Polynucleotides for causing RNA interference and method for inhibiting gene expression using the same

• US 20080113351A1
• Filed: 11/13/2006
• Published: 05/15/2008
• Est. Priority Date: 05/11/2004
• Status: Abandoned Application

• Current Assignee: alphaGEN Co., Ltd.
• Original Assignee: alphaGEN Co., Ltd.
• Inventors: Natori, Yukikazu, Naito, Yuki, Fujino, Masato, Oguchi, Shinobu
• Application Number:
  US11/598,052
• Publication Number:
  US 20080113351A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: A61K 31/713 Double-stranded nucleic acids or oligonucleotides
• CPC Class Codes: A61K 48/00 Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
• CPC Class Codes: A61P 21/00 Drugs for disorders of the muscular or neuromuscular system
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 25/24 Antidepressants
• CPC Class Codes: A61P 25/28 for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• 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 3/10 for hyperglycaemia, e.g. antidiabetics
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 35/02 specific for leukemia
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: A61P 5/26 Androgens
• CPC Class Codes: A61P 7/06 Antianaemics
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2320/11 for the determination of target sites, i.e. of active nucleic acids
• CPC Class Codes: C12N 2330/30 chemically synthesised

Abstract

The present invention provides a polynucleotide that not only has a high RNA interference effect on its target gene, but also has a very small risk of causing RNA interference against a gene unrelated to the target gene. A sequence segment conforming to the following rules (a) to (d) is searched from the base sequences of a target gene for RNA interference and, based on the search results, a polynucleotide capable of causing RNAi is designed, synthesized, etc.:

• (a) The 3′ end base is adenine, thymine, or uracil,
• (b) The 5′ end base is guanine or cytosine,
• (c) A 7-base sequence from the 3′ end is rich in one or more types of bases selected from the group consisting of adenine, thymine, and uracil, and
• (d) The number of bases is within a range that allows RNA interference to occur without causing cytotoxicity.

Claims

1. A polynucleotide for causing RNA interference against a target gene selected from the genes of a target organism, which has at least a double-stranded region, wherein one strand in the double-stranded region consists of a base sequence homologous to a prescribed sequence which is contained in the base sequences of the target gene and which conforms to the following rules (a) to (d):

(a) The 3′

end base is adenine, thymine or uracil;

(b) The 5′

end base is guanine or cytosine;

(c) A 7-base sequence from the 3′

end is rich in one or more types of bases selected from the group consisting of adenine, thymine and uracil; and

(d) The number of bases is within a range that allows RNA interference to occur without causing cytotoxicity, and

wherein the other strand in the double-stranded region consists of a base sequence having a sequence complementary to the base sequence homologous to the prescribed sequence.

2. The polynucleotide according to claim 1, wherein at least 80% of bases in the base sequence homologous to the prescribed sequence corresponds to the base sequence of the prescribed sequence.

3. The polynucleotide according to claim 1, wherein, in the rule (c), at least three bases among the seven bases are one or more types of bases selected from the group consisting of adenine, thymine and uracil.

4. The polynucleotide according to claim 1, wherein, in the rule (d), the number of bases is 13 to 28.

5. The polynucleotide according to claim 1, wherein the prescribed sequence further conforms to the following rule (e):

(e) A sequence in which 10 or more bases of guanine or cytosine are continuously present is not contained.

6. The polynucleotide according to claim 5, wherein the prescribed sequence further conforms to the following rule (f):

(f) A sequence sharing at least 90% homology with the prescribed sequence is not contained in the base sequences of genes other than the target gene among all gene sequences of the target organism.

7. The polynucleotide according to claim 6, wherein the prescribed sequence consists of the base sequence shown in any of SEQ ID NOs:

47 to 817081.

8. The polynucleotide according to claim 6, wherein the prescribed sequence is any of the sequences listed in the column “

Target Sequence”

of FIG. 46.

9. The polynucleotide according to claim 6, which has any of the base sequences shown in SEQ ID NOs:

817102 to 817651.

10. The polynucleotide according to claim 1, which is a double-stranded polynucleotide.

11. The polynucleotide according to claim 10, wherein

one strand of the double-stranded polynucleotide consists of a base sequence having an overhanging portion at the 3′

end of the base sequence homologous to the prescribed sequence, and the other strand of the double-stranded polynucleotide consists of a base sequence having an overhanging portion at the 3′

end of the sequence complementary to the base sequence homologous to the prescribed sequence.

12. The polynucleotide according to claim 1, which is a single-stranded polynucleotide having a hairpin structure, wherein the single-stranded polynucleotide has a loop segment linking the 3′

end of one strand in the double-stranded region and the 5′

end of the other strand in the double-stranded region.

15. A method for inhibiting gene expression, which comprises introducing the polynucleotide according to claim 1 into an expression system for a target gene whose expression is to be inhibited, thereby inhibiting the expression of the target gene.

17. The method for inhibiting gene expression according to claim 15, wherein the expression is inhibited to 50% or below.

18. A pharmaceutical composition which comprises a pharmaceutically effective amount of the polynucleotide according to claim 1.

19. The pharmaceutical composition according to claim 18, which is for use in treating or preventing the diseases listed in the column “

Related Disease”

of FIG. 46.

20. The pharmaceutical composition according to claim 18, which is for use in treating or preventing diseases related to the genes listed in the column “

Gene Name”

of FIG. 46.

21. The pharmaceutical composition according to claim 18, which is for use in treating or preventing a disease in which a gene belonging to any of the following 1) to 9) is involved:

1) an apoptosis-related gene;

2) phosphatase or a phosphatase activity-related gene;

3) a cell cycle-related gene;

4) a receptor-related gene;

5) an ion channel-related gene;

6) a signal transduction system-related gene;

7) kinase or a kinase activity-related gene;

8) a transcription regulation-related gene;

or

9) G protein-coupled receptor or a G protein-coupled receptor-related gene.

22. The pharmaceutical composition according to claim 18, which comprises a polynucleotide targeting the base sequence shown in any of SEQ ID NOs listed in the column “

SEQ ID NO (human)”

or “

SEQ ID NO (mouse)”

of FIG. 46.

23. The pharmaceutical composition according to claim 18, which is for use in treating or preventing diseases related to the genes listed in the column “

Gene Name”

of Table 1.

24. The pharmaceutical composition according to claim 18, which is for use in treating or preventing any cancer selected from bladder cancer, breast cancer, colorectal cancer, gastric cancer, hepatoma, lung cancer, melanoma, ovarian cancer, pancreas cancer, prostate cancer, oral cancer, skin cancer, and thyroid gland cancer.

25. The pharmaceutical composition according to claim 18, which comprises a polynucleotide having any of the base sequences shown in SEQ ID NOs:

817102 to 817651.

26. A composition for inhibiting gene expression to inhibit the expression of a target gene, which comprises the polynucleotide according to claim 1.

27. The composition for inhibiting gene expression according to claim 26, wherein the target gene is related to any of the diseases listed in the column “

Related Disease”

of FIG. 46.

28. The composition for inhibiting gene expression according to claim 26, wherein the target gene is any of the genes listed in the column “

Gene Name”

of FIG. 46.

29. The composition for inhibiting gene expression according to claim 26, wherein the target gene is a gene belonging to any of the following 1) to 9):

1) an apoptosis-related gene;

2) phosphatase or a phosphatase activity-related gene;

3) a cell cycle-related gene;

4) a receptor-related gene;

5) an ion channel-related gene;

6) a signal transduction system-related gene;

7) kinase or a kinase activity-related gene;

8) a transcription regulation-related gene;

or

9) G protein-coupled receptor or a G protein-coupled receptor-related gene.

30. The composition for inhibiting gene expression according to claim 26, wherein the target gene is any of the genes listed in the column “

Gene Name”

of Table 1.

31. The composition for inhibiting gene expression according to claim 26, wherein the target gene is related to any cancer selected from bladder cancer, breast cancer, colorectal cancer, gastric cancer, hepatoma, lung cancer, melanoma, ovarian cancer, pancreas cancer, prostate cancer, oral cancer, skin cancer, and thyroid gland cancer.

32. A method for treating or preventing the diseases listed in the column “

Related Disease”

of FIG. 46, which comprises administering a pharmaceutically effective amount of the polynucleotide according to claim 1.

13. A method for selecting a polynucleotide to be introduced into an expression system for a target gene whose expression is to be inhibited, wherein the polynucleotide has at least a double-stranded region, wherein one strand in the double-stranded region consists of a base sequence homologous to a prescribed sequence which is contained in the base sequences of the target gene and which conforms to the following rules (a) to (f):

(a) The 3′

end base is adenine, thymine or uracil;

(b) The 5′

end base is guanine or cytosine;

(c) A 7-base sequence from the 3′

end is rich in one or more types of bases selected from the group consisting of adenine, thymine and uracil;

(d) The number of bases is within a range that allows RNA interference to occur without causing cytotoxicity;

(e) A sequence in which 10 or more bases of guanine or cytosine are continuously present is not contained; and

(f) A sequence sharing at least 90% homology with the prescribed sequence is not contained in the base sequences of genes other than the target gene among all gene sequences of the target organism, and

wherein the other strand in the double-stranded region consists of a base sequence having a sequence complementary to the base sequence homologous to the prescribed sequence.

14. A method for selecting a polynucleotide according to claim 13, wherein a polynucleotide having a sequence, wherein the base sequence homologous to the prescribed sequence of the target gene contains mismatches of at least 3 bases against the base sequences of genes other than the target gene, and for which there is only a minimum number of other genes having a base sequence containing the mismatches of at least 3 bases, is further selected from the selected polynucleotides.

16. A method for inhibiting gene expression, which comprises introducing a polynucleotide selected by the method according to claim 13 into an expression system for a target gene whose expression is to be inhibited, thereby inhibiting the expression of the target gene.