OLIGOMERS TARGETING HEXANUCLEOTIDE REPEAT EXPANSION IN HUMAN C9ORF72 GENE

• US 20160108396A1
• Filed: 08/14/2015
• Published: 04/21/2016
• Est. Priority Date: 08/15/2014
• Status: Abandoned Application

• Current Assignee: Pfizer Inc.
• Original Assignee: Pfizer Inc.
• Inventors: Jensen, Mads Aaboe, Lindow, Morten
• Application Number:
  US14/826,829
• Publication Number:
  US 20160108396A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• 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 2310/322 2'-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 2310/3525 MOE, methoxyethoxy
• CPC Class Codes: C12N 2320/30 Special therapeutic applications
• CPC Class Codes: C12N 2320/34 Allele or polymorphism specific uses

Abstract

The disclosure relates to oligomers capable of targeting RNA expressed from the human C9ORF72 gene containing a pathogenic hexanucleotide repeat expansion. Such oligomers are useful for, among other things, reducing or eliminating C9ORF72 RNA and/or proteins translated therefrom, and treating or preventing diseases or disorders caused by, or associated with, hexanucleotide repeat expansion, including familial frontotemporal dementia (FTD) and familial amyotrophic lateral sclerosis (ALS).

Claims

1. A gapmer comprising between 12 to 30 nucleosides, complementary to at least a 12 contiguous nucleobase portion of SEQ ID NO:

187, wherein the gapmer further comprises in 5′

to 3′

order;

(a) a 5′

flanking region consisting of 1 to 5 contiguously linked nucleosides, at least one of which is an LNA monomer,

(b) a gap region consisting of contiguously linked deoxyribonucleosides; and

(c) a 3′

flanking region consisting of 1 to 5 contiguously linked nucleosides, at least one of which is an LNA monomer.

wherein the gapmer is capable of preferentially inhibiting expression of C9ORF72 sense transcript containing an expanded hexanucleotide repeat region when compared with inhibiting expression of a wild-type C9ORF72 sense transcript, and

wherein the gapmer is further capable of inhibiting expression of C9ORF72 antisense transcript containing an expanded hexanucleotide repeat region.

2. The gapmer of claim 1, having a sequence that is identical to at least a 12 nucleobase portion of a nucleobase sequence selected from the group consisting of SEQ ID NO:

1 to SEQ ID NO;

175.

3. The gapmer of any of the preceding claims, wherein all internucleoside linkages are phosphorothioate.

4. The gapmer of claim 1, wherein all of the nucleosides in the 5′

flanking region and 3′

flanking region are modified.

5. The gapmer of claim 1, wherein all modified nucleosides are LNA monomers.

6. The gapmer of claim 1, wherein all cytosine nucleosides in the 5′

flanking region and 3′

flanking region are 5-methylcytosines.

7. The gapmer of claim 1, wherein the nucleobase sequence of said gapmer is GGc ccc ggc ccC GG (SEQ ID NO:

109), wherein the 5′

flanking region and 3′

flanking region are each respectively indicated by capital letters, and wherein the gap region is indicated by lower case letters.

8. The gapmer of claim 7, wherein cytosines at positions 6 and 12 are 5-methylcytosines.

9. The gapmer of claim 8, wherein all the nucleosides in the 5′

flanking region and 3′

flanking region are LAN monomers.

11. A composition comprising the gapmer of any of the preceding claims and a pharmaceutically acceptable carrier.

12. A method of treating a disorder in a subject in need thereof wherein the subject is suffering from a disease or disorder mediated by or associated with repeat expansion in a C9ORF72 sequence, comprising administering to said subject a therapeutically effective amount of the gapmer of any of the preceding claims.

13. The method of any of claim 12, wherein said neurological disorder is selected from amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD).

14. The method of any of claim 13, wherein the gapmer is administered into the central nervous system intrathecally or intraventricularly.

15. A method of reducing the amount of RNA in a cell from a C9ORF72 gene containing an expanded hexanucleotide repeat region, the method comprising contacting a cell containing C9ORF72 RNA with an effective amount of the gapmer of claim 1, thereby reducing the amount of C9ORF72 RNA in the cell.

16. The method of claim 15, wherein the RNA is a C9ORF72 sense transcript.

17. The method of any of claim 15, wherein the RNA is a C9ORF72 antisense transcript.

18. A method of simultaneously down-regulating the expression of C9ORF72 sense transcript containing an expanded hexanucleotide repeat region and C9ORF72 antisense transcript containing an expanded hexanucleotide repeat region in a cell, tissue or organism comprising contacting or administering said cell, tissue or organism with an effective amount of one or more of the gapmers of claim 1.

10. A gapmer consisting of 14 nucleotides wherein the nucleobase sequence consists of the sequence of SEQ ID NO:

109, and the 5′

flanking region consists of two nucleosides that are LNA monomers, the 3′

flanking region consists of three nucleosides that are LNA monomers, wherein all internucleoside linkages are phosphorothioate linkages, and each cytosine at positions 6 and 12 is a 5-methylcytosine.