Sterol regulatory element binding protein (SREBP) chaperone (SCAP) iRNA compositions and methods of use thereof

1. A double stranded ribonucleic acid (RNAi) agent for inhibiting expression of a sterol regulatory element binding protein (SREBP) chaperone (SCAP) gene, wherein the dsRNA agent comprises a sense strand and an antisense strand forming a double stranded region, and

wherein the antisense strand comprises a region of complementarity to an mRNA encoding SCAP, wherein the region of complementarity comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from nucleotides 1132-1156 of SEQ ID NO:1.

2. The double stranded RNAi agent of claim 1 , wherein the double stranded RNAi agent comprises at least one modified nucleotide.

3. The double stranded RNAi agent of claim 2 , wherein at least one of the modified nucleotides is selected from the group consisting of a deoxy-nucleotide, a 3′-terminal deoxy-thymine (dT) nucleotide, a 2′-O-methyl modified nucleotide, a 2′-fluoro modified nucleotide, a 2′-deoxy-modified nucleotide, a locked nucleotide, an unlocked nucleotide, a conformationally restricted nucleotide, a constrained ethyl nucleotide, an abasic nucleotide, a 2′-amino-modified nucleotide, a 2′-O-allyl-modified nucleotide, 2′-C-alkyl-modified nucleotide, 2′-hydroxly-modified nucleotide, a 2′-methoxyethyl modified nucleotide, a 2′-O-alkyl-modified nucleotide, a morpholino nucleotide, a phosphoramidate, a non-natural base comprising nucleotide, a tetrahydropyran modified nucleotide, a 1,5-anhydrohexitol modified nucleotide, a cyclohexenyl modified nucleotide, a nucleotide comprising a 5′-phosphorothioate group, a nucleotide comprising a 5′-methylphosphonate group, a nucleotide comprising a 5′ phosphate or 5′ phosphate mimic, a nucleotide comprising vinyl phosphate, a nucleotide comprising adenosine-glycol nucleic acid (GNA), a nucleotide comprising thymidine-glycol nucleic acid (GNA) S-Isomer, a nucleotide comprising 2-hydroxymethyl-tetrahydrofurane-5-phosphate, a nucleotide comprising 2′-deoxythymidine-3′phosphate, a nucleotide comprising 2′-deoxyguanosine-3′-phosphate, and a terminal nucleotide linked to a cholesteryl derivative and a dodecanoic acid bisdecylamide group.

4. The double stranded RNAi agent of claim 2 , further comprising at least one phosphorothioate internucleotide linkage.

5. The double stranded RNAi agent of claim 1 , wherein the region of complementarity is at least 17 nucleotides in length; 19-23 nucleotides in length; or 19 nucleotides in length.

6. The double stranded RNAi agent of claim 1 , wherein each strand is no more than 30 nucleotides in length.

7. The double stranded RNAi agent of claim 1 , wherein at least one strand comprises a 3′ overhang of at least 1 nucleotide; or a 3′ overhang of at least 2 nucleotides.

8. The double stranded RNAi agent of claim 1 , wherein the double stranded RNAi agent further comprises a ligand.

9. The double stranded RNAi agent of claim 8 , wherein the ligand is

10. The double stranded RNAi agent of claim 8 , wherein the double stranded RNAi agent is conjugated to the ligand as shown in the following schematic

and, wherein X is O or S.

11. The double stranded RNAi agent of claim 10 , wherein the X is O.

12. The double stranded RNAi agent of claim 8 , wherein the ligand is a cholesterol.

13. A double stranded ribonucleic acid (RNAi) agent for inhibiting expression of a sterol regulatory element binding protein (SREBP) chaperone (SCAP) gene, wherein said double stranded RNAi agent comprises a sense strand complementary to an antisense strand, wherein said antisense strand comprises a region complementary to nucleotides 1132-1156 of SEQ ID NO:1, wherein each strand is about 14 to about 30 nucleotides in length, wherein said double stranded RNAi agent is represented by formula (III):

sense:5′n p -N a -(XXX) i -N b -YYY-N b -(ZZZ) i -N a -n q 3′

antisense:3′n p ′-N a ′-(X′X′X′) k -N b ′-Y′Y′Y′-N b ′-(Z′Z′Z′) l —N a ′-n q ′5′  (III)

wherein:

j, k, and 1 are each independently 0 or 1;

p, p′, q, and q′ are each independently 0-6;

each N a and N a ′ independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified nucleotides;

each N b and N b ′ independently represents an oligonucleotide sequence comprising 0-10 nucleotides which are either modified or unmodified or combinations thereof;

each n p , n p ′, n q , and n q ′, each of which may or may not be present, independently represents an overhang nucleotide;

XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides;

modifications on N b differ from the modification on Y and modifications on N b ′ differ from the modification on Y′; and

wherein the sense strand is conjugated to at least one ligand.

14. The double stranded RNAi agent of claim 13 , wherein formula (III) is represented by formula (Ma):

sense: 5′ n p -N a -YYY-N a -n q 3′

antisense: 3′ n p ′-N a ′-Y′Y′Y′-N a ′-n q ′5′  (IIIa);

wherein formula (III) is represented by formula (IIIb):

sense: 5′n p -N a -YYY-N b -ZZZ-N a -n q 3′

antisense: 3′n p ′-N a ′-N a ′-n q ′5′  (IIIb)

wherein each N b and N b ′ independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides;

wherein formula (III) is represented by formula (IIIc):

sense: 5′n p -N a XXX-N b -YYY-N a -n q 3′

antisense: 3′ n p ′-N a ′-X′X′X′-N b ′-Y′Y′Y′-N a ′-n q ′5′  (IIIc)

wherein each N b and N b ′ independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides; or

wherein formula (III) is represented by formula (Ind):

sense: 5′n p -N a -XXX-N b -YYY-N b -ZZZ-N a -n q 3′

antisense: 3′n p ′-N a ′-X′X′X′-N b ′-Y′Y′Y′-N b ′-Z′Z′Z′-N a ′-n q ′5′  (IIId)

wherein each N b and N b ′ independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides and each N a and N a ′ independently represents an oligonucleotide sequence comprising 2-10 modified nucleotides.

15. The double stranded RNAi agent of claim 13 , wherein the double stranded region is 15-30 nucleotide pairs in length; 17-23 nucleotide pairs in length; 17-25 nucleotide pairs in length; 23-27 nucleotide pairs in length; 19-21 nucleotide pairs in length; or 21-23 nucleotide pairs in length.

16. The double stranded RNAi agent of claim 13 , wherein the modifications on the nucleotides are selected from the group consisting of LNA, HNA, CeNA, 2′-methoxyethyl, 2′-O-alkyl, 2′-O-allyl, 2′-C-allyl, 2′-fluoro, 2′-deoxy, 2′-hydroxyl, and combinations thereof.

17. The double stranded RNAi agent of claim 13 , wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker; or a cholesterol.

18. The double stranded RNAi agent of claim 13 , wherein said agent further comprises at least one phosphorothioate or methylphosphonate internucleotide linkage.

19. A cell containing the double stranded RNAi agent of claim 1 or 13 .

20. A pharmaceutical composition for inhibiting expression of a SCAP gene comprising the double stranded RNAi agent of claim 1 .

21. A method of inhibiting for inhibiting expression of a sterol regulatory element binding protein (SREBP) chaperone (SCAP) gene in a cell, the method comprising:

(a) contacting the cell with the double stranded RNAi agent of claim 1 or the pharmaceutical composition of claim 20 ; and

(b) maintaining the cell produced in step (a) for a time sufficient to obtain degradation of the mRNA transcript of a SCAP gene, thereby inhibiting expression of the SCAP gene in the cell.

22. The method of claim 21 , wherein said cell is within a subject.

23. The method of claim 22 , wherein the subject is a human.

24. The method of claim 23 , wherein the human subject suffers from a SCAP-associated disorder.

25. The method of claim 24 , wherein the SCAP-associated disease is nonalcoholic fatty liver disease (NAFLD; fatty liver (steatosis); or nonalcoholic steatohepatitis (NASH).

26. The method of claim 21 , wherein the SCAP expression is inhibited by at least about 30%.

27. A method of treating a subject having a disorder that would benefit from a reduction in SCAP expression, comprising administering to the subject a therapeutically effective amount of the double stranded RNAi agent of claim 1 or the pharmaceutical composition of claim 20 , thereby treating said subject.

28. The method of claim 27 , wherein the subject suffers from a SCAP-associated disorder.

29. The method of claim 27 , wherein the subject is a human.

30. The method of claim 28 , wherein the SCAP-associated disease is nonalcoholic fatty liver disease (NAFLD); fatty liver (steatosis); nonalcoholic steatohepatitis (NASH).

31. The method of claim 27 , wherein the SCAP expression is inhibited by at least about 30%.

32. The method of claim 27 , further comprising administering an additional therapeutic agent to the subject.

33. The method of claim 27 , wherein the double stranded RNAi agent is administered at a dose of about 0.01 mg/kg to about 50 mg/kg.

34. The method of claim 27 , wherein the double stranded RNAi agent is administered to the subject subcutaneously.

35. The method of claim 27 , wherein the administration of the double stranded RNAi to the subject causes a decrease in one or more serum lipid and a decrease in SCAP protein accumulation; PNPLA3 protein accumulation; or SREBP double stranded RNAi accumulation.

36. A kit for inhibiting expression of a SCAP gene , comprising

a) the double stranded RNAi agent of claim 1 or 13 , and

b) instructions for use, and

c) optionally, means for administering the double stranded RNAi agent to the subject.

37. The double stranded RNAi agent of claim 1 , wherein the antisense strand comprises the nucleotide sequence 5′-UAUGUAGGCAAACAAGAUGAUGU-3′ (SEQ ID NO:194).

38. The double stranded RNAi agent of claim 1 , wherein the antisense strand comprises the nucleotide sequence 5′-UAGAUGUAGGCAAACAAGAUGAU-3′ (SEQ ID NO:196).

39. The double stranded RNAi agent of claim 1 , wherein the antisense strand comprises the nucleotide sequence 5′-AGUAGAUGUAGGCAAACAAGAUG-3′ (SEQ ID NO:198).

40. The double stranded RNAi agent of claim 37 , wherein the sense strand comprises the nucleotide sequence 5′-AUCAUCUUGUUUGCCUACAUA-3′ (SEQ ID NO:193) and the antisense strand comprises the nucleotide sequence 5′-UAUGUAGGCAAACAAGAUGAUGU-3′ (SEQ ID NO:194).

41. The double stranded RNAi agent of claim 38 , wherein the sense strand comprises the nucleotide sequence 5′-CAUCUUGUUUGCCUACAUCUAA-3′ (SEQ ID NO:195) and the antisense strand comprises the nucleotide sequence 5′-UAGAUGUAGGCAAACAAGAUGAU-3′ (SEQ ID NO:196).

42. The double stranded RNAi agent of claim 39 , wherein the sense strand comprises the nucleotide sequence 5′-UCUUGUUUGCCUACAUCUACU-3′ (SEQ ID NO:197) and the antisense strand comprises the nucleotide sequence 5′-AGUAGAUGUAGGCAAACAAGAUG-3′ (SEQ ID NO:198).

43. The double stranded RNAi agent of claim 8 , wherein the ligand is an N-acetylgalactosamine (GalNAc) derivative conjugated to the 3′ end of the sense strand through a monovalent or branched bivalent or trivalent linker.

44. A pharmaceutical composition for inhibiting expression of a SCAP gene comprising the double stranded RNAi agent of claim 13 .

45. A method of inhibiting for inhibiting expression of a sterol regulatory element binding protein (SREBP) chaperone (SCAP) gene in a cell, the method comprising:

(a) contacting the cell with the double stranded RNAi agent of claim 13 or the pharmaceutical composition of claim 44 ; and

(b) maintaining the cell produced in step (a) for a time sufficient to obtain degradation of the mRNA transcript of a SCAP gene, thereby inhibiting expression of the SCAP gene in the cell.

46. The method of claim 45 , wherein said cell is within a subject.

47. The method of claim 46 , wherein the subject is a human.

48. The method of claim 47 , wherein the human subject suffers from a SCAP-associated disorder.

49. The method of claim 48 , wherein the SCAP-associated disease is nonalcoholic fatty liver disease (NAFLD; fatty liver (steatosis); or nonalcoholic steatohepatitis (NASH).

50. The method of claim 45 , wherein the SCAP expression is inhibited by at least about 30%.

51. A method of treating a subject having a disorder that would benefit from a reduction in SCAP expression, comprising administering to the subject a therapeutically effective amount of the double stranded RNAi agent of claim 13 or the pharmaceutical composition of claim 44 , thereby treating said subject.

52. The method of claim 51 , wherein the subject suffers from a SCAP-associated disorder.

53. The method of claim 51 , wherein the subject is a human.

54. The method of claim 52 , wherein the SCAP-associated disease is nonalcoholic fatty liver disease (NAFLD); fatty liver (steatosis); nonalcoholic steatohepatitis (NASH).

55. The method of claim 51 , wherein the SCAP expression is inhibited by at least about 30%.

56. The method of claim 51 , further comprising administering an additional therapeutic agent to the subject.

57. The method of claim 51 , wherein the double stranded RNAi agent is administered at a dose of about 0.01 mg/kg to about 50 mg/kg.

58. The method of claim 51 , wherein the double stranded RNAi agent is administered to the subject subcutaneously.

59. The method of claim 51 , wherein the administration of the double stranded RNAi to the subject causes a decrease in one or more serum lipid and a decrease in SCAP protein accumulation; PNPLA3 protein accumulation; or SREBP double stranded RNAi accumulation.