Compositions and uses for treatment thereof

• US 10,669,542 B2
• Filed: 11/07/2016
• Issued: 06/02/2020
• Est. Priority Date: 05/07/2014
• Status: Active Grant

• Current Assignee: Board of Supervisors of Louisiana State University Agricultural & Mechanical College (Louisiana State University System)
• Original Assignee: Board of Supervisors of Louisiana State University Agricultural & Mechanical College (Louisiana State University System)
• Inventors: Grabczyk, Edward L., Fuselier, Kayla T.
• Primary Examiner(s): Gibbs, Terra C
• Application Number:
  US15/345,058
• Publication Number:
  US 20170183655A1
• Time in Patent Office: 1,303 Days
• 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 2320/33 Alteration of splicing

Abstract

The invention is directed generally to oligonucleotide compositions for the treatment of DNA repeat expansion diseases. The invention also relates to oligonucleotides directed to subunits of the DNA mismatch repair system.

Claims

1. An isolated nuclease-resistant oligonucleotide comprising a nucleic acid sequence that hybridizes to a complementary target nucleic acid sequence of a gene or gene product to modulate the expression of a component of a mismatch repair (MMR) complex, wherein the component of the MMR complex comprises exon 7 of MLH3 of MutLgamma, further wherein the isolated nuclease resistant oligonucleotide does not impact the total cellular ratios of MLH1 and its binding partners.

2. The nuclease-resistant oligonucleotide of claim 1, wherein MLH3 comprises SEQ ID NO:

1.

3. The nuclease-resistant oligonucleotide of claim 1, wherein the oligonucleotide directs skipping of exon 7 of MLH3.

4. The nuclease-resistant oligonucleotide of claim 1, wherein the oligonucleotide hybridizes to the target complementary nucleic acid sequence comprising SEQ ID NO:

2.

5. The nuclease-resistant oligonucleotide of claim 1, wherein the oligonucleotide is at least 80% identical to a nucleic acid sequence comprising SEQ ID NO:

3, SEQ ID NO;

4, SEQ ID NO;

7, SEQ ID NO;

8, SEQ ID NO;

9, SEQ ID NO;

10, SEQ ID NO;

11, SEQ ID NO;

12, SEQ ID NO;

13, SEQ ID NO;

14, SEQ ID NO;

15, SEQ ID NO;

16, SEQ ID NO;

17, SEQ ID NO;

18, SEQ ID NO;

19, SEQ ID NO;

20, SEQ ID NO;

21, SEQ ID NO;

22, SEQ ID NO;

23, SEQ ID NO;

24, SEQ ID NO;

25, SEQ ID NO;

26, SEQ ID NO;

27, or SEQ ID NO;

28.

6. The nuclease-resistant oligonucleotide of claim 1, wherein the oligonucleotide comprises one or more morpholino subunits, one or more locked nucleic acid subunits, one or more 2-O-methyl moieties, or one or more peptide moieties.

15. The nuclease-resistant oligonucleotide of claim 1, wherein the oligonucleotide comprises a pharmaceutical composition administered to a subject in a pharmaceutically acceptable carrier.

7. A pharmaceutical composition comprising a nuclease-resistant oligonucleotide 15 to 30 nucleotide bases in length targeted to a complementary nucleic acid sequence of exon 7 a gene encoding a MLH3 subunit of MutLgamma, wherein the oligonucleotide hybridizes with and modulates the expression of the human MutL subunit by at least 20%, wherein the oligonucleotide comprises at least one modification, and further wherein the nuclease resistant oligonucleotide does not impact the total cellular ratios of MLH1 and its binding partners.

8. The pharmaceutical composition of claim 7, wherein the modification comprises a phosphorothioate backbone, a phosphorodiamidate morpholino nucleotide, a charge-negative oligonucleotide, a charge-neutral oligonucleotide, a 2-aminoethylglycine functionalized nucleotide phosphorothioate backbone, a 5-methylcytosine nucleotide, a 2′

-O-methoxyethyl sugar moiety, a locked nucleic acid subunit, an ethylene-bridged nucleic acid subunit, or a combination thereof.

14. The composition of claim 7, wherein the oligonucleotide decreases the expression of the human MutL subunit by at least 20%.

9. An oligonucleotide complex for modulating the expression or activity of a gene or gene product encoding a component of a mismatch repair (MMR) system, the complex comprising a first oligonucleotide and a second oligonucleotide, wherein the first oligonucleotide comprises a sequence complementary to an acceptor region of exon 7 of a gene encoding a MLH3 subunit, and wherein the first oligonucleotide comprises a nuclease-resistant modification, and wherein the second oligonucleotide comprises a sequence complementary to a donor region of exon 7 of a gene encoding a MLH3 subunit, and wherein the second oligonucleotide comprises a nuclease-resistant modification.

10. An oligonucleotide complex for modulating the expression or activity of a gene or gene product encoding a component of a mismatch repair (MMR) system, the complex comprising a first oligonucleotide and a second oligonucleotide, wherein the first oligonucleotide comprises a sequence complementary to an acceptor region of exon 7 of a gene encoding a MLH3 subunit, and wherein the first oligonucleotide comprises a nuclease-resistant modification, and wherein the second oligonucleotide comprises a sequence complementary to a donor region of exon 7 of a gene encoding a MLH3 subunit.

12. The oligonucleotide complex of claim 9, 10, or 11, wherein the nuclease-resistant modification comprises one or more morpholino subunits, one or more locked nucleic acid subunits, one or more 2-O-methyl moieties, one or more peptide moieties, or a combination thereof.

13. The oligonucleotide complex of claim 9, 10, or 11, wherein the first or second oligonucleotide comprises a nucleic acid sequence having at least 90% identity to SEQ ID NO:

3 or SEQ ID NO;

4.

11. An oligonucleotide complex for modulating the expression or activity of a gene or gene product encoding a component of a mismatch repair (MMR) system, the complex comprising a first oligonucleotide and a second oligonucleotide, wherein the first oligonucleotide comprises a sequence complementary to an acceptor region of exon 7 of a gene encoding a MLH3 subunit, and wherein the second oligonucleotide comprises a sequence complementary to a donor region of exon 7 of a gene encoding a MLH3 subunit, and wherein the second oligonucleotide comprises a nuclease-resistant modification.