Splice switch oligomers for TNF superfamily receptors and their use in treatment of disease

• US 20070105807A1
• Filed: 11/10/2006
• Published: 05/10/2007
• Est. Priority Date: 11/10/2005
• Status: Abandoned Application

• Current Assignee: Marvell Semiconductor, Inc. (Marvell Technology Group Limited), Santaris Pharma A/S (Roche Holding AG), Ercole Biotech, Inc. (Sarepta Therapeutics, Inc.), University of North Carolina At Chapel Hill (University of North Carolina System)
• Original Assignee: Ercole Biotech, Inc. (Sarepta Therapeutics, Inc.), University of North Carolina At Chapel Hill (University of North Carolina System)
• Inventors: Kole, Ryszard, Orum, Henrik, Sazani, Peter
• Application Number:
  US11/595,485
• Publication Number:
  US 20070105807A1
• Time in Patent Office: Days
• US Class Current: 514/44.A
• CPC Class Codes: A61P 1/04 for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
• CPC Class Codes: A61P 1/16 for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
• CPC Class Codes: A61P 17/06 Antipsoriatics
• CPC Class Codes: A61P 19/02 for joint disorders, e.g. arthritis, arthrosis
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 31/00 Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 31/04 Antibacterial agents
• CPC Class Codes: A61P 31/14 for RNA viruses
• CPC Class Codes: A61P 31/20 for DNA viruses
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• CPC Class Codes: C12N 15/1138 against receptors or cell surface proteins
• 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 2310/346 having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2320/33 Alteration of splicing

Abstract

Methods and compositions are disclosed for controlling expression of TNF receptors (TNFR1 and TNFR2) and of other receptors in the TNFR superfamily using compounds that modulate splicing of pre-mRNA encoding these receptors. More specifically these compounds cause the removal of the transmembrane domains of these receptors and produce soluble forms of the receptor which act as an antagonist to reduce TNF-α activity or activity of the relevant ligand. Reducing TNF-α activity provides a method of treating or ameliorating inflammatory diseases or conditions associated with TNF-α activity. Similarly, diseases associated with other ligands can be treated in like manner. In particular, the compounds of the invention are splice-splice switching oligomers (SSOs) which are small molecules that are stable in vivo, hybridize to the RNA in a sequence specific manner and, in conjunction with their target, are not degraded by RNAse H.

Claims

1. A method of treating an inflammatory disease or condition which comprises administering one or more splice switching oligomers (SSOs) to a subject for a time and in an amount to reduce the activity of a ligand for a receptor of the tumor necrosis factor receptor (TNFR) superfamily, wherein said one or more SSOs are capable of altering the splicing of a pre-mRNA encoding said receptor to increase production of a stable, secreted, ligand-binding form of said receptor.

2. The method of claim 1, wherein said receptor is a mammalian receptor selected from the group consisting of TNFRSF1A, TNFRSF1B, TNFRSF3, TNFRSF5, TNFRSF8, and TNFRSF11A.

3. The method of claim 2, wherein said receptor is a human TNFRSF1A or a human TNFRSF1B.

4. The method of claim 3, wherein said receptor is a human TNFRSF1B.

5. The method of claim 1, wherein said ligand is TNF-α

, RANKL, CD40L, LT-α

, or LT-β

.

6. The method of claim 1, wherein said disease or condition is selected from the group consisting of rheumatoid arthritis, juvenile rheumatoid arthritis, psoriasis, psoriatic arthritis, ankylosing spondylitis, inflammatory bowel disease (Crohn'"'"'s disease or ulcerative colitis), hepatitis, sepsis, alcoholic liver disease, and non-alcoholic steatosis.

7. The method of claim 1, wherein two or more SSOs are administered.

8. The method of claim 1, wherein said receptor is TNFRSF1A, TNFRSF1B, TNFRSF3, TNFRSF5, or TNFRSF11A, and said altering the splicing of said pre-mRNA comprises excising exon 7, exon 8, or both from said pre-mRNA.

9. The method of claim 8, wherein said altering the splicing of said pre-mRNA comprises excising exon 7.

10. The method of claim 1, wherein said receptor is a human TNFRSF1A or a human TNFRSF1B, and said SSO comprises from at least 10 to at least 20 nucleotides which are complementary to a contiguous sequence from SEQ ID Nos:

1, 2, 3 or 4.

11. The method of claim 10 wherein the sequence of said SSO comprises a sequence selected from the group consisting of SEQ ID Nos:

74, 75, 77, 78, 80, 82, 84, and 86-89.

12. The method of claim 1, wherein said SSOs comprise one or more nucleotides or nucleosides independently selected from the group consisting of 2′

-deoxyribonucleotides, 2′

O-Me ribonucleotides, 2′

O-MOE ribonucleotides, hexitol (HNA) nucleotides or nucleosides, 2′

O-4′

C-linked bicyclic ribofuranosyl (LNA) nucleotides or nucleosides, phosphorothioate analogs of any of the foregoing, peptide nucleic acid (PNA) analogs of any of the foregoing;

methylphosponate analogs of any of the foregoing, peptide nucleic acid analogs of any of the foregoing, N3′

→

P5′

phosphoramidate analogs of any of the foregoing, and phosphorodiamidate morpholino nucleotide analogs of any of the foregoing, and combinations thereof.

13. The method of claim 12, wherein said SSOs comprise one or more nucleotides or nucleosides independently selected from the group consisting of 2′

O-Me ribonucleotides and 2′

O-4′

C-linked bicyclic ribofuranosyl (LNA) nucleotides or nucleosides.

14. The method of claim 1, wherein said administration is parenteral, topical, oral, rectal, or pulmonary.

15. A method of increasing the production of a stable, secreted, ligand-binding form of a receptor from the TNFR superfamily in a cell, which comprises administering one or more splice switching oligomers (SSOs) to said cell, wherein said one or more SSOs are capable of altering the splicing of a pre-mRNA encoding said receptor to increase production of a stable, secreted, ligand-binding form of said receptor.

16. The method of claim 15, wherein said method is performed in vivo.

17. The method of claim 15, wherein said receptor is a mammalian receptor selected from the group consisting of TNFRSF1A, TNFRSF1B, TNFRSF3, TNFRSF5, TNFRSF8, and TNFRSF1A.

18. The method of claim 17, wherein said receptor is a human TNFRSF1A or a human TNFRSF1B.

19. The method of claim 18, wherein said receptor is a human TNFRSF1B.

20. The method of claim 18, wherein said SSO comprises from at least 10 to at least 20 nucleotides which are complementary to a contiguous sequence from SEQ ID Nos:

1, 2, 3 or 4.

21. A splice switching oligomer (SSO) comprising from at least 10 to at least 20 nucleotides, said SSO capable of altering the splicing of a pre-mRNA encoding a receptor from the TNFR superfamily to produce a stable, secreted, ligand-binding form of said receptor.

22. The SSO of claim 21, wherein said receptor is a mammalian receptor selected from the group consisting of TNFRSF1A, TNFRSF1B, TNFRSF3, TNFRSF5, TNFRSF8, and TNFRSF11A.

23. The SSO of claim 22, wherein said receptor is a human TNFSF1A or a human TNFRSF1B.

24. The method of claim 23, wherein said receptor is a human TNFRSF1B.

25. The SSO of claim 23, which comprises from at least 10 to at least 20 nucleotides which are complementary to a contiguous sequence from SEQ ID Nos:

1, 2, 3 or 4.

26. The SSO of claim 21, wherein said SSO comprises one or more nucleotides or nucleosides independently selected from the group consisting of 2′

-deoxyribonucleotides, 2′

O-Me ribonucleotides, 2′

O-MOE ribonucleotides, hexitol (HNA) nucleotides or nucleosides, 2′

O-4′

C-linked bicyclic ribofuranosyl (LNA) nucleotides or nucleosides, phosphorothioate analogs of any of the foregoing, peptide nucleic acid (PNA) analogs of any of the foregoing;

methylphosponate analogs of any of the foregoing, peptide nucleic acid analogs of any of the foregoing, N3′

→

P5′

phosphoramidate analogs of any of the foregoing, and phosphorodiamidate morpholino nucleotide analogs of any of the foregoing, and combinations thereof.

27. The SSO of claim 26, wherein said 2′

O-4′

C-linked bicyclic ribofuranosyl (LNA) nucleotides or nucleosides are 2′

O-4′

C-(methylene)-ribofuranosyl nucleotides or nucleosides, respectively, or 2′

O-4′

C-(ethylene)-ribofuranosyl nucleotides or nucleosides, respectively.

28. The SSO of claim 26, wherein said SSOs comprise one or more nucleotides or nucleosides independently selected from the group consisting of 2′

O-Me ribonucleotides and 2′

O-4′

C-linked bicyclic ribofuranosyl (LNA) nucleotides or nucleosides.

29. The SSO of claim 21, wherein the sequence of said SSO comprises a sequence selected from the group consisting of SEQ ID Nos:

8, 9, 14, 17-21, 24-29, 32, 33, 38-42, 44-46, 50-52, 55-57, 60, 68-71, 74, 75, 77, 78, 80, 82, 84, and 86-89.

30. A pharmaceutical composition comprising the SSO of claim 21 and a pharmaceutically acceptable carrier.

31. The pharmaceutical composition of claim 30, wherein said SSO comprises from at least 10 to at least 20 nucleotides which are complementary to a contiguous sequence from SEQ ID Nos:

1, 2, 3 or 4.