Compositions and methods for inhibiting expression of klf-1 and bcl11a genes

1. A double-stranded ribonucleic acid (dsRNA) for inhibiting expression of BCL11A, wherein said dsRNA comprises a sense strand and an antisense strand, wherein said antisense strand comprises a region of complementarity to a BCL11A variant RNA transcript consisting of SEQ ID NO:667 or SEQ ID NO:633, and wherein said dsRNA comprises at least one modified nucleotide.

2. The dsRNA of claim 1 , wherein the sense strand consists of the sequence of SEQ ID NO:666 or SEQ ID NO:632.

3. The dsRNA of claim 1 , wherein at least one of said modified nucleotide is chosen from: a 2′-O-methyl modified nucleotide, a nucleotide comprising a 5′-phosphorothioate group, or a terminal nucleotide linked to a cholesteryl derivative or dodecanoic acid bisdecylamide group.

4. The dsRNA of claim 1 , wherein said modified nucleotide is chosen from: a 2′-deoxy-2′-fluoro modified nucleotide, a 2′-deoxy-modified nucleotide, a locked nucleotide, an abasic nucleotide, 2′-amino-modified nucleotide, 2′-alkyl-modified nucleotide, morpholino nucleotide, a phosphoramidate, or a non-natural base comprising nucleotide.

5. The dsRNA of claim 1 , wherein the antisense strand has a region of complementarity to a BCL11A variant transcript of at least 17 nucleotides in length.

6. The dsRNA of claim 5 , wherein the region of complementarity is between 19 and 21 nucleotides in length.

7. The dsRNA of claim 1 , wherein the sense strand is no more than 30 nucleotides in length.

8. The dsRNA of claim 1 , wherein at least one strand comprises a 3′ overhang of at least 1 or 2 nucleotides.

9. The dsRNA of claim 1 , further comprising a ligand.

10. The dsRNA of claim 9 , wherein the ligand is conjugated to the 3′ end of the sense strand of the dsRNA.

11. The dsRNA of claim 7 , wherein the sense strand is between 19 and 24 nucleotides in length.

12. A cell containing the dsRNA of claim 1 .

13. A pharmaceutical composition for inhibiting expression of a BCL11A gene comprising the dsRNA of claim 1 .

14. The pharmaceutical composition of claim 13 , further comprising a lipid formulation.

15. The pharmaceutical composition of claim 14 , wherein the lipid formulation is a MC3 formulation.

16. A method of inhibiting BCL11A expression in a cell, the method comprising:

(a) introducing into the cell the dsRNA of claim 1 ; and

(b) maintaining the cell produced in step (a) for a time sufficient to obtain degradation of the mRNA transcript of a BCL11A gene, thereby inhibiting expression of the BCL11A gene, or a combination thereof, in the cell.

17. The method of claim 16 , wherein the cell is present in a subject in need of treatment, prevention and/or management of a hemoglobinopathy.

18. The method of claim 16 , wherein the BCL11A expression is inhibited by at least 30%.

19. The method of claim 16 , wherein the dsRNA of claim 1 has an IC 50 in the range of 0.001-7 nM.

20. A method of treating a disorder mediated by BCL11A expression comprising administering to a human in need of such treatment a therapeutically effective amount of the dsRNA of claim 1 .

21. The method of claim 20 , wherein the human is at risk, or is diagnosed with a hemoglobinopathy chosen from a β-hemoglobinopathy, sickle cell disease, or a β-thalassemia.

22. A methods for increasing fetal hemoglobin levels in an erythroid cell, comprising contacting the cell with one or more of the dsRNA of claim 1 , in an amount effective to increase fetal hemoglobin levels in the cell, or its progeny.

23. The method of claim 22 , wherein the cell is present in a subject at risk of having or having a β-hemoglobin disorders, sickle cell anemia or β-thalassemia.

24. A method for decreasing β-globin levels in an erythroid cell, comprising contacting the cell with one or more of the dsRNA of claim 1 , in an amount effective to reduce expression of BCL11A, thereby decreasing the expression of β-globin in the cell, or its progeny.

25. The method of claim 24 , wherein the dsRNA is administered at a concentration of 0.01 mg/kg-5 mg/kg bodyweight of the subject.

26. A vector encoding the dsRNA of claim 1 .

27. A cell comprising the vector of claim 26 .

28. The dsRNA of claim 1 , wherein at least one end of the dsRNA is blunt.

29. The dsRNA of claim 1 , wherein the dsRNA comprises a duplex region between 15-30 base pairs.

30. The dsRNA of claim 9 , wherein the ligand is a cell or tissue targeting group chosen from a lectin, a glycoprotein, a lipid, or an antibody that binds to a specified cell type.

31. The dsRNA of claim 9 , wherein the ligand is a multivalent galactose, N-acetyl-galactosamine, an N-acetyl-galacosamine multivalent mannose, or a cholesterol.

32. A double-stranded ribonucleic acid (dsRNA) for inhibiting expression of BCL11A, wherein said dsRNA comprises a sense strand sequence consisting of SEQ ID NO:626 and an antisense strand sequence consisting of SEQ ID NO:627.

33. The dsRNA of claim 32 , further comprising a ligand.

34. The dsRNA of claim 33 , wherein the ligand is conjugated to the 3′ end of the sense strand of the dsRNA.

35. The dsRNA of claim 33 , wherein the ligand is a cell or tissue targeting group chosen from a lectin, a glycoprotein, a lipid, or an antibody that binds to a specified cell type.

36. The dsRNA of claim 33 , wherein the ligand is a multivalent galactose, N-acetyl-galactosamine, an N-acetyl-galacosamine multivalent mannose, or a cholesterol.

37. A cell containing the dsRNA of claim 32 .

38. A pharmaceutical composition for inhibiting expression of a BCL11A gene comprising the dsRNA of claim 32 .

39. The pharmaceutical composition of claim 38 , further comprising a lipid formulation.

40. The pharmaceutical composition of claim 39 , wherein the lipid formulation is a MC3 formulation.

41. A vector encoding the dsRNA of claim 32 .

42. A cell comprising the vector of claim 41 .

43. The dsRNA of claim 1 , wherein the antisense strand consists of SEQ ID NO:627.

44. The dsRNA of claim 1 , wherein the antisense strand consists of SEQ ID NO:639.