Alteration of cellular behavior by antisense modulation of mRNA processing

• US 6,210,892 B1
• Filed: 03/26/1999
• Issued: 04/03/2001
• Est. Priority Date: 10/07/1998
• Status: Expired due to Term

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Wyatt, Jacqueline R., Cooke, Stanley T., Monia, Brett P., McKay, Robert, Freier, Susan M., Karras, James G., Baker, Brenda F., Manoharan, Muthiah, Bennett, C. Frank
• Primary Examiner(s): Schwartzman, Robert A.
• Assistant Examiner(s): EPPS -SMITH, JANET L
• Application Number:
  US09/277,020
• Time in Patent Office: 739 Days
• Field of Search: 536/24.5, 536/23.1, 435/6, 435/325, 435/375, 435/91.1, 435/91.31, 514/44
• US Class Current: 435/6.14
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: C12N 15/1135 against oncogenes or tumor suppressor genes
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/3181 Peptide nucleic acid, PNA
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/3233 Morpholino-type ring
• CPC Class Codes: C12N 2310/334 Modified C
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/345 having at least two different backbone modifications
• CPC Class Codes: C12N 2310/346 having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/3525 MOE, methoxyethoxy
• CPC Class Codes: Y02P 20/582 Recycling of unreacted starting or intermediate materials

Abstract

The present invention provides compositions and methods for controlling the behavior of a cell, tissue or organism through antisense modulation of mRNA processing, using antisense compounds which does not support cleavage of the mRNA target.

Claims

1. A method of modulation of processing of a selected wild-type cellular mRNA target, said method comprising binding to said target an antisense compound having at least one 2′

-methoxyethoxy, 2′

-dimethylaminooxyethoxy, 2′

-dimethylaminoethoxyethoxy, 2′

-acetamide, morpholino, or peptide nucleic acid modification which is specifically hybridizable with said mRNA target and which does not elicit cleavage of the mRNA target upon binding, so that processing of said mRNA target is modulated.

2. The method of claim 1 wherein said modulation of the processing of a selected wild-type cellular mRNA target is modulation of splicing of said mRNA target.

3. The method of claim 1 wherein said antisense compound has a 2′

-methoxyethoxy, 2′

-dimethylaminooxyethoxy, 2′

-dimethylaminoethoxyethoxy or 2′

-acetamide modification on substantially every sugar.

4. The method of claim 3 wherein said antisense compound has at least one phosphorothioate backbone linkage.

5. The method of claim 1 wherein said antisense compound is an antisense oligonucleotide.

6. The method of claim 2 wherein said modulation of splicing is a redirection of splicing.

7. The method of claim 2 wherein said modulation of splicing results in an altered ratio of splice products.

8. The method of claim 2 wherein said modulation of splicing results in exclusion of one or more exons from a mature mRNA.

9. The method of claim 8 wherein said antisense compound is targeted to at least a portion of an exon to be excluded.

10. The method of claim 9 wherein said antisense compound is targeted to an intron-exon junction.

11. The method of claim 6 wherein said antisense compound is targeted to at least a portion of a region up to 50 nucleobases upstream from a 5′

splice site.

12. The method of claim 11 wherein said redirection of splicing is a decreased frequency of use of said 5′

splice site.

13. The method of claim 1 wherein said processing of a selected wild-type cellular mRNA target is polyadenylation of said mRNA target.

14. The method of claim 1 wherein said antisense compound is targeted to a polyadenylation signal or polyadenylation site.

15. The method of claim 1 wherein said processing of a selected wild-type cellular mRNA target is regulating stability of said mRNA target, by targeting said antisense compound to a sequence which controls the stability of said mRNA target.

16. The method of claim 1 wherein said antisense compound which does not elicit cleavage of the mRNA target upon binding contains at least one modification which increases binding affinity for the mRNA target and which increases nuclease resistance of the antisense compound.

17. The method of claim 1 wherein said antisense compound which does not elicit cleavage of the mRNA target upon binding contains at least one nucleoside having a 2′

modification of its sugar moiety.

18. The method of claim 17 wherein every nucleoside of said antisense compound has a 2′

modification of its sugar moiety.

19. The method of claim 17 wherein said 2′

modification is selected from the group consisting of 2′

-O-methoxyethyl and 2′

-dimethylaminooxyethoxy.

20. The method of claim 1 wherein said antisense compound which does not elicit cleavage of the mRNA target upon binding contains at least one modified backbone linkage other than a phosphorothioate backbone linkage.

21. The method of claim 20 wherein said antisense compound which does not elicit cleavage of the mRNA target upon binding contains a plurality of modified backbone linkages other than phosphorothioate backbone linkages.

22. The method of claim 21 wherein said antisense compound also contains at least one phosphodiester or phosphorothioate backbone linkage.

23. The method of claim 21 wherein said modified backbone linkages alternate with phosphodiester and/or phosphorothioate backbone linkages.

24. The method of claim 20 wherein every backbone linkage is a modified backbone linkage other than a phosphorothioate linkage.

25. The method of claim 20 wherein said modified backbone linkage is a morpholino, peptide nucleic acid or methylene (methylimino) backbone linkage.

26. The method of claim 1 wherein said antisense compound which does not elicit cleavage of the mRNA target upon binding contains at least one modified nucleobase.

27. The method of claim 26 wherein said modified nucleobase is a C-5 propyne.

28. The method of claim 7 wherein said altered ratio of splice products results from an increase or a decrease in the amount of a splice product encoding a membrane form of a protein relative to a soluble form of a protein.

29. The method of claim 28 wherein said protein is a receptor.

30. The method of claim 29 wherein said receptor is a hormone or cytokine receptor.

31. The method of claim 1 wherein said antisense compound has a morpholino or peptide nucleic acid modification at substantially every backbone linkage.