Compositions and methods for modulation of SMN2 splicing in a subject

• US 9,717,750 B2
• Filed: 02/09/2015
• Issued: 08/01/2017
• Est. Priority Date: 06/17/2009
• Status: Active Grant

• Current Assignee: Biogen MA Inc. (Biogen, Inc.), Cold Spring Harbor Laboratory
• Original Assignee: Biogen MA Inc. (Biogen, Inc.), Cold Spring Harbor Laboratory
• Inventors: Bennett, C. Frank, Krainer, Adrian R., Shihabuddin, Lamya, Cheng, Seng H., Hua, Yimin, Passini, Marco A., Klinger, Katherine W., Rigo, Frank, Hung, Gene
• Primary Examiner(s): McGarry, Sean
• Application Number:
  US14/617,388
• Publication Number:
  US 20170015995A1
• Time in Patent Office: 904 Days
• Field of Search: None
• CPC Class Codes: A61K 31/7088 Compounds having three or more nucleosides or nucleotides
• CPC Class Codes: A61K 31/712 Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose
• CPC Class Codes: A61P 11/00 Drugs for disorders of the respiratory system
• CPC Class Codes: A61P 21/00 Drugs for disorders of the muscular or neuromuscular system
• CPC Class Codes: A61P 21/02 Muscle relaxants, e.g. for tetanus or cramps
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 25/02 for peripheral neuropathies
• CPC Class Codes: A61P 25/28 for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/3525 MOE, methoxyethoxy
• CPC Class Codes: C12N 2320/32 Special delivery means, e.g. tissue-specific
• CPC Class Codes: C12N 2320/33 Alteration of splicing

Abstract

Disclosed herein are compounds, compositions and methods for modulating splicing of SMN2 mRNA in a subject. Also provided are uses of disclosed compounds and compositions in the manufacture of a medicament for treatment of diseases and disorders, including spinal muscular atrophy.

Claims

1. A method comprising administering by a bolus injection into the intrathecal space of a human subject having type II spinal muscular atrophy (SMA) an antisense compound comprising an antisense oligonucleotide consisting of 18 linked nucleosides, wherein the oligonucleotide has a nucleobase sequence consisting of the nucleobase sequence SEQ ID NO:

1, wherein each internucleoside linkage of the oligonucleotide is a phosphorothioate linkage, wherein each nucleoside of the oligonucleotide is a 2′

-MOE nucleoside, and wherein the administering of the antisense compound ameliorates at least one symptom of SMA in the human subject.

2. The method of claim 1, wherein the antisense compound is administered at a dose from 0.01 to 10 milligrams of antisense compound per kilogram of body weight of the subject.

3. The method of claim 1, wherein inclusion of exon 7 of SMN2 mRNA in a motoneuron in the subject is increased.

4. The method of claim 1, wherein a 5 mg to 20 mg dose of the antisense compound is administered.

5. The method of claim 1, wherein a first dose of the antisense compound is administered when the subject is from 1 to 2 years of age.

6. The method of claim 1, wherein a first dose of the antisense compound is administered when the subject is from 1 to 15 years of age.

7. The method of claim 4, wherein a first dose of the antisense compound is administered when the subject is from 1 to 2 years of age.

8. The method of claim 4, wherein a first dose of the antisense compound is administered when the subject is from 1 to 15 years of age.

9. The method of claim 1, wherein inclusion of exon 7 amino acids in SMN2 polypeptide in a motoneuron in the subject is increased.

10. The method of claim 4, wherein inclusion of exon 7 amino acids in SMN2 polypeptide in a motoneuron in the subject is increased.

11. A method comprising administering by a bolus injection into the intrathecal space of a human subject having type III spinal muscular atrophy (SMA) an antisense compound comprising an antisense oligonucleotide consisting of 18 linked nucleosides, wherein the oligonucleotide has a nucleobase sequence consisting of the nucleobase sequence SEQ ID NO:

1, wherein each internucleoside linkage of the oligonucleotide is a phosphorothioate linkage, wherein each nucleoside of the oligonucleotide is a 2′

-MOE nucleoside, and wherein the administering of the antisense compound ameliorates at least one symptom of SMA in the human subject.

12. The method of claim 11, wherein the antisense compound is administered at a dose from 0.01 to 10 milligrams of antisense compound per kilogram of body weight of the subject.

13. The method of claim 11, wherein inclusion of exon 7 of SMN2 mRNA in a motoneuron in the subject is increased.

14. The method of claim 11, wherein a 5 mg to 20 mg dose of the antisense compound is administered.

15. The method of claim 11, wherein a first dose of the antisense compound is administered when the subject is from 1 to 2 years of age.

16. The method of claim 11, wherein a first dose of the antisense compound is administered when the subject is from 1 to 15 years of age.

17. The method of claim 14, wherein a first dose of the antisense compound is administered when the subject is from 1 to 2 years of age.

18. The method of claim 14, wherein a first dose of the antisense compound is administered when the subject is from 1 to 15 years of age.

19. The method of claim 11, wherein inclusion of exon 7 amino acids in SMN2 polypeptide in a motoneuron in the subject is increased.

20. The method of claim 14, wherein inclusion of exon 7 amino acids in SMN2 polypeptide in a motoneuron in the subject is increased.

21. A method of increasing inclusion of exon 7 in SMN2 messenger ribonucleic acid (mRNA) transcripts in a human subject having loss of both functional copies of the SMN1 gene, the method comprising administering by a bolus injection into the intrathecal space of the human subject an antisense compound comprising an antisense oligonucleotide consisting of 18 linked nucleosides, wherein the oligonucleotide has a nucleobase sequence consisting of the nucleobase sequence SEQ ID NO:

1, wherein each internucleoside linkage of the oligonucleotide is a phosphorothioate linkage, wherein each nucleoside of the oligonucleotide is a 2′

-MOE nucleoside, and wherein the administering of the antisense compound increases inclusion of exon 7 in SMN2 mRNA transcripts in the human subject.

22. The method of claim 21, wherein the human subject is identified by a genetic test as having a mutation in the SMN1 gene.

23. The method of claim 21, wherein the antisense compound is administered at a dose from 0.01 to 10 milligrams of antisense compound per kilogram of body weight of the subject.

24. The method of claim 21, wherein a 5 mg to 20 mg dose of the antisense compound is administered.

25. A method of increasing exon 7 inclusion in SMN2 messenger ribonucleic acid (mRNA) transcripts in a human subject having mutations in the SMN1 gene that lead to functional SMN protein deficiency, the method comprising administering by a bolus injection into the intrathecal space of the human subject an antisense compound comprising an antisense oligonucleotide consisting of 18 linked nucleosides, wherein the oligonucleotide has a nucleobase sequence consisting of the nucleobase sequence SEQ ID NO:

1, wherein each internucleoside linkage of the oligonucleotide is a phosphorothioate linkage, wherein each nucleoside of the oligonucleotide is a 2′

-MOE nucleoside, and wherein the administering of the antisense compound increases exon 7 inclusion in SMN2 mRNA transcripts in the human subject.

26. The method of claim 25, wherein the antisense compound is administered at a dose from 0.01 to 10 milligrams of antisense compound per kilogram of body weight of the subj ect.

27. The method of claim 25, wherein a 5 mg to 20 mg dose of the antisense compound is administered.

28. The method of claim 25, wherein a first dose of the antisense compound is administered within one week of birth of the subject.

29. The method of claim 25, wherein a first dose of the antisense compound is administered within one month of birth of the subject.

30. The method of claim 25, wherein a first dose of the antisense compound is administered within three months of birth of the subject.

31. The method of claim 25, wherein a first dose of the antisense compound is administered within six months of birth of the subject.

32. The method of claim 25, wherein a first dose of the antisense compound is administered when the subject is from 1 to 2 years of age.

33. The method of claim 25, wherein a first dose of the antisense compound is administered when the subject is from 1 to 15 years of age.

34. A method of treating spinal muscular atrophy (SMA) in a human subject having SMA, the method comprising administering by a bolus injection into the intrathecal space of the human subject an antisense compound comprising an antisense oligonucleotide consisting of 18 linked nucleosides, wherein the oligonucleotide has a nucleobase sequence consisting of the nucleobase sequence SEQ ID NO:

1, wherein each internucleoside linkage of the oligonucleotide is a phosphorothioate linkage, wherein each nucleoside of the oligonucleotide is a 2′

-MOE nucleoside, and wherein the administering of the antisense compound increases inclusion of exon 7 in SMN2 messenger ribonucleic acid (mRNA) transcripts in the human subject.

35. The method of claim 34, wherein the antisense compound is administered at a dose from 0.01 to 10 milligrams of antisense compound per kilogram of body weight of the subj ect.

36. The method of claim 34, wherein a 5 mg to 20 mg dose of the antisense compound is administered.

37. The method of claim 34, wherein a first dose of the antisense compound is administered within one week of birth of the subject.

38. The method of claim 34, wherein a first dose of the antisense compound is administered within one month of birth of the subject.

39. The method of claim 34, wherein a first dose of the antisense compound is administered within three months of birth of the subject.

40. The method of claim 34, wherein a first dose of the antisense compound is administered within six months of birth of the subject.

41. The method of claim 34, wherein a first dose of the antisense compound is administered when the subject is from 1 to 2 years of age.

42. The method of claim 34, wherein a first dose of the antisense compound is administered when the subject is from 1 to 15 years of age.