Compositions for modulating C9ORF72 expression

• US 10,221,414 B2
• Filed: 10/11/2014
• Issued: 03/05/2019
• Est. Priority Date: 10/11/2013
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: Ionis Pharmaceuticals, Inc.
• Inventors: Freier, Susan M., Rigo, Frank
• Primary Examiner(s): Vivlemore, Tracy
• Application Number:
  US15/028,626
• Publication Number:
  US 20160251655A1
• Time in Patent Office: 1,606 Days
• Field of Search: None
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 25/16 Anti-Parkinson drugs
• 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: 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 2310/3231 having an additional ring, e.g. LNA, ENA
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/343 having patterns, e.g. ==--==--==--
• CPC Class Codes: G01N 33/6896 Neurological disorders, e.g. Alzheimer's disease

Abstract

Disclosed herein are compositions and methods for reducing expression of C90RF72 mRNA and protein in an animal with C90RF72 specific inhibitors. Also disclosed herein are compositions and methods of selectively inhibiting a C90RF72 pathogenic associated mRNA variant by administering an antisense compound targeting the region beginning at the start site of exon 1A to the start site of exon 1B of a C90RF72 pre-mRNA. Such methods are useful to treat, prevent, or ameliorate neurodegenerative diseases in an individual in need thereof. Such C90RF72 specific inhibitors include antisense compounds.

Claims

1. A compound comprising a modified oligonucleotide consisting of 15 to 30 linked nucleosides and having a nucleobase sequence that is at least 90% complementary to an equal length portion of nucleobases 8213-8325 of SEQ ID NO:

2.

2. The compound of claim 1, wherein the modified oligonucleotide is a single-stranded modified oligonucleotide.

3. The compound of claim 1, wherein at least one internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.

4. The compound of claim 3, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

5. The compound of claim 1, wherein each internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.

6. The compound of claim 4, wherein at least one internucleoside linkage of the modified oligonucleotide is a phosphodiester internucleoside linkage.

7. The compound of claim 1, wherein at least one nucleobase of the modified oligonucleotide is a modified nucleobase.

8. The compound of claim 7, wherein the modified nucleobase is a 5-methylcytosine.

9. The compound of claim 1, wherein at least one nucleoside of the modified oligonucleotide comprises a modified sugar.

10. The compound of claim 9, wherein the modified sugar is a bicyclic sugar.

11. The compound of claim 10, wherein each bicyclic sugar comprises a chemical bridge between the 4′

and 2′

positions of the sugar, wherein each chemical bridge is independently selected from;

4-CH(R)—

O-2′ and

4′

(CH₂)₂—

O-2′

, wherein R is independently selected from H, C₁-C₆ alkyl, and C₁-C₆.

12. The compound of claim 9, wherein at least one modified sugar comprises a 2′

-O-methoxyethyl group.

13. The compound of claim 9, wherein at least one modified sugar comprises a 2′

-O-methyl group.

14. The compound of claim 1, wherein the modified oligonucleotide comprises:

a gap segment consisting of 10 linked deoxynucleosides;

a 5′

wing segment consisting of 5 linked nucleosides; and

a 3′

wing segment consisting of 5 linked nucleosides;

wherein the gap segment is positioned between the 5′

wing segment and the 3′

wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.

15. The compound of claim 1, wherein the modified oligonucleotide comprises:

a gap segment consisting of 8 linked deoxynucleosides;

a 5′

wing segment consisting of 5 linked nucleosides; and

a 3′

wing segment consisting of 5 linked nucleosides;

wherein the gap segment is positioned between the 5′

wing segment and the 3′

wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.

16. The compound of claim 1, wherein the modified oligonucleotide comprises sugar modifications in any of the following patterns:

eeekkdddddddkkeee, eekkddddddddkkeee, ekddddddddekekeee, kekeddddddddekeke, and ekekddddddddkekee;

wherein,

e=a 2′

-O-methoxyethyl modified nucleoside

d=a 2′

-deoxynucleoside, and

k=a cEt nucleoside.

17. The compound of claim 1, wherein the modified oligonucleotide comprises internucleoside linkages in any of the following patterns:

soooossssssssssooss, sooosssssssssooss, soosssssssssooss, and sosssssssssoooss;

wherein,

s=a phosphorothioate linkage, and

o=a phosphodiester linkage.

18. The compound of claim 1, wherein the modified oligonucleotide consists of 17, 18, 19, or 20 linked nucleosides.

19. A composition comprising the compound of claim 1 and a pharmaceutically acceptable carrier or diluent.

20. A method comprising administering to an animal the compound of claim 1.

21. The compound of claim 9, wherein each nucleoside of the modified oligonucleotide comprises a modified sugar.

22. The compound of claim 11, wherein at least one chemical bridge is 4′

-CH(R)—

O-2′ and

wherein R is methyl.

23. The compound of claim 11, wherein at least one chemical bridge is 4′

-CH(R)—

O-2′ and

wherein R is H.

24. The compound of claim 11, wherein at least one chemical bridge is 4′

-CH(R)—

O-2′ and

wherein R is —

CH₂—

O—

CH₃.

25. The compound of claim 21, wherein each modified sugar comprises a 2′

-O-methoxyethyl group or a 2′

-O-methy group.

26. The compound of claim 1, wherein the modified oligonucleotide is a gapmer.

27. The compound of claim 1, wherein the modified oligonucleotide has a nucleobase sequence complementary to a region of a C9ORF72 nucleic acid other than a hexanucleotide expansion, wherein the hexanucleotide repeat expansion comprises any of GGGGCC, GGGGGG, GGGGCG, and GGGGGC.

28. The compound of claim 1, wherein the compound comprises a conjugate group.

29. The compound of claim 1, consisting of the modified oligonucleotide.

30. A double-stranded compound comprising the compound of claim 1.

31. The double-stranded compound of claim 30, wherein the double-stranded compound comprises a conjugate group.

32. A compound comprising a modified oligonucleotide consisting of 14 to 30 linked nucleosides, wherein the modified oligonucleotide comprises at least 14 consecutive nucleobases of a sequence selected from SEQ ID NOs:

555 to 590, 1054, 1319 to 1365, and 1489 to 1491.

33. The compound of claim 32, wherein the modified oligonucleotide comprises at least 15 consecutive nucleobases of a sequence selected from SEQ ID NOs:

555 to 590, 1054, 1319 to 1365, and 1489 to 1491.

34. The compound of claim 32, wherein the modified oligonucleotide comprises a nucleobase sequence selected from SEQ ID NOs:

555 to 590, 1054, 1319 to 1365, and 1489 to 1491.