmaceutically acceptable carrier.

20. A method of treating hemophilia B comprising administering to a subject in need thereof a therapeutically effective amount of the pharmaceutical preparation of claim 19.

21. A DNA sequence encoding the polypeptide of any one of claims 1-18.

22. A eukaryotic host cell transfected with the DNA sequence according to claim 20 in a manner allowing the host cell to express a Factor IX polypeptide.

23. A method for producing a Factor IX polypeptide comprising (i) modifying the amino acid sequence of the polypeptide by introducing one or more glycosylation sites; (ii) expressing the polypeptide in a manner which allows glycosylation at the one or more glycosylation sites; and (iii) purifying the polypeptide. 61