Reducing intron retention

• US 10,538,764 B2
• Filed: 06/12/2017
• Issued: 01/21/2020
• Est. Priority Date: 06/16/2014
• Status: Active Grant

• Current Assignee: University of Southampton
• Original Assignee: University of Southampton
• Inventors: Vorechovsky, Igor, Kralovicova, Jana
• Primary Examiner(s): Bowman, Amy H
• Application Number:
  US15/619,984
• Publication Number:
  US 20180002694A1
• Time in Patent Office: 953 Days
• CPC Class Codes: A61P 3/10 for hyperglycaemia, e.g. antidiabetics
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• 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 2310/113 targeting other non-coding nucleic acids, e.g. antagomirs
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/346 having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2320/33 Alteration of splicing
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material

Abstract

Disclosed herein are methods, compositions, polynucleic acid polymers, assays, and kits for inducing processing of a partially processed mRNA transcript to remove a retained intron to produce a fully processed mRNA transcript that encodes a full-length functional form of a protein. Also described herein are methods and compositions for treating a disease or condition characterized by impaired production of a full-length functional form of a protein or for treating a disease or condition characterized by a defective splicing in a subject.

Claims

1. A method of treating or preventing a disease or condition characterized by an impaired production of a functional protein or by a defective splicing in a subject comprising correction of intron retention in gene transcripts, the method comprising:

administering to the subject a pharmaceutical composition comprising;

(i) a therapeutic agent that induces splicing out of an entire intron in a partially processed mRNA transcript, wherein the therapeutic agent comprises a polynucleic acid polymer or a small molecule; and

(ii) a pharmaceutically acceptable excipient and/or a delivery vehicle;

wherein the disease or condition characterized by an impaired production of a functional protein or by a defective splicing is treated or prevented in the subject by the administration of the therapeutic agent.

2. The method of claim 1, wherein the disease or condition or a predisposition to the disease or condition is associated with a defective protein expression caused by the intron retention in the gene transcripts.

3. The method of claim 1, wherein the disease or condition is a hereditary disease, diabetes, or cancer.

4. The method of claim 1, wherein the therapeutic agent is a polynucleic acid polymer is an anti-sense sequence that hybridizes to a retained intron of the partially processed mRNA transcript.

5. The method of claim 1, wherein the pharmaceutical composition comprises:

a polynucleic acid polymer that hybridizes to a target sequence of a partially processed mRNA transcript, wherein the partially processed mRNA transcript encodes a protein and comprises an entire retained intron, wherein the polynucleic acid polymer induces splicing out of the entire retained intron from the partially processed mRNA transcript; and

a pharmaceutically acceptable excipient and/or a delivery vehicle.

6. The method of claim 5, wherein the target sequence is a binding motif that forms a hairpin structure.

7. The method of claim 5, wherein the target sequence is between two G quadruplexes of a partially processed mRNA transcript.

8. The method of claim 5, wherein the target sequence is within the entire retained intron of the partially processed mRNA transcript.

9. The method of claim 5, wherein the target sequence does not form a G quadruplex.

10. The method of claim 5, wherein the target sequence is an intronic sequence.

11. The method of claim 10, wherein the intronic sequence comprises an intronic splicing regulatory element comprising a first CCC motif or a second CCC motif.

12. The method of claim 5, wherein the polynucleic acid polymer is from about 10 to about 50 nucleotides in length, or is from about 10 to about 30 nucleotides in length.

13. The method of claim 5, wherein the polynucleic acid polymer comprises a sequence that is at least 60% complementary to the target sequence of the partially processed mRNA transcript.

14. The method of claim 5, wherein the polynucleic acid polymer is modified at a nucleoside moiety, at a phosphate moiety, at a 5′

terminus, at a 3′

terminus, or a combination thereof.

15. The method of claim 14, wherein the polynucleic acid polymer comprises an artificial nucleotide.

16. The method of claim 15, wherein the artificial nucleotide is selected from the group consisting of 2′

-O-methyl, 2′

-O-methoxyethyl (2′

-O-MOE), 2′

-O-aminopropyl, 2′

-deoxy, T-deoxy-2′

-fluoro, 2′

-O-aminopropyl (2′

-O-AP), 2′

-O-dimethylaminoethyl (2′

-O-DMAOE), 2′

-O-dimethylaminopropyl (2′

-O-DMAP), T-O-dimethylaminoethyloxyethyl (2′

-O-DMAEOE), 2′

-O—

N-methylacetamido (2′

-O-NMA), a locked nucleic acid (LNA), an ethylene nucleic acid (ENA), a peptide nucleic acid (PNA), a 1′

,5′

-anhydrohexitol nucleic acid (HNA), a morpholino, a methylphosphonate nucleotide, a thiolphosphonate nucleotide, and a 2′

-fluoro N3-P5′

-phosphoramidite.

17. The method of claim 5, wherein the polynucleic acid polymer comprises a sequence that is complementary to a sequence with:

(i) at least 80% sequence identity to at least 13 contiguous bases of SEQ ID NO;

46;

(ii) at least 10 contiguous bases of SEQ ID NO;

46;

(iii) at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO;

6, SEQ ID NO;

9, SEQ ID NO;

12, SEQ ID NO;

15, SEQID NO;

18, SEQ ID NO;

21, SEQ ID NO;

24, SEQ ID NO;

27, SEQ ID NO;

30, SEQID NO;

33, SEQ ID NO;

36, SEQ ID NO;

39, SEQ ID NO;

42, and SEQ ID NO;

45;

(iv) at least 60% sequence identity to SEQ ID NO;

3;

or

(v) at least 80% sequence identity to at least 13 contiguous bases of a sequence selected from the group consisting of SEQ ID NOs;

47-434.

18. The method of claim 5, wherein the delivery vehicle comprises a cell penetrating peptide or a peptide-based nanoparticle.

19. The method of claim 1, wherein the subject is human.

20. The method of claim 1, wherein the small molecule has a molecular weight of less than 900 Daltons.

21. The method of claim 1, wherein the small molecule modulates a protein that regulates intron splicing activity.

22. The method of claim 1, wherein the therapeutic agent comprises a vector comprising the polynucleic acid polymer.

23. The method of claim 22, wherein the vector is a viral vector.

24. The method of claim 23, wherein the viral vector is adeno-associated viral vector.