Coagulation factor ix compositions and methods of making and using same

Abstract

The present invention relates to compositions comprising factor IX coagulation factors linked to extended recombinant polypeptide (XTEN), isolated nucleic acids encoding the compositions and vectors and host cells containing the same, and methods of making and using such compositions in treatment of coagulation factor-related diseases, disorders, and conditions.

What is claimed is: 
     
         1 . An isolated factor VII polypeptide comprising an extended recombinant polypeptide (XTEN), said XTEN comprising at least 200 amino acid residues, wherein said factor IX polypeptide exhibits a terminal half-life that is longer than about 12 hours when administered to a subject. 
     
     
         2 . The isolated factor IX polypeptide of  claim 1 , wherein the factor IX polypeptide exhibits at least 90% sequence identity compared to a sequence selected from Table 2 when optimally aligned. 
     
     
         3 . The isolated factor IX polypeptide of  claim 1  or  2 , wherein said factor VII is linked at its C-terminus to the XTEN. 
     
     
         4 . The isolated factor IX polypeptide of  claim 1  that is linked to the XTEN via a cleavage sequence that is cleavable by a mammalian protease selected from the group consisting of factor XIa, factor XIIa, kallikrein, factor VIIa, factor IXa, factor Xa, factor IIa (thrombin), Elastase-2, MMP-12, MMP13, MMP-17 and MMP-20. 
     
     
         5 . The isolated factor IX polypeptide of  claim 4 , wherein cleavage at the cleavage sequence by the mammalian protease releases said XTEN from said factor IX polypeptide. 
     
     
         6 . The isolated factor IX polypeptide of  claim 1 , wherein said XTEN is characterized in that:
 (a) the cumulative total of XTEN amino acid residues is greater than 200 to about 3000 amino acid residues:   (b) the sum of asparagine and glutamine residues is less than 10% of the total amino acid sequence of the XTEN;   (c) the sum of methionine and tryptophan residues is less than 2% of the total amino acid sequence of the XTEN;   (d) the XTEN sequence has a subsequence score less than 10;   (e) the XTEN sequence has greater than 90% random coil formation as determined by GOR algorithm; and   (f) the XTEN sequence has less than 2% alpha helices and 2% beta-sheets as determined by Chou-Fasman algorithm.   
     
     
         7 . The isolated factor IX polypeptide of  claim 1  exhibiting an apparent molecular weight factor of at least about 4. 
     
     
         8 . The isolated factor IX polypeptide of  claim 1 , wherein said XTEN exhibits at least 90% sequence identity to a comparable length of an amino acid sequence selected from Table 4, Table 9, Table 10, Table 11, Table 12, or Table 13. 
     
     
         9 . The isolated factor IX polypeptide of  claim 1  that is configured according to formula VII:
   (Gla)-(XTEN) u -(EGF1)-(XTEN) v -(EGF2)-(AP1)-(XTEN) w -(AP2)-(XTEN) x -(Pro)-(S) y -(XTEN) z   VII
 
 
       wherein independently for each occurrence,
 (a) Gla is a Gla domain of factor IX; 
 (b) EGF1 is an EGF1 domain of factor IX; 
 (c) EGF2 is an EFG2 domain of factor IXI; 
 (d) AP1 is a portion of an activator peptide domain of factor IX; 
 (e) AP2 is a portion of an activator peptide domain of factor IX that includes at least a first cleavage sequence; 
 (f) PRO is a protease domain of factor IX; 
 (g) S is a spacer sequence having between 1 to about 50 amino acid residues that can optionally include a cleavage sequence; 
 (h) XTEN is an extended recombinant polypeptide that exhibits at least 90% sequence identity to a comparable length of an amino acid sequence selected from Table 4, Table 9, Table 10, Table 11, Table 12, or Table 13, 
 (i) u is either 0 or 1; 
 (j) v is either 0 or 1; 
 (k) x is either 0 or 1; 
 (l) y is either 0 or 1; and 
 (m) z is either 0 or 1, with the proviso that u+v+x+y+z≧1. 
 
     
     
         10 . The isolated factor IX polypeptide of  claim 9 , wherein y=1 and S comprises a cleavage sequence that is cleavable by a mammalian protease selected from the group consisting of FXIa, FXIIa, kallikrein, FVIIa, FIXa, FXa, FIIa (thrombin), Elastase-2, MMP-12, MMP13, MMP-17 and MMP-20. 
     
     
         11 . The isolated factor IX polypeptide of  claim 1  comprising more than one XTEN. 
     
     
         12 . The isolated factor IX polypeptide of  claim 1 , wherein said XTEN is incorporated between any two adjacent domains contained in said factor IX, wherein said two adjacent domains are selected from the group consisting of Gla, EGF1, EGF2, AP, and peptidase S1 (Pro). 
     
     
         13 . The isolated factor IX polypeptide of  claim 1 , characterized in that:
 (i) it has a longer terminal half-life when administered to a mammal compared to the corresponding factor IX that lacks the XTEN when administered to a mammal at a comparable molar dose;   (ii) when a smaller molar amount of the factor IX polypeptide is administered to a mammal in comparison to the corresponding factor IX that lacks the XTEN administered to a mammal under an otherwise equivalent dose regimen, the factor IX polypeptide achieves a comparable area under the curve (AUC) as the corresponding factor IX that lacks the XTEN;   (iii) when a smaller molar amount of the factor IX polypeptide is administered to a mammal in comparison to the corresponding factor IX that lacks the XTEN administered to a mammal under an otherwise equivalent dose regimen, the factor IX polypeptide achieves a comparable therapeutic effect as the corresponding factor IX that lacks the XTEN;   (iv) when the factor IX polypeptide is administered to a mammal less frequently in comparison to the corresponding factor IX that lacks the XTEN administered to a mammal using an otherwise equivalent molar amount, the factor IX polypeptide achieves a comparable area under the curve (AUC) as the corresponding factor IX that lacks the XTEN;   (v) when the factor IX polypeptide is administered to a mammal less frequently in comparison to the corresponding factor IX that lacks the XTEN administered to a mammal using an otherwise equivalent molar amount, the factor IX polypeptide achieves a comparable therapeutic effect as the corresponding factor IX that lacks the XTEN;   (vi) when an accumulatively smaller molar amount of the factor IX polypeptide is administered to a mammal in comparison to the corresponding factor IX that lacks the XTEN administered to a mammal under an otherwise equivalent dose period, the factor IX polypeptide achieves comparable area under the curve (AUC) as the corresponding factor IX that lacks the XTEN; or   (vii) when an accumulatively smaller molar amount of the factor IX polypeptide is administered to a mammal in comparison to the corresponding factor IX that lacks the XTEN administered to a mammal under an otherwise equivalent dose period, the factor IX polypeptide achieves comparable therapeutic effect as the corresponding factor IX that lacks the XTEN.   
     
     
         14 . A method of treating coagulopathy in a subject, comprising administering to said subject a composition comprising a therapeutically effective amount of the factor IX polypeptide of any of  claim 1 . 
     
     
         15 . The method of  claim 14 , wherein said coagulopathy is hemophilia B. 
     
     
         16 . A method of treating a bleeding episode in a subject comprising administering to said subject a composition comprising a therapeutically effective amount of the factor IX polypeptide of  claim 1 . 
     
     
         17 . A method of treating a subject deficient in a clotting protein, comprising: administering to said subject a composition comprising a therapeutically effective amount of the factor IX of any of  claim 1 . 
     
     
         18 . The method of  claim 17 , wherein the clotting protein substitutes wildtype factor VII, factor IX, or factor XI.