SG189790A1

SG189790A1 - Modified factor ix polypeptides and uses thereof

Info

Publication number: SG189790A1
Application number: SG2013028790A
Authority: SG
Inventors: Alan Brooks; John E Murphy; Marian Seto; Xiaoqiao Jiang; Chandra Patel; Uwe Gritzan; Kornelia Kirchner; Ulrich Haupts
Original assignee: Bayer Healthcare Llc; Bayer Schering Pharma Ag
Priority date: 2008-04-16
Filing date: 2009-04-16
Publication date: 2013-05-31
Also published as: CO6311000A2; CN102083856A; WO2009137254A2; CR11737A; MX2010011345A; JP2011517951A; EP2288622A2; CA2721683A1; WO2009137254A3; EP2288622A4; DOP2010000311A; RU2010146387A; KR20110005862A; AU2009244633A1; IL208718A0; BRPI0910702A2; ECSP10010551A; SV2010003704A

Abstract

MODIFIED FACTOR IX POLYPEPTIDES AND USES THEREOFDisclosed are 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. Also, methods are disclosed of making modified Factor IX polypeptides, and methods of using modified Factor IX polypeptides, for example, to treat patients afflicted with hemophilia B.FIGURE 1

Description

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 10 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, Experi 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 {

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 aot 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 iniroducing 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 unan 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. [0081 The one or more glycosylation sites may be introduced via one or more amino acid substitutions. The substitulions may be at surface exposed residues and/or be limited to substitutions that do not introduce a mutation known to be associated with hemophilia IB.

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; D85SN; VB6A; K91T; A103T; V107T;

K122N; K122T; S138N; A146N; T148N; F150T; P151N; T159N; A161T; A161N; T169N;

QL70N; T172N; D177N; DI77E; F178T; K201N; K201T; K214T; V223N; G226N; Y226T;

K228N; K228T; B239N; E242N; 1251T; A262T; E294N; R338A; R338N; K341N; F353N;

H354V; H3541; E355T; V370N; T371V; T3711; E372T; E374N; M391N; K392V; G393T;

E410N; K413N; L4141; {b) YIN and S3T; S3N and K5T; G4N and L6T, KSN and E7T; L6N and EST; E7N and FT; FON and Q11T; VION and G12T; Q11N and N13T; G12N and L14T; N13 and E15T; L14N and R16T;

E15N and E17T; M19N and E21T; E20N and K22T; 524N and E26T; F25N and E27T; E26N and

A2Z8T; E27N and R29T; A28N and E30T; R29N and V31T; E30N and F32T; V31N and E33T;

F32N and N34T; T35N and R37T; T38N and F40T; 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; 853N and P55T; G59N and S61T; K63N and D65T; I66N and S68T; S68N and

E707: G76N and E78T; E78N and K80T;, E83N and D85T; L84N and V86T; I90N and N92T;

K100N and S102T; S102N and D104T; A103N and N105T; D104N and K106T; K106N and

VI108T; R116N and A118T; E119N and Q121T; QI21N and S123T; A127N and P129T; V135N and V137T; S136N and S138T; VI37N and Q139T; Q139N and S141T; T140N and K142T;

S141N and L143T; E147N and V149T; T148N and F150T; V145N and P151T; P151N and

VI53T; DI5S2ZN and D154T; VI33N and Y155T; D154N and V156T; Y155N and N157T; V156N and S138T; S158N and E160T; T1539N and A161T; E160N and E162T; E162N and 1164T; T163N and L165T; 1164N and D166T; L165N and N167T; D166N and I1168T; [168N and Q170T; T169N and S171T; 8171N 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 B242T; T241N and H243T; H243N and B245T; K247N and N249T; V250N and R252T;

I251N and 1253T; [253N and P255T; A261N and 1263T; A262N and N264T; D276N and P273T;

V280N 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; G336N 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

ALl61IN; PI5IN, VI53T, 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; M391IN, K392V, and G393T; D85N, P151N, VI53T, and K228N; D85N,

PI5IN, V153T, and E242N; K122T, P151N, V153T, and K228N; K122T, P15IN, V153T, and

E242N; K122T, P15IN, V153T, and 1251T; T148N, F150T, G226N, and K228T; P151N, V153T,

T172N, and R338A; P151N, V1353T, D177E, and FU78T; P151IN, V153T, G226N, and K228T;

T172N, G226N, K228T, and R338A; D85SN, K122T, P151N, V153T, and E242N; D85N, P15IN,

V153T, G226N, and K228T; K122T, P15IN, V153T, G226N, and K228T; S138N, Pi51N,

V153T, G226N, and K2258T; 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. [oe7] 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: R3I7N; D85N; K122T; S138N; A146N; A161N; Q170N;

TI172N; DI77N; F178T; K20IN; 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 S61T; 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;

P151IN and V153T; DI52N and D154T; V133N and Y155T; D154N and V156T; V156N and

S158T; S158N and E160T; E160N and E162T; E162N and 1164T; T163N and L165T; I164N and

DI166T, D166N and I168T; I168N and Q170T; S171N and Q173T; T172N and S174T; Q173N and F175T; $174N and N176T; K201N and D203T; V202N and A204T; E224N and G226T;

T225N and V227T; G226N and K228T; T241N and H243T; I1251N and 1253T; 1253N and P255T;

A262N and N264T; V280N and N282T; T343N and Y345T; and E372N and E374T; F150N,

Pi51A, 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.

[068] The one or more glycosylation sites may be introduced by converting an O-linked glycosylation site 10 an N-linked glycosylation site. Exemplary embodiments include substitutions such as, but not limited to TI69N; 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 VE6A. In some embodiments, the modified polypeptides may further comprise both the R338A and V86A substitutions.

[0609] The one or more glycosylation sites may be introduced by inserting between | and 12 amino acid residues between amino acid residues 160-164. The glycosylation sites may be imroduced 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,

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 P151N,

V153T, and T172N. In some embodiments, the polypeptide may further comprise amino acid substitutions T148N and F1507T. In some cmbodiments, 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 VB6A. In some embodiments, the modified polypeptides may further comprise both the R338A and VR6A substitutions.

[010] In exemplary embodiments, modified FIX polypeptides are provided comprising one or more substitutions such as: D8SN; K122T; S138N; T172N; K201IN; K228N; E239N; E242N; 12517; A262T; E294N; G59N and S61T; G76N and E78T; S102N and D104T; A103N and

N105T; D104N and K106T; ELI9N and QI21T; Q121N and 8123T;, S136N and S138T; Q139N and S141T; T140N and K142T; T148N and F150T; V149N and P151T; P15IN 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; V280ON 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 R338A and V86A substitutions.

[011] The application also provides FIX polypeptides comprising an R338A substitution and a

VBGA 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 10 a subject in need thereof a therapeutically effective amount of the phanmaceutical preparations described herein. {014] The application also provides DNA sequences encoding modified polypeptides, as well as eukaryotic host cells transfected with the DNA sequences.

[015] The application also provides metheds 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

[018] Figure I depicts a multiple sequence alignment of FIX sequences within the activation pepiide from eight species [0171 Figure 2 depicts Western Blot analysis of media from HKB11 cells transfected with glycosylation sile muteins of FIX. FIX protein was detected using an anii-FIX-HRP antibody.

[018] Figure 3 depicts a table of expression and activity of FIX glycosylation site muteins in

HKBI1 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 iransfection experiment. (none): no change in mobility, (+): decreased mobility with the number of + indicating degree, (-): increased mability.

[018] Figure 4 depicts expression level, coagulation activity, and specific activity of FIX glycosylation site muieins 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 O- 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 hemnophilia BB patients to achieve protection against 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 VEGA substitution (Chang, et al., J. Biol. Chem. 273:12089-12054, 1998 and Chang, ct al, J. Biol. Chem, 277:25393-25399, 2002). The combination with onc 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 donaing: 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 amine acids and undergoes extensive posttranslational modification during passage ihrough 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 (853, S61, T159, T169,

T172, T179), and one site each for Ser phosphorylation (S158), tyrosine sulfation (Y'155) 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 Xla (FXIa) or the tissue factor (TF)/Factor VIIa complex to generate the catalytically active molecule, Factor IXa (FIXa). FIXa and Factor Villa

(FVIIa) 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 m vivo pharmacokinetic profile, an ectopic glycosylation site may be infroduced at a position that does not affect these other modifications. Once produced, FIX should retain enzymatic activity and interact with FVIII, FX, 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 Tesult 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 VE6A 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 luman 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 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 gluiamate; cysteine to serine; glutamine to asparagine; glutamate to aspartate; glycine to proline; histidine to asparagine or glutamine; isoleucine io 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); I, aspartic acid (Asp); E, glutamic acid (Glu); F, phenylalanine (Phe); G, glycine (Gly); H, histidine (His); I, isoleucine (Ile); K, lysine (Lys); L, leucine (Lew); M, methionine (Met); N, asparagine {Asn}; P, proline (Pro); Q, glutamine (Gln); R, arginine (Arg); 5, serine (Ser); T, threonine (Thr), V, valine (Val); W, tryptophan (Tip); Y, tyrosine (Tyr); and norleucine (Nie).

[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 polypeplide 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 1s Asp; X2 is lle; 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 serine 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 ane or more endogenous FIX amino acid residues with another amino acid(s), or adding one or more amine acid residues. The addition of an amino acid residue may be

Q 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 hwman 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 huinan 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 ihe 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 kel.ac.uk/ip/petergreen/hacmBdatabase. htinl and in Table l.

TABLE 1

Residue Mutation Residue Mutation Residue Mutation

LE

2 wen || ow Jee [| ow fem

Cs few [fw few [ow fem os (ow lve [ow fer lke || ow flow [| ow fnew

IE PI PE

0 lew [| ow low [| ow Jo

Cs lew [| os Jess [| ow fem 0 lew [os eer [ow ues ou Joe [| os es || ow Jew

EE ET

Cw fee [low Jos Jom few on lew |] ow Jes [| owe few so Jew || oe Jew [| ows [ve

Cw Jew || ow low ow fiw a ew ow fen ous aw on Jew [| ow ew [om [ew

Cs les [|e lve || oo om x leo [| on Jes || om ew

Cw lew [| 0m Jes || ome Jew

Cw Jew [| on Jew || om ae

Cw les [low Jew |] oms Jew on few || om fees [ow es os lea low few || ow Jew a lew Iw Jew [om lew 1t

Residue Mutation Residue Mutation Residue Mutation

RE ws les [oar lve [ow [wen vie fae [| ows lew [| ow paw few ows far ow ee wo free [| oa lar [| om aw ow ver [oe lew [| oom few ow vw [| om es [| om few ie Joss || ome Jew || om pa ow Jom || ow [El] ms fio 184 G—R 227 E 275 L—Q aw fan [| ome Jer || ome [pw ow Joe || oa fver [| om [ew fo || ler || oow [ew we few [ome es || [iw wn fees |] ome men || ow [ne is wen [| oa len || ow [vee ws ow || aw few || oom [eer iow Jes [ows few || li os fav || as Jou [| ow Jem we oom || as ne || owe few ow Jor || ome [ves || ow aw we Joos [| oaw few || xem mo fer [| ows leew || ows vee a ver || few [oes ea we Dex || ome ven oes few os wer [| owo fwes | ew

IE FE I PR YB I

Residue Mutation Residue Mutation Residue Mutation a

I PE PO I PE ow Joe || owe Jew [| sw few ws Joop || owe Jen [| ose fer

Cw fer || fees || owe ew ae [sn || oae fee Joan fun woos || oaws [vee || ow [ai"F 309 GS 345 YC 371 G.I oo wer || ows wen || om Jew

ES EEE EE se reo || owe bew || owe [mw ow vee || owe [ew [| owe few ae ea || Jew [aw [iw as eos || aw aw [ww [re sw aw || oso fos || ow fom 0 fae ose [en J] ose fee a Jee oa [er Fl] ow [ee 323 IL—F 354 Gq, 1 384 5=C

Joe || oss [er || owe fun as ves [owe Jem [| owe fos as ve || oes fee J] own few

Cw fer [oa fer [ow fee

Cw Jer || ow [ow J] ow few

EEE I

IES PS I PO I sw ree || ose ew [| ow [G7 333 R—G 363 G—=R 392 Gg, ae far ose ow [ow fer oe Jen || ose {so |] ow [res

Residue Mutation Residue Mutation Residue Mutation

LN as ven owe Jew [| ow wen ws or [| ow [sw [| ow iw

Ca fee [ow few [| owe [rk

Ca ves [oan lew [| ows few

Cw lew [Lows few [ae [GF 399 TN 405 V—F 414 G,1 [0371 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, ihe control polypeptide may be identical io 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 cerfain 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 (wo, 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 2 patient to be reduced by one half. Methods for pharmacckinelic 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.,

Pharmacokinet 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). y

[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

FVIlia on an activated platelet, or support the formation of a blood clol. The aclivily may be assessed in vitro by fechniques 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 aninal 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 Departinent of Pathology, University of North Carolina, Chapel Hill, N.C.

Both of these sources, for example, provide canines suffering froin canine hemophilia B.

Allernatively, 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 lime 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. I. 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 postiranslational modification, and is then secreted by the cells into the extracellutar milien. 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 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 FVII, FXJ, or EX. For example, a modified FIX polypeptide may interact with at least one of FVIII, FX, 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 FVII, 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 O-linked sites on Ser53 and Ser61) and in the activation peptide (four O-linked sites al Thrl159, Thrl69, 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 indroduced inio 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: ES3T; DS5N; VE6A;

K91T; A103T; VIO7T, K122N; K122T; S138N; A146N; T148N; F150T; P151N; T159N; Al161T;

ALGIN; T160ON; Q170N; T172N; D177N; D177E; F178T; K201N; K201T; K214T; V223N;

G226N; Y226T; K228N; K228T; E239N; E242N; 1251T; A262T; E294N; R338A; R338N;

K341IN; F353N; H354V,; H354I; E355T,; V370N; T371V; T3711; E372T; E374N; M39IN;

K392V; G393T; E410N; K413N; L414I; or any combination thereof.

[048] In some embodiments, FIX polypeptides are provided comprising one or more substitutions selected from YIN and S3T; S3N and K5T; G4N and L&T; K5N and ETT; L6N and

EST; E7N and FOT; F9N and QL1T; VION and G12T; Q11N and N13T; G12N and L14T; N13 and E15T; LI14N and R16T; E15N and E177; 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; FAIN and K43T; W42N and Q44T; K43N and Y45T; Q44N and V46T; Y45N and D47T; V46N and G48T; E52N and N34T; S53N and P55T; G59N and $61T; K63N and

D65T, 166N and S68T; S68N and E70T; G76N and E78T; E78N and K80T; E83N and DSST;

L84N and V86T; [90N and N92T; K100N and S102T; S102N and D104T; A103N and N105T;

D104N and K106T; K106N and V10ST; R116N and A118T; EI19N and Q121T; Q12IN and

St23T; A127N and P129T; V135N and V137T; S136N and S138T; V137N and Q139T; QI39N and S141T; T140N and K142T; S141N and L143T; E147N and V149T; T148N and F150T:

V149N and P151T; P1SIN 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 [168T; 1168N and QL70T; T169N and S171T; S17I1N and Q173T; T172N and S174T; Q173N and F175T; S174N and N176T; G184N and Di186T; E185N and A187T; D186N and K188T;

Al18TN 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; [251N and 1253T; 1253N and P255T; A26IN and 1263T; A262N and N264T; D276N and P278T; V280N and N282T; F302N and 3304T; 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; or any combination thereof

[047] Tn some embodiments, FIX polypeptides are provided comprising one or more substitutions selected from D83N, K122T, and 1251T; D85N, K122T, and E242N; E125N, P126A, and A127T; P126N, V128T, and P129A; T148N, F150T, and P151A; F150N, P151A, and D152T;

P15IN, VI53T, and A161N; P15IN, V153T, and T172N; Vi53N, Y155T, and E294N; T172N, (G226N, and K228T; F3533N, H354V, and E355T; F353N, H3541, and E355T; V370N, T371V, and

E372T; V370N, T3711, and E372T; M391N, K392V, and G393T; D8SN, P151N, V153T, and

K228N; DSN, P151IN, V153T, and E242N; K122T, P151IN, VI153T, and K228N; K122T, P15iN,

V153T, and E242N; K122T, P151N, V153T, and 1251T; T148N, F150T, G226N, and K228T;

PLSIN, VIS3T, T172N, and R338A; P15IN, V153T, DI77E, and F178T; P151IN, VI53T, G226N, and K228T; T172N, G226N, K228T, and R338A; D8SN, K122T, P151N, V153T, and E242N,;

D85N, P151IN, V153T, G226N, and K228T; KI122T, P151N, V133T, (G226N, and K228T; 3138N,

PISIN, V153T, G226N, and K228T; T148N, F150T, G226N, K228T, and R338A; P151N,

V153T, T172N, G226N, and K228T; P151IN, V153T, D177E, F178T, and R338A; P151IN,

V153T, G226N, K228T, and R338A; and PI15IN, V153T, T172N, (3226N, 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,; B36N; R37N; F75N; F77T; E83T, D85SN; V86A; KOI T; A103T, V107T;

K122N; K122T; S138N; A146N; T148N; F150T; P15IN; TI59N; A161T; A161N; TI69N;

QI70N; T172N; DITIN; DI77E; F178T; K201N; K201T; K214T; V223N; G226N; Y226T;

K228N; K228T; E239N; E242N; 1251T; A262T; E204N; R338A; R338N; K341N; F353N;

H354V; H3541; E355T; V370N; T371V; T371L E3721; E374N; M391N; K392V; G393T;

E410N; K413N: L414[,; {(b} YIN and S3T; S3N and K5T; G4N and L6T: K5N and E7T; L6N and EST; E7N and FOT; FON and Q11T; VION and G12T; QF IN and N13T; G12N and L147; N13 and E15T; L14N and R16T;

El5N and E17T; M19N and E21T; E20N and K22T; $24N 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; I66N and S68T; S68N and

E70T; G76N and E78T; E78N and K80T; E83N and D85T; L84N and V86T; I90N and N92T:

K100N and S102T; S102N and D104T; A103N and N105T; D104N and K106T: K106N and

V108T; R116N and A118T; E119N and Q121T; QI12IN and S123T; A127N and P129T; V135N and V137T; S136N and S138T; VI37N 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; DI166N and 1168T; I[168N and Q170T; T169N i8 and S171T; S171N and Q173T; T172N and S174T; Q173N and F175T; S174N and N176T;

G184N and D186T; EL85N and A187T; D186N and K188T; AI187N and P189T; P189N and

QI9IT; G200N and V202T; K201N and D203T; V202N and A204T; E224N and G226T; T225N and V227T; G226N and K228T; V227N and 1229T; H236N and I238T; I238N and E240T; E240N and E242T; T241N and H243T; H243N and E245T; K247N and N249T; V250N and R252T;

I251N and 1253T; I253N and P255T; A261 N and 1263T; A262N and N264T; D276N and P278T;

V280N 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 L32IT; A320N and V322T; R327N and P329T; P329N and V331T; D332N and A334T;

L.337N 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) D8SN, K122T, and I25tT; D85N, K122T, and E242N; E125N, P126A, and A127T; P126N,

V128T, and P129A; TE48N, FI50T, and P151A; FIS0N, PI151A, and DIS2T; PISIN, VI53T, and

Al6IN; P151IN, V153T, and T172N; V153N, Y155T, and E294N; T172N, G226N, and K228T:

T3711, and E372T; M391N, K392V, and G393T; D85N, P151N, V153T, and K228N; D85N,

P15IN, V153T, and E242N; K122T, P15IN, V153T, and K228N; K122T, P151N, V153T, and

E242N; K122T, P151N, V153T, and 1251 T; T148N, F150T, G226N, and K228T; P151N, V153T,

T172N, and R338A; P151IN, V153T, D177E, and F1787T; P151N, V153T, G226N, and K228T;

T172N, G226N, K228T, and R3384; D85N, K122T, P151N, V153T, and E242N; D§5N, P151N,

V153T, G226N, and K228T; K122T, P15IN, V153T, G226N, and K228T; S138N, P151N,

V153T, G226N, and K228T; T148N, F150T, G226N, K228T, and R338A; P15IN, V153T,

T172N, G226N, and K228T; P151N, V153T, D177E, F178T, and R338A; P151IN, VI53T,

G226N, K228T, and R338A; and P151N, V153T, T172N, G226N, K228T, and R338A; and any combination thereof.

[048] The application provides, in part, FIX polypeptides comprising one more glycosylation sites introduced by converting en 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 TI69N substitution. In some embodiments, FIX polypeptides are provided comprising a T172N substitution. In some embodiments, FIX polypeptides are provided 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 amine 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, 4, 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 aligmment 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

Al6l 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 Al61 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 may be 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 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 catalylic 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; AI46N; AI61N; QL70N; 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 S61T; K63N and D65T; G76N and E78T;

S102N and D104T; AL03N and N105T; D104N and K106T; E119N and Q121T; Q121N and

S123T; S136N and SI138T; Q139N and S141T; TI40N and K142T; T148N and F150T; V149N and P151T; P151N and V153T; DI52N and D154T; V153N and Y155T; D154N and V156T;

V136N and S158T; S158N and E160T; E160N and E162T; E162N and [164T; T163N and L165T, 1164N and DI166T; DI66N 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 and H243T; 1251N and 1253T; 1253N and

P255T; A262N and N264T; V280N 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 emnbodiments, the modified polypeptides may further comprise at least one substitution such as, for example, R338A and VE6A. 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-ierminus 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.

[054] One aspect of the application provides modified FIX polypeptides comprising al 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, medified FIX polypeptides may comprise both the R338A and the V86A substitution.

[055] A farther aspect of the application provides FIX polypeptides with increased specific activity. In some embodiments, FIX polypeptides may comprise an R338 A 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, £100, 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

LNGGSCKDDINSYECWCPFGFEGKNCEL X35 Xs TCNIKNGRCEQFCKNS AX, ,NKVV

CSCTEGYRLAENX 2 KSCEPAVPFPCUGRVSVX 3:QTSKLTRAEX 145 VX 50X15: % 152X530

YVNSX 5sEZ X161Z,EZ3 TZ LDNIX 165Q 5X 172QX17sFNX 2X s TRVVGGEDAKPGQFPW

QVVLNGKVDAFCGGSIVNEKWIVTAAHCVET Xa15 VXag TVVAGEHNIEETEHTEQK

RNVIRIIPHANYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGY

VSGWGRVFHKGRSALVEQYLRVPLYVDRATCLX 5s STKFTIYNNMFECAGX 353X535: X55

GGRDSCQGDSGGPHX:70X37m1 X57 VEGTSFLTGISWGEECAX 591 X302Ge:s KYGIYTKVS

RYVNWIKE KTX, 3X45 T (SEQ ID NO: 3); wherein Xgs is selected from D and E; wherein Xe 18 selected from ALE, P, S, and V; wherein Xo is selected from D, N, and T; wherein X,;) is selected from N, Q, and T; wherein X33 is selected from N, S, and T; wherein X44 and Xs are selected from: {i} Kia is T and Kiso is F;

(1) Xpugis Nand Xjs50is T; and (iii) Kiss is N and Kiso is S: wherein Xs; is selected from A, P, and T; wherein Xs and Xs; are selected from: (1) Xin is P and Xiss is Vv: (il) Xs is Nand X53 is T; and (iii) Xis1 is N and Xs; i$ S; wherein Z,, Z,, Zs, and Z, are independently selected from {iy zero to twelve amino acid residues and (ii} SEQIDNO: 2; wherein X;s: is selected from D, N, and T; wherein Xs and X,¢, are selected from: (i) X30 is T and Xist is A; (ii) Hisois Nand Xj4, is T; and (111) Xisois Nand Kiel is S; wherein Xo is selected from T and N; wherein X, 1; is selected from T and N; wherein X44 is selected from S and T; wherein X77 and X75 are selected from; (iy XyrisDandX55isF (il) Xinris E and X75 1s T; and (iii) Xi sEorD and Xs is Ss; wherein Xai and Xaog are selected from: (i) Kang is Gand Kang 18 K; (in) Kong is N and Kars is T: and (111) Kang 1s N and Xan is S; wherein Xas5 is selected from R and A; wherein Xsss, Xasq, and ysss are selected from: (iy sis F, Xyseis H, Xj55 is E; (i1) Kasay 18 N, Kise is V, Kass is T: (iii} Kasay i8 N, X34 is I X55 is T; and (iv) Kass 18 N, Xssa is H, V. or I, Kiss is S;

wherein Xs, X371, and X;7; are selected from: (1) XKnisV,XmnisT, XsnisE; (if) XsisN, Xin is V, Xn is T; (ill) XKswpisN, Xzypis [, Xs is T; and (iv) XspisN,XanisT,V,or, Xs is S; wherein Xjg1, Xagz, and Xa: are selected fiom: (1) Kiser is M, Xser 18 K, Xsny 18 Gj (i) Kiso isN, Xs is K, Xap is T; (iii) Kio is N, Xzaz2 18 V, Xags is T; and (iv) X391isN,X392isVorK,X393 is §; wherein X43 and X.4 are selected from: (1) XKysisKand XyzisL; (ity Xuzis Nand Xy5isL; and (iii) Xi3is Nand Xy4isT; and wherein the FIX polypeptide comprises at least one introduced glycosylation sile 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. Tn some embodiments, the modified polypeptide is at least about 80, 85, 90, 95, or 99% identical to SEQ ID NO: | 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 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 consiracl, 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 imto 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 veclor may be derived from plasinid or viral DNA, or may conlain 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 mnamimalian cells are, for example, the SV40 promoter (Subramani, et al.,

Mol. Cell Biol. 1:854-864, 1981), the MT-I (inetallothionein 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 (Kaufman et al,,, Mol. Cell Biol, 2:1304-1319, 1982).

[064] The DNA sequences encoding the FIX polypeptide may also, if necessary, be operably connecled lo 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

(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 Elb region, the human growth hormone gene tenminator (DeNoto, et al., Nucl. Acids

Res. %:3719-3730, 1981), or the polyadenylation signal from the hurnan FIX gene. The expression vectors may also include enhancer sequences, such as the SV40 enhancer. f065] 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 mown as a leader sequence, prepro sequence, or pre sequence) may be provided in the recombinant vector. The sceretory 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° 10 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 tenninator 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, Kaufinan, 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, (Celi 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 inay be introduced into cultured mammalian cells by, for example, lipofection, DEAE-dexiran-mediated transfection, microinjection, protoplast fusion, calcium phosphate precipitation, retroviral delivery, electroporation, sonoporation, laser irradiation, magnetofeciion, natural transformation, and bioclistic 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 io 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 adenosine deaminase. It is within the purview of one skilled in the art to choose suitable selectable markers (see, ¢.g., US Patent No. 5,238,820). [0681 After cells have been transfected with DNA, they are grown in an appropriate growth medium lo 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), HKIB311 cells (Cho, et al., J. Biomed. Sci, 9:631-638, 2002), and HEK-293 (ATCC CRL 1573; Graham, et al., I. Gen. Viral. 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-K1 (ATCC

CCL 61), and CHO-DUKX cells {Urlaub and Chasin, 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 kmown 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] Generaily, “purified” shall refer to a protein or peplide composition that has been subjected fo fractionation to remove various other components, and which substantially retains its xy 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 chernical 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 bela-galactoside alpha-2,6 sialyliransferase, 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 10 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., bryophyle 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-manmose N-linked oligosaccharide chains, among others. Polypeptides produced in mammalian cell culture are usually glycosylated differently depending upon, for 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, 1s 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 forin of the polypeptide.

[078] A variety of inethods 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, O-glycans are linked primarily to serine 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. Fora 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 Giycoanalysis 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 stalus 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-glycosaiminyl) asparagine amidase (PNGase F), endoglycosidase Fl, endoglycosidase F2, endoglycosidase F3, and the like. For example, sodium docecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the protein, either pre-ireated with PNGaseF or untreated with PNGaseF, may be conducted. A marked decrease in band width and change in migration position afler treaiment 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 separated by SDS-PAGE and transferred {o 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 (Curnmings,

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, 0 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 witliin 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 io an antennary N-acetylglucosamine residue.

[082] The patlern 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; Hellergvist,

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),

Pharmaceutical Compositions

[083] Based on well known assays used to determine the efficacy for treatment of conditions identified above in marmmals, 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 accepiable 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 nnnan, As used herein, “pharmaceutically acceptable carries” 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 inveniion 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, inlramarmmary, intraperitoneal, intrathecal, retrobulbar, intrapulmonary, oral, sublingual, nasal, anal, vaginal, or transdermal delivery, or by surgical implantation at a particular site, The freatinent 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 hydroxypropyleellulose. 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 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, pelysorbate 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 sedivin 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 slerile-filtered solulion 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 (o 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 forns, 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

FIX per ml of plasma, that is, 100%. Mild cases of hemophilia B are defined by FIX plasma concentrations between 6-60%, 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 15-30%.

Treatment of moderate hemorrhaging usually requires raising levels to between 30-50%, while treatment of major frawma 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 unitkg 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., 20 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. Fusther 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,

[084] 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 invention include benzalkonium chloride, benzethonium chloride, benzyl alcohol, cetylpyridiatum 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 F838 (both of which are available from BASF, Mount Olive, N.1.); sorbitan esters; lipids such as phospholipids such as lecithin and other phosphatidylcholings, phosphatidylethanolamines, faity 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, potassiwin 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, froma 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 Pharnaceutical Association,

Washinglon, D.C., 2000.

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 trawma- 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 uncontroiled 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.

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 predicied sites of interaction with both FVII 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 (G226N, K228T Gly226-Val227-Lys228 Asn226-Val227-Thr228

F353N, H354V, E355T Phe353-His354-Glu3ss Asn353-Val354-Thr355

F353N, H3541, E355T Asn353-1le354-Thr355

V370N, T371V, E372T Val370-Thr371-Glu372 Asn370-Val371-Thr372

V370N, T3711, E372T Asn370-11e371-Thr372

M391IN, G393T Met391-Lys392-Gly3o3 Asn391- Lys392- Thr393

M39iN, K392V, G393T Asn39l- Val392- Thr393

K413N Lys413-Leud14-Thr415 Asndi3-Leud14-Thr415

K413N, L414] Asnd13-Tle414-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 other N-linked sites and the consensus sequence for tyrosine sulfation so as not to disrupt these positranslational 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

Example 3: Insertion of Amino Acids to Generate N-linked Glycosylation Sites {1091 The multiple sequence alignment (Figure 1) also revealed that mouse, rat, and guinea pig have additional amino acids between residues A161 and E162 relative to human, thesus 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 aligmment 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 thai the site can be either between E160 and A161, between A161 and E162, between E162 and T163, or between T163 and [164 of human FIX.

[110] Nine exira amino acids with the sequence N-8-T-Q-D-N-I.T-Q {SEQ ID NO: 2) were inserted in the activation peptide between A161 and E162. The sequences “ N-5-T™ and “N-1-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 I and 3 consensus sequences for N-glycosylation site (N-X-5/T) may also be inserted between A161 and E162,

[111] Additional examples of modified FIX polypeptides are described in Tables 4a, 4b, and 4c.

TABLE 4a

Constroct Substitution Description Specific Activity {% of Control)

HOW | DSN [CresteslnewNlikedsitenEGFL | 99

HGI12 S138N Creates 1 new N-linked site in EGF2- 73

ET ermine catalytic domain

HGl4 E242N Creates | new N-linked site in 183

EY edna catalytic domain

Hoe catalytic domain catalytic domain

HG18 E83T Creates 1 new N-linked consensus in NT

RE LET ame

HGL9 K214T Creates [ new N-linked consensus in NT

PET dome catalytic domain catalytic domain

E355T catalytic domain

HG23 V3ITON-T371V- | Creates 1 new N-linked consensus in NT

PTET | edna (G393T catalytic domain

HG25 415 - T-N-8-T-T : Adds | new N-linked consensus 57

PP Smo |weneeComme

HG26 415 - T-N-8-T- Adds 2 new N-linked consensus 42

RR

(SEQ ID NO: 5)

HG27 415 - T-N-8-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-8-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 (SEQIDNO: 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.

TABLE 4b

Construct Residue Substitution | Specific Activity | Specific Activity (Ye of WT) (%o of Control)

HG3/9 PISIN, V153T, G226N, 270 40

K228T

HG8/9 Insertion of SEQ ID NO: 350 55 2 between Al6] and

E162, G226N, K228T

HG3/9/12 S138N, P151N, V153T, 200 26 (G226N, K228T

HG3/5/9 Pi5IN, V153T, T172N, 190 38 (G226N, K228T

HG3/9/10 D35N, P151N, Vi53T, 200 26 (G226N, K228T

HG3/10/13 D85N, P15IN, V133T, 200 20

K228N

HG3/11/13 K122T, P15IN, V153T, 400 40

K228N

HG3/10/14 DEBSN, P151N, V153T, 210 21

E242N

HG3/11/14 K122T, P151N, V153T,

E242N

HG10/11/14 D33N, K122T, E242N

HG3/11/1251T KI122T, PISIN, V153T, 540 47 1251T

HG3/10/11/14 D85N, K122T, P15IN, 400 40

V153T, E242N

TABLE 4c rs | spe | cos [ct

Construct Substitution (relative to control)* (relative to control)*

Te Emer Ty

CC Cc I AL

Ce ewe

Con mew |r| 1

E125N, P126A,

P126N, VI28T,

V128N, P129A,

Con | me |e

T148N, F150T,

F150N, P151A,

Cow | memmer | = [om meow |v

KISSN, P189A,

R252N, 1254T, 1254N, P255A,

Com [eawmwr | 1 |r

L275N, E277T, on |e

E277N, P2T8A,

Cow [mwa | 1

L326N, V328T,

V328N, P3294,

Com [mw |r

Co [weer |r

[ow owes | wT

Expression and activity relative to the wild type control are expressed on a scale of 1 to 5 where 1 = <10%; 2 = 10-50%; 3 = 50-100%; 4 = 100-200%; 5 = >200%.

Example 4: Substitutions to Convert O-linked to N-linked Glycosylation Sites

[112] Table 5 shows the substitutions that were designed lo convert O-linked glycosylation sites to N-linked glycosylation sites.

TABLE 5 (O-linked site underlined) | created

F150T

Example 5: Expression of FIX Variunts in HEBII Cells {1131 In order to determine if the FIX gencs 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

HEKI311 cells. HKB11 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, R338 A, as shown for HG1 through HGS 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 resulls 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 R338 A substitution (Figure 2).

[115] The activity of the FIX muteins was also tested using the aPPT assay. The results demonstrated thai 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 [4% and 109%. In particular, muteins HG1, HG3, HG4, HGS, HG6, HG7, HGS, and HG3 plus

HGS 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 HEB11 cells

[116] An initial analysis of muteing HG through HGS (Figure 3) and HG9 (Figure 5) demonstrated that HG2, HG3, HGS, HGS, HGS, and HGY 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, HGS, HG6, and HGS. For example, the following combinations were created: HG2/HG3,

HG8/HG2, HG8/HG3, HGR/HG2/HG3. Other possible combinations include, for example,

HG3/HGS, HGS/HGS, HG3/HGS/HGS. HG3/HGS, HGS/HG6, HGE/HG6, HG3/HGS/HGE,

HG3/HG6/HGS, HGS/HG6/HGS, and HG3/HGS/HG6/HGS. 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, HGS, HG6, HGS, and HGY resulted in reduced mobility on a SDS-PAGE gel.

Among these eight single muteins, HGE which has two additional N-linked consensus sequences inserted between A161 and E162, exhibited the greatest increase in apparent molecular weigit 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 Nelinked site. In contrast, HGS and

HG6 exhibited reduced mobility on the gel demonstrating that the substitutions in these clones did create fimetional 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 O- linked site and thus increase the mobility on the gel, ihe 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, HGS/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 R3384 and V86A4 Substitutions

[119] Amino acid V86 of FIX was changed 10 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 HKBI11 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 sumninarized in Table 6a. Table 6b summarizes the average of {liree experiments.

TABLE 6a (mU/mL) (ng/mL) (1U/mg) ween | ow | ow | ow]

TABLE 6b {(% of WT-FIX) | (% of WT-FIX) (%% of WT-FIX)

R33sA [3% of 90 [450

[120] The results demonstrate that the VS6A substitution alone resulls 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 resulied 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-VE6A 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 crealing 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 {o 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

HindIII 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 HindIII 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 HindlIIl, the PCR product was gel purified and then cloned into the HindIII site of the plasmid pAGE16. Clones in which the FIX cDNA was inserted in the forward orientation relative lo 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 pAGE16-Factor IX (pAGE16-FIX).

Exumple 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 Quickchange™ primer design program available from Stratagene. These primers were used to generate mutations in the pAGE16-FEX plasmid employing the

Quickchange™ 11 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

G226N/K228T CTGCTGCCCACTGTGTTGAAACTAACGTTACCATTACA mms amon

F353N/H354V/E355T | CACCATCTATAACAACATGTTCTGTGCTGGCAACGTGA

CCGGAGGTAGAGATTCATGTCAAGGAGATAGTG

(SEQID NO: 11)

V3TON/T37IV/EZT2T | GATTCATGTCAAGGAGATAGTGGGGGACCCCATAACG

TGACCGTGGAAGGGACCAGTTTCTTAACTGGAATTA

(SEQ ID NO: 12)

M39IN/K392V/G393T | GGAATTATTAGCTGGGGTGAAGAGTGTGCAAACGTGA

CCAAATATGGAATATATACCAAGGTATCCCGG

(SEQ ID NO: 13)

K413N TCAACTGGATTAAGGAAAAAACAAACCTCACTTAATG em amon

AlGIN CTGATGTGGACTATGTAAATTCTACTGAAAATGAAACC

TT meme momo

DI77E/F178T ACTCAAAGCACCCAATCATTTAATGAGACCACTCGGGT

Be

P15SIN/V153T ACTTCTAAGCTCACCCGTGCTGAGACTGTTTTTAATGA

TT soca samo

T169N GAAGCTCGAAACCATTTTGGATAACATCAATCAAAGCA 7 Joo samen

TI72N ATTTTGGATAACATCACTCAAAGCAACCAATCATTITAA eon mmo rome mmol

Ti59N/AL161T GTTTTTCCTGATGTGGACTATGTAAATTCTAATGAAAC mone mon

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 peplide between residues A161 and E162. To generate this variant of FIX, unique restriction sites for SnaB1 and

Xba] at Y155 and 1164 were created without altering the amino acid sequence by site directed mutagenesis with primers 18216¢_g8218a and t8188c¢ (Table 3). The resulting plasmid was digested with SnaB1 and Xbal to remove the 27 bp fragment corresponding to residues V156 to 1164 and then ligated to a double stranded fragment created by anncaling of oligonucleotides 2Primerl? and 2PrimerR (Table 8). The sequence of the resulting plasmid was detennined 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 2a (SEQ ID NO: 22) (SEQ ID NO: 23)

AAACCATT (SEQ ID NO: 24)

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] HEKBII cells (a hybrid of HEK293 and a Burkitt 3 cell lymphoma line, 2B8) were grown in suspension culture on an orbital shaker (100-125 rpm) in a CO, (5%) incubator at 37°C in senun free media (RF#277) supplemented with 10 ng/mL soluble vitamin K; (Sigma-Aldrich, St.

Louis, MO) and maintained at a density between 0.25 and 1.5 x 10° cells/mL.

[125] Cells for transfection were collected by centrifugation at 1000 rpm for 5 minudes then resuspended in FreeStyle™ 293 Expression Medium (Invitrogen, Carlsbad, CA) at 1.1 x 10° cells/mL. The celis were seeded in 6 well plates (4.6 mL/well) and incubated on an orbital rotator (125 rpin) in a 37°C CO; incubator. For each well, 5 ug plasmid DNA was mixed with 0.2 mL

Opti-MEM® I medium (Invitrogen). For each well, 7 pL 293fectin™ reagent (Invitrogen) was mixed gently with 0.2 mL Opti-MEM® I medium and incubated at room temperature for minutes. The diluted 293fectin™ 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 10° (4.6 mL) HKB11 cells. The cells were then incubated on an orbital rotator (125 rpm) in a CO, incubator at 37°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°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°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,

Swampscott, Massachusetts, Catalog No. FO017-07B) for 60 minutes at room temperature. Afeer washing with phosphate-buifered saline with 0.1% Tween®-20 buffer, the signal from HRP was detected using SuperSignal® Pico (Pierce, Rockford, IL) and exposure 10 x-ray film,

Example 12: FIX ELISA [t28] 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 io the ELISA plate that is pre-coated with a polyclonal anti-FIX capture antibody. After adding the polyclonal detection antibody, the plate wag 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.

[129] FIX expression levels were also quantitated using commercially available FIX ELISA reagents (Haemochrom Diagnostica GinbH, Essen, Germany) according to the manufacturer’s instructions, Wheat germ agghitinin (Sigma-Aldrich, St, Louis, MO) was coated on 384 well

MaxiSorp™ plates (Nunc™, 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 Electra™ 1800C automatic coagulation analyzer (Beckman Coulter, Fullerton,

CA). Briefly, three dilutions of supernatant samples in coagulation diluent were created by the instrument, and 100 pF was then mixed with 100 pL FIX deficient plasma (Aniara, Mason, OH) and 100 pL automated aPTT reagent (rabbit brain phospholipid and micronized silica {(bioMérieux,

Inc., Durham, NC). After the addition of 100 pL 25 mM CaCl, 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 vive 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, AdSmut, which conlains mutations in the fiber knob domain, does not bind to FIX. Ad5mut has significanily 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 (Shayaklimetov, 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 halflife 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, inamimalian cells are incubated with adenovirus in the presence or absence of FIX or FIX variants. Viral uptake is mediated by wild-type FIX and 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 a subject by intravenous injection. Blood samples are taken at a number of time points afier 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 cotnpared to the FIX concentration expected or measured immediately afler 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 morc 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.

MSB7324_5T25

SEQUENCE LISTING

<110> Bayer HealthCare LLC

Bayer HealthCare AG

Brooks, Alan

Murphy, John E.

Seto, Marian

Jiang, Xiaogiao

Patel, Chandra

Gritzan, Uwe i

Kirchner, Kornelia

Haupts, Ulrich <120> MODIFIED FACTOR IX POLYPEPTIDES AND USES THEREOF <130> MSB-7324 <150> US 61/124,567 <151> 2008-04-16 <150> US 61/045,961 <151> 2008-04-17 <160> 26 <170> PatentIn version 3.5 <210> 1 <211> 415 <212> PRT <213> Homo sapiens <400> 1

Tyr Asn Ser Gly Lys Leu Glu Glu Phe val Gln Gly Asn Leu Glu Arg 1 5 10 15

Glu Cys Met Glu Glu Lys Cys Ser Phe Glu Glu Ala Arg Glu val Phe

Glu Asn Thr Glu Arg Thr Thr Glu Phe Trp Lys Gln Tyr val Asp Gly 40 45

Asp GIn Cys Glu Ser Asn Pro Cys Leu Asn Gly Gly Ser Cys Lys Asp 50 55 60

Asp Ile Asn Ser Tyr Glu Cys Trp Cys Pro Phe Gly Phe Glu Gly Lys 65 70 75 80

Asn Cys Glu Leu Asp val Thr Cys Asn Ile Lys Asn Gly Arg Cys Glu 85 90 95

Gln Phe Cys Lys Asn Ser Ala Asp Asn Lys val val Cys Ser Cys Thr 100 105 110

Glu Gly Tyr Arg Leu Ala Glu Asn Gln Lys Ser Cys Glu Pro Ala val 115 120 125

Pro Phe Pro Cys Gly Arg val Ser val Ser GIn Thr Ser Lys Leu Thr 130 135 140

Page 1

MSB7324_ST25

Arg Ala Glu Thr val Phe Pro Asp val Asp Tyr val Asn Ser Thr Glu 145 150 155 160

Ala Glu Thr Ile Leu Asp Asn Ile Thr GIn Ser Thr GIn Ser Phe Asn 165 170 175

Asp Phe Thr Arg val val Gly Gly Glu Asp Ala Lys Pro Gly GIn Phe 180 185 190

Pro Trp Gln val val Leu Asn Gly Lys val Asp Ala Phe Cys Gly Gly 195 200 205

Ser Ile val Asn Glu Lys Trp Ile val Thr Ala Ala His Cys val Glu 210 215 220

Thr Gly val Lys Ile Thr val val Ala Gly Glu His Asn Ile Glu Glu 225 230 235 240

Thr Glu His Thr Glu GIn Lys Arg Asn val Ile Arg Ile Ile Pro His 245 250 255

His Asn Tyr Asn Ala Ala ITe Asn Lys Tyr Asn His Asp Ite Ala Leu 260 265 270

Leu Glu Leu Asp Glu Pro Leu val Leu Asn Ser Tyr val Thr Pro Ile 275 280 285

Cys Ile Ala Asp Lys Glu Tyr Thr Asn Ile Phe Leu Lys Phe Gly Ser 290 295 300

Gly Tyr val Ser Gly Trp Gly Arg val Phe His Lys Gly Arg Ser Ala 305 310 315 320

Leu val Leu Glin Tyr Leu Arg val Pro Leu Val Asp Arg Ala Thr Cys 325 330 335

Leu Arg Ser Thr Lys Phe Thr Ile Tyr Asn Asn Met Phe Cys Ala Gly 340 345 350

Phe His Glu Gly Gly Arg Asp Ser Cys Gin Gly Asp Ser Gly Gly Pro 355 360 365

His val Thr Glu val Glu Gly Thr Ser Phe Leu Thr Gly Ile Ile Ser 370 375 380

Trp Gly Glu Glu Cys Ala Met Lys Gly Lys Tyr Gly Ile Tyr Thr Lys 385 390 385 400 val Ser Arg Tyr val Asn Trp Ile Lys Glu Lys Thr Lys Leu Thr 405 410 415

Page 2

MSB7324_ST25 <210> 2 ’ <211> 9 <212> PRT <213> Artificial Sequence <220> <223> Insertion sequence <400> 2

Asn Ser Thr Gln Asp Asn Ile Thr Gln 1 5 <210> 3 <211> 415 <212> PRT <213> Artificial sequence <220> <223> Peptide variant <220> <221> MISC_FEATURE <222> (85)..(85) <223> X is selected from D and E. <220> <221> MISC FEATURE <222> (86)..(86) <223> X is selected from aA, E, P, S, and Vv. <220> <221> MISC_FEATURE <222> (104)..(104) <223> X is selected from D, N, and T. <220> <221> MISC_FEATURE <222> (121)..¢(121) <223> X is selected from N, Q, and T. <220> <221> MISC_FEATURE <222> (138)..(138) <223> X is selected from N, S, and T. <220> <221> MISC_FEATURE <222> (148)..(148) <223> (i) X148 is T and X150 is F; (ii) x148 is N and X150 is T; and (iii) X148 is N and X150 is Ss; <220> <221> MISC_FEATURE <222> (150)..(150) <223> (i) x148 is T and x150 is FE; (ii) X148 is N and X150 is T; and (i414) X148 is N and X150 is S;

Page 3

MSB7324_ST25 <220> <221> MISC_FEATURE <222> (151)..(15D) <223> X is selected from A, P, and T. <220> <221> MISC_FEATURE <222> (151)..(151) <223> (i) X151 is P and X153 is v; (ii) X151 is N and X153 is T; and (iii) Xi51 is N and X153 is Ss. <220> <221> MISC_FEATURE <222> (152)..(152) <223> X is selected from D, N, and T. <220> <221> MISC_FEATURE <222> (153)..(153) <223> (i) X151 is P and X153 is v; (11) X151 is N and X153 is T; and (iii) X151 is N and X153 is s. <220> <221> MISC_FEATURE <222> (159)..(159) <223> (i) x159 is T and xX16l is A; (ii) X159 is N and x161 is T; and (iii) X159 is N and xX161 is Ss. <220> <221> MISC_FEATURE <222> (160)..{164) <223> Z1, ZZ, Z3, and Z4 are independently selected from (i) zero to twelve amino acid residues and (ii) SEQ ID NO: 2; <220> <221> MISC_FEATURE <222> (161)..(161) <223> (1) X159 is T and X161 is A; (ii) X159 is N and X161 is T; and (iii) X159 4s N and X161 is S. <220> <221> MISC_FEATURE <222> (169)..(169) <223> X is selected from T and N. <220> <221> MISC FEATURE <222> (172)..(172) <223> X is selected from C, T, and N. <220> <221> MISC_FEATURE <222> (174)..(174)

Page 4

MSB7324_ST25 <223> X is selected from Ss and T. <220> <221> MISC_FEATURE <222> (177)..(177) <223> (i) X177 is p and X178 is F; (ii) x177 is E and X178 is T; and (iii) X177 is E or b and X178 is S. <220> <221> MISC_FEATURE <222> (178)..(178) <223> (i) X177 is D and x178 is F; (i1) X177 is E and X178 is T; and (i491) X177 4s E or D and X178 is s. <220> <221> MISC_FEATURE <222> (226)..(226) <223> (i) X226 is G and X228 is K; (ii) X226 is N and X228 is T:; and (iii) X226 is N and x228 is Ss. <220> <221> MISC_FEATURE <222> (228)..(228) <223> (i) X226 is G and X228 is K; (i1) X226 is N and X228 is T; and (iii) X226 is N and X228 is S. <220> <221> MISC_FEATURE <222> (338)..(33% <223> X is selected from R and A <220> <221> MISC_FEATURE <222> (353)..(355) <223> (i) X353 is F, X354 is H, X355 is E; (ii) x353 is N, X354 is v, x355 is T; (iii) X353 is N, X354 is TI, X355 is T; and (iv) X353 is N, X354 is H, v, or I, X355 is Ss. : <220> <221> MISC_FEATURE <222> (370)..(372) <223> (i) X370 is v, X371 is T, X372 is E; (i) X370 is N, X371 is Vv, X372 is T; (iii) X370 is N, X371 is I, X372 is T; and (iv) X370 is N, X371 is T, v, or I, X372 is Ss. <220> <221> MISC_FEATURE «222> (391)..(393)

Page 5

} MSB7324_ST25 <223> (i) X391 is M, X392 is K, X393 is G; (ii) X391 is N, X392 is K, X393 is T; (iii) X391 is N, x392 is Vv, x393 is T; and (iv) X391 is N, X392 is V or K, X393 is S. <220> <221> MISC_FEATURE <222> (413)..(414) <223> (1) X413 is K and X414 is L; (ii) X413 is N and x414 is L; and (111) Xx413 is N and X414 is I. <400> 3

Tyr Asn Ser Gly Lys Leu Glu Glu Phe val GIn Gly Asn Leu Glu Arg 1 5 10 15

Glu Cys Met Glu Glu Lys Cys Ser Phe Glu Glu Ala Arg Glu val Phe

Glu Asn Thr Glu Arg Thr Thr Glu Phe Trp Lys Gln Tyr val Asp Gly 40 45

Asp Gln Cys Glu Ser Asn Pro Cys Leu Asn Gly Gly Ser Cys Lys Asp 50 55 60

Asp Ile Asn Ser Tyr Glu Cys Trp Cys Pro Phe Gly Phe Glu Gly Lys 65 70 75 80

Ash Cys Glu Leu Xaa Xaa Thr Cys Asn Ile Lys Asn Gly Arg Cys Glu 85 a0 95

Gln Phe Cys Lys Asn Ser Ala Xaa Asn Lys val val Cys Ser Cys Thr 100 105 110

Glu Gly Tyr Arg Leu Ala Glu Asn Xaa Lys Ser Cys Glu Pro Ala val 115 120 125

Pro Phe Pro Cys Gly Arg val Ser val Xaa GIn Thr Ser Lys Leu Thr 130 135 140

Arg Ala Glu Xaa val Xaa Xaa Xaa Xaa Asp Tyr val Asn Ser Xaa Glu 145 150 155 160

Xaa Glu Thr Ile Leu Asp Asn Ile Xaa GIn Ser Xaa Gln Xaa Phe Asn 165 170 175

Xaa Xaa Thr Arg val val Gly Gly Glu Asp Ala Lys Pro Gly Gin Phe 180 185 190

Pro Trp GIn val val Leu Asn Gly Lys val Asp Ala Phe Cys Gly Gly

Page 6

MSB7324_ST25 195 200 205

Ser Ile val Asn Glu Lys Trp Ile val Thr Ala Ala His Cys val Glu 210 215 220

Thr Xaa val Xaa Ile Thr val val Ala Gly Glu His Asn ITe Glu Glu 225 230 235 240

Thr Glu His Thr Glu Gln Lys Arg Asn val Ile Arg Ile Ile Pro His 245 250 255

His Asn Tyr Asn Ala Ala Ile Asn Lys Tyr Asn His Asp Ile Ala Leu 260 265 270

Leu Glu Leu Asp Glu Pro Leu val Leu Asn Ser Tyr val Thr Pro Ile 275 280 285

Cys Ile Ala Asp Lys Glu Tyr Thr Asn Ile Phe Leu Lys Phe Gly Ser 290 295 300

Gly Tyr val Ser Gly Trp Gly Arg val Phe His Lys Gly Arg Ser Ala 305 310 315 320 teu val Leu Gln Tyr Leu Arg val Pro Leu val Asp Arg Ala Thr Cys 325 330 335

Leu Xaa Ser Thr Lys Phe Thr Ile Tyr Asn Asn Met Phe Cys Ala Gly 340 345 350

Xaa Xaa Xaa Gly Gly Arg Asp Ser Cys Gin Gly Asp Ser Gly Gly Pro 355 360 365

His Xaa Xaa Xaa val Glu Gly Thr Ser phe Leu Thr Gly Ile Ile Ser 370 375 380

Trp Gly Glu Glu Cys Ala Xaa Xaa Xaa Lys Tyr Gly Ile Tyr Thr Lys 385 390 395 400 val Ser Arg Tyr val Asn Trp Ile Lys Glu Lys Thr Xaa Xaa Thr 405 410 415 <210> 4 <211> 5 <212> PRT <213> Artificial sequence <220> <223> Insertion sequence <400> 4

Thr Asn ser Thr Thr 1 5 page 7

MSB7324_ST25 <210> 5 <211> 9 <212> PRT <213> Artificial Sequence <220> <223> Insertion sequence <400> 5

Thr Asn Ser Thr Gln Asn Ile Thr Thr 1 5 <210> 6 <211> 15 <212> PRT <213> Artificial Sequence <220> <223> Insertion sequence <400> 6

Thr Asn Ser Thr Gln Asn Ile Thr Gly Asn Asp Thr Glu Lys Thr 1 5 10 15 <210> 7 <211> 18 <212> PRT <213> Artificial Sequence <220> <223> Insertion sequence <400> 7

Thr Asn Ser Thr Gln Asn Ile Thr Gly Asn Asp Thr Glu Asn Gly Thr 1 5 10 15

Lys Thr <210> 8 <211> 35 <212> DNA <213> Artificial Sequence <220> <223> FIXFl - 5' primer <400> 8 atcataagct tgccaccatg cagcgcgtga acatg 35 <210> 9 <211> 33 <212> DNA <213> Artificial Sequence <220> <223> FIXR3- 3' primer <400> 9

Page 8

MSB7324_5T25 atcataagct tgattagtta gtgagaggcc ctg 33 <210> 10 <211> 54 <212> DNA <213> Artificial Sequence <220> <223> Oligonucleotide sequence <400> 10 ctgctgccca ctgtgttgaa actaacgtta ccattacagt tgtcgcaggt gaac 54 <210> 11 <211l> 71 <212> DNA <213> Artificial Sequence <220> <223> Oligonucleotide sequence <400> 11 caccatctat aacaacatgt tctgtgctgg caacgtgacc ggaggtagag attcatgtca 60 aggagatagt g 71 <210> 12 <211> 73 <212> DNA <213> Artificial Sequence <220> <223> Oligonucleotide sequence <400> 12 gattcatgtc aaggagatag tgggggaccc cataacgtga ccgtggaagg gaccagtttce 60 ttaactggaa tta 73 <210> 13 <211> 69 <212> DNA <213> Artificial Sequence <220> <223> 0Qligonucleotide sequence <400> 13 ggaattatta gctggggtga agagtgtgca aacgtgacca aatatggaat atataccaag 60 gtatcccgg 69 <210> 14 <211> 50 <212> DNA <213> Artificial Sequence <220> <223> oOligonucleotide sequence <400> 14 tcaactggat taaggaaaaa acaaacctca cttaatgaaa gatggattte 50

Page 9

MSB7324_ST25 <210> 15 <211> 55 <212> DNA <213> Artificial Sequence <220> <223> Oligonucleotide sequence <400> 15 ctgatgtgga ctatgtaaat tctactgaaa atgaaaccat tttggataac atcac 55 <210> 16 <211> 47 <212> DNA <213> Artificial sequence <220> <223> Oligonucleotide sequence <400> 16 actcaaagca cccaatcatt taatgagacc actcgggttg ttggtgg 47 <210> 17 <211> 61 <212> DNA <213> Artificial Sequence <220> <223> oligonucleotide sequence <400> 17 acttctaagc tcacccgtgc tgagactgtt tttaatgata cggactatgt aaattctact 60 a 61 <210> 18 <211> 44 <212> DNA <213> Artificial Sequence <220> } <223> Oligonucleotide sequence <400> 18 gaagctgaaa ccattttgga taacatcaat caaagcaccc aatc 44 <210> 19 <211> 47 <212> DNA <213> Artificial Sequence <220> <223> Oligonucleotide sequence <400> 19 attttggata acatcactca aagcaaccaa tcatttaatg acttcac 47 <210> 20 <211> 45 <212> DNA <213> Artificial Sequence

Page 10

MSB7324.5725 <220> <223> Oligonucleotide sequence <400> 20 acttctaage tcacccgtgce tgagaatgtt actcctgatg tggac 45 <210> 21 <211> 57 <212> DNA <213> Artificial Sequence <220> <223> Oligonucleotide sequence <400> 21 gtttttcctg atgtggacta tgtaaattct aatgaaactg aaaccatttt ggataac 57 <210> 22 <211> 47 <212> DNA <213> Artificial Sequence <220> <223> Primer T8216c¢c_g8212a <400> 22 ttctactgaa gctgaaacca ttctagataa catcactcaa agcaccc 47 <210> 23 <211> 45 <212> DNA <213> Artificial sequence <220> <223> Primer T8188c <400> 23 ctatttttcc tgatgtggac tacgtaaatt ctactgaage tgaaa 45 <210> 24 <211> 54 <212> DNA <213> Artificial Sequence <220> <223> 2PrimerF <400> 24 gtaaattcta ctgaagctaa ctccacacag gataatatca cacaagaaac catt 54 <210> 25 <211> 58 <212> DNA <213> Artificial sequence <220> <223> 2PrimerR <400> 25 ctagaatggt ttcttgtgtg atattatcct gtgtggagtt agcttcagta gaatttac 58 <210> 26

Page 11

MSB7324_ST25 <211> 461 <212> PRT <213> Homo sapiens <400> 26

Met Gln Arg val Asn Met Ile Met Ala Glu Ser Pro Gly Leu Ile Thr 1 5 10 15

Ile Cys Leu Leu Gly Tyr Leu Leu Ser Ala Glu Cys Thr val Phe Leu

Asp His Glu Asn Ala Asn Lys Ile Leu Asn Arg Pro Lys Arg Tyr Ash 40 45

Ser Gly Lys Leu Glu Glu Phe val GIn Gly Asn Leu Glu Arg GTu Cys 50 55 60

Met Glu Glu Lys Cys Ser phe Glu Glu Ala Arg Glu val Phe Glu Asn 65 70 75 80

Thr Glu Arg Thr Thr Glu Phe Trp Lys GIn Tyr val Asp Gly Asp Gln 85 90 95

Cys Glu Ser Asn Pro Cys Leu Asn Gly Gly Ser Cys Lys Asp Asp Ile 100 105 110

Asn Ser Tyr Glu Cys Trp Cys Pro Phe Gly phe Glu Gly Lys Asn Cys 115 120 125

Glu Leu Asp val Thr Cys Asn Ile Lys Asn Gly Arg Cys Glu GIn Phe 130 135 140

Cys Lys Asn Ser Ala Asp Asn Lys val val Cys Ser Cys Thr Glu Gly 145 150 155 160

Tyr Arg Leu Ala Glu Asn Gln Lys Ser Cys Glu Pro Ala val Pro Phe 165 170 175

Pro Cys Gly Arg val Ser val Ser GIn Thr Ser Lys Leu Thr Arg Ala 180 185 190

Glu Thr val phe Pro Asp val Asp Tyr val Asn Ser Thr Glu Ala Glu 195 200 205

Thr Ile Leu Asp Asn Ile Thr GIn Ser Thr Gin Ser Phe Asn Asp Phe 210 215 220

Thr Arg val val Gly Gly Glu Asp Ala Lys Pro Gly GIn Phe Pro Trp 225 230 235 240

Gln val val Leu Asn Gly Lys val asp Ala Phe Cys Gly Gly Ser Ile 245 250 255

Page 12

MSB7324_ST25 val Asn Glu Lys Trp Ile val Thr Ala Ala His Cys val Glu Thr Gly 260 265 270 val Lys Ite Thr val val Ala Gly Glu His Asn Ile Glu Glu Thr Glu 275 280 285

His Thr Glu GIn Lys Arg Asn val Ile Arg Ile Ile Pro His His Asn 290 295 300

Tyr Asn Ala Ala Ile Asn Lys Tyr Asn His Asp Ile Ala Leu Leu Glu 305 310 315 320

Leu Asp Glu Pro Leu val Leu Asn Ser Tyr val Thr Pro Ile Cys Ile 325 330 335

Ala Asp Lys Glu Tyr Thr Asn Ile Phe Leu Lys Phe Gly Ser Gly Tyr 340 345 350 val Ser Gly Trp Gly Arg val Phe His Lys Gly Arg Ser Ala Leu val 355 360 365

Leu GIn Tyr Leu Arg val Pro Leu val Asp Arg Ala Thr Cys Leu Arg 370 375 380

Ser Thr Lys Phe Thr Ile Tyr Asn Asn Met Phe Cys Ala Gly Phe His 385 390 395 400

Glu Gly Gly Arg Asp Ser Cys GIn Gly Asp Ser Gly Gly Pro His val 405 410 415

Thr Glu val Glu Gly Thr Ser Phe Leu Thr Gly Ile Tle Ser Trp Gly 420 425 430

Glu Glu Cys Ala Met Lys Gly Lys Tyr Gly Ile Tyr Thr Lys val ser 435 440 445

Arg Tyr val Asn Trp Ile Lys Glu Lys Thr Lys Leu Thr 450 455 460

Page 13

Claims

CLAIMS:

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; VIO7T; K122N; K122T; S138N; A146N; T148N; F150T; PISIN; T159N; A161T; A161IN; TI69N; QL70N; T172N; D177N; DI77E; F178T; K201N; K201T; K214T; V223N; G226N; Y226T; K228N; K228T; E239N, E242N,; [251T; A262T; E294N; R338A; R338N; K341N; F353N; H354V; H3541; E355T; V370N; T371V; T3711; E372T; E374N; M391N; K392V; G393T; E410N; K413N; L414L YIN and S3T; 83N and K5T; G4N and L6T; K5N and E7T; L6N and EST; E/N and FOT; FIN and QLIT; VION and G12T; Q11N and N13T; GI12N and L14T; N13 and EIST; 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 GA8T; ES2N and N54T; S53N and P55T; G59N and 561T; K63N and D65T; 166N and S68T; S68N and E70T; G76N and E78T; E78N and K80T; E§3N and D85T; L.84N and V86T; I190N and N92T; K100N and S102T; S102N and D104T; A103N and N105T; D104N and K106T; K106N and VI08T; R116N and A118T; E119N 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; PI5SIN and V153T; D152N and D154T; V153N and Y155T; D154N and V156T; Y155N and NI157T; V156N and S158T; S158N and E160T; T159N and A161T; E160N and E162T; E162N and 1164T; T163N and L165T; T164N and D166T; L165N and N167T; D166N and [168T; I1168N and Q170T; TI69N and S171T; S171N and Q173T; T172N and S174T; QI73N and F175T; S174N and N176T; G184N and D186T; E185N and A187T; D186N and K188T; A187N and P189T; P18IN and Q191T; G200N and V202T; K20IN and

D203T; V202N and A204T; E224N and G226T; T225N and V227T, G226N and K228T; V227N and 1229T; H236N and 1238T; [238N and E2407; E240N and E242T; T241N and H243T; H243N and E245T; K247N and N249T; V250N and R252T; 1251N and 12537; [253N and P255T; A261N and 1263T; A262N and N264T; D276N and P278T; V280N 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; D85N, K122T, and 1251T; D8SN, Ki22T, and E242N; E125N, P126A, and A127T; P126N, V128T, and P129A; T148N, F150T, and P151A; F1530N, P151A, and D15S2T; P15S1IN, V153T, and A161N; P151N, V133T, and TI72N; VI153N, Y155T, and E294N; T172N, G226N, and K228T; F353N, H354V, and E355T; F353N, H3541, and E355T; V370N, T371V, and E372T; V370N, T3711, and E372T; M391IN, K392V, and G393T; DSSN, P15IN, V153T, and K228N; D&5N, P151N, V153T, and E242N; K122T, P151IN, V153T, and K228N; K122T, P151N, V153T, and E242N; K122T,P15IN, V153T, and 1251T; T148N, Fi150T, G226N, and K228T; P151N, VI53T, T172N, and R338A; PISIN, V153T, DI77E, and F178T; P15IN, V133T, G226N, and K228T; T172N, G226N, K228T, and R338A; D8SN, KI122T, PI51N, VI53T, and E242N; D&5N, P15IN, V153T, G226N, and K228T; K122T, P151IN, V153T, G226N, and K228T; S138N, P15SIN, V153T, G226N, and K228T; T148N, F150T, G226N, K228T, and R338A; PI5IN, VI53T, TI72N, G226N, and K228T; P151N, V153T, DI77E, F178T, and R338A; PISIN, VI53T, G226N, K228T, and R338A; and P151IN, V153T, T172N, G226N, K228T, and R338A,; and any combination thereof,

6. The polypeptide according to any one of claims 1 to 4, wherein ihe one or more amino acid substitutions are selected from R37N; D83N; K122T; S138N; Al46N; Al61N; QI170N; Ti72N; D177N; F178T; K201N; K228N; E239N; E242N; 1251T; A262T; E294N; E374N; E410N; G59N and S61T; K63N and D65T; G76N and E78T; S102N and D104T; A103N and N105T; D104N and K106T; E119N and Q121T; Q121N and S123T; SI36N and S138T; Q139N and S141T; TI40N and K142T; T148N and F150T; V149N and PI51T; 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 [168T; 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 and H243T; [251N and 1253T; 1253N and P255T; A262N and N264T; V280N and N282T; T343N and Y345T; E372N and E3747; D85N, K122T, and E242N; DSN, K122T, and 1251T; F150N, P151A, and D152T; T172N, G226N, and K228T; D85N, P151N, VI53T, and K228N; DSSN, P151N, V153T, and E242N; K122T, P151N, V153T, and K228N; K122T, P15IN, Vi53T, and E242N; K122T, P151N, V153T, and I251T; 151, Vi53T, G226N, and K228T; DSN, K122T, P151N, V153T, and E242N; D85N, P151IN, VIS53T, (G226N, and K228T; SI38N, P151N, V153T, G226N, and K228T; P151IN, VI53T, T172N, (G226N, and K228T.

7. The polypeptide according 1o any ore of clans 1 to 4, wherein the one or more amino acid substitutions are selected from DSN; K122T; §138N; TI72N; K201N; K228N; E239N; E2421; 1251T; A262T; E294N,; G59N and S61T; G76N and E78T; S102N and D104T; ALO3N and N105T; D104N and K106T; E119N and Q121T; Q121IN and S123T; S136N and S138T; Q139N and S141T; T140N and K142T; T148N and F150T; V149N and P151T; P151N and Vi53T; DI52N and D154T; S158N and B160T; E162N and 1164T; TI63N 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; and D85N, K122T, and E242N; D85N, K122T, and 1251T; F150N, P151A, and D152T; T172N, G226N, and K228T; D85N, P151N, V153T, and K228N; D&5N, P1S1IN, V153T, and E242N; K122T, P15IN, VI53T, and K228N; K122T, P151N, V153T, and E242N; K122T, P151IN, V153T, and I1251T; P151, V153T, G226N, and K228T; D85N, K122T, P151N, V153T, and E242N; D85N, P151N, V153T, G226N, and K228T; 8138N, P151IN, V153T, G226N, and K228T; P151N, V153T, T172N, G226N, and K228T.

8. A Factor IX polypeptide comprising the amino acid sequence YNSGKLEEFVQGNLERECMEEKCSFEEAREVFENTERTTEFWEQYVDGDQCE SNPCLNGGSCKDDINSYECWCPFGFEGKNCEL Xs Xo TCNIKNGRCEQFCKNSA XiuNKVVCSCTEGYRLAENX; KSCEPAVPFPCGRVSVX 5:QTSKLTRAEX 14s V XisoX15:X150X153DYVNSX5eEZ1 X16: Zo EZ TZILDNIX 1 60QS8 Xi: 72QX 1aFNX 77X75 TR VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVET X02 VXans ITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNS YVTPICIADKEYTNIFLKEGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATC LX33sSTKFTIYNNMFCAGX 553 X35 X35: GGRDSCQGDSGGPHX 370X371 Xan VEGTSFE LTGIISWGEECAX 301 X30: X50: KYGIYTKVSRYVNWIKE KTX, 3X01. T (SEQ ID NO: 3);

wherein Xgs is selected from D and E; wherein Xs is selected from A, E, P, §, and V; wherein Xo. is selected from D, N, and T; wherein Xa; is selected from N, Q, and T; wherein X15 is selected from N, S, and T; wherein X45 and Xs are selected from:

(1) Xugis Tand Xjspis F;

(ii) Xusis Nand Xis018 T; and

(iii) Xias 1s N and Xiso is S; wherein Xs; is selected from A, P, and T; wherein Xs; and Xs, are selected from:

O Xis1 is P and Xis3 is V;

(ii) Xis) 15 N and Xs is T; and

(iii) Xist is N and Xis3 is S; wherein Z,, Zy, Zs, and Z,4 are independently selected from

{i} zero to twelve amino acid residues and

(ii) SEQIDNO:2; wherein Xs» is selected from D, N, and T; wherein X so and X4; are selected from:

(i) Kiso is T and Kiss 18 A;

(ii) Kiso is N and Xisi is TT; and

(iti) Kiso is N and Xia) is S; wherein X40 is selected from T and N; wherein X41, is selected from T and N: wherein Xz, is selected from S and T; wherein X,; and X75 are selected from:

(i) XymisDand X5sis TF,

(ii) Xy7isE and X 751s T; and

(itl) X;yisEorDand Xj55is S; wherein Xs» and Xaag are selected from:

(i) Xso6 is G and Kang 18 K;

(ii) Kagis Nand Xyegis T; and (iil) Kaze is Nand Xie is S; wherein X35 is selected from R and A; wherein Xaiss, Xasq, and x1ss are selected from; (i) KisnisF,Xanis H, Xsssis Ej an Kis is N, Kissa is V, Kiss is T; (iii) Kas is N, Kissa is I, Xass is T; and (iv) Kaisa is N, Kaisa is H, V, or I, Kiss is S; wherein Xsq0, Xs71, and Xs, are selected from: (i) XapisV, X37 i8T, Xan is E; (if) XzisN, X37 18 V, Xn is T; (iii) X90 is N, Xan is I, Xin is T; and (iv) XewisN, XagnisT,V, orl, Xsn is S; wherein Xag,, Xap, and Xie; are selected from: (i) Kao is M, Kaa is K, X303 18 Gy (ii) Xag is N, Xio0z is K, Xsoz is T; (iii) X30 18 N, Xam i8 V, Xi03 is T and (Gv) X391isN, X392isVorK, X393 is S; wherein Xu; and X44 are selected from: (i) XypisKandXy,isL; (i) XuaisNand Xay4isL; and (ii) XsaisNandXy., isl; and wherein the FIX polypeptide comprises at least one introduced glycosylation siic as compared to the FIX polypeptide having SEQ ID NO: 1.

9S. 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 ¢laiins 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.

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 infroducing 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 1 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 1 fo 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 cne of claims 1-18 and a pharmaceutically acceptable carrier.

20. The pharmaceutical preparation of claim 19 for freating hemophilia B.

21. Use of the pharmaceutical preparation of claim 19 in the manufacture of a medicament for treating hemophilia B.

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

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

24. 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.