Treatment of tumor suppressor gene related diseases by inhibition of natural antisense transcript to the gene

• US 10,358,646 B2
• Filed: 11/05/2014
• Issued: 07/23/2019
• Est. Priority Date: 12/04/2008
• Status: Active Grant

• Current Assignee: CURNA, Inc. (Opko Health, Inc.)
• Original Assignee: CURNA, Inc. (Opko Health, Inc.)
• Inventors: Collard, Joseph, Khorkova Sherman, Olga
• Primary Examiner(s): Poliakova-Georgantas, Ekaterina
• Application Number:
  US14/533,371
• Publication Number:
  US 20150159162A1
• Time in Patent Office: 1,721 Days
• Field of Search: None
• CPC Class Codes: A61K 31/712 Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose
• CPC Class Codes: A61P 13/12 of the kidneys
• CPC Class Codes: A61P 17/02 for treating wounds, ulcers, burns, scars, keloids, or the like
• CPC Class Codes: A61P 19/02 for joint disorders, e.g. arthritis, arthrosis
• CPC Class Codes: A61P 19/08 for bone diseases, e.g. rachitism, Paget's disease
• CPC Class Codes: A61P 19/10 for osteoporosis
• CPC Class Codes: A61P 21/02 Muscle relaxants, e.g. for tetanus or cramps
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 25/14 for treating abnormal movements, e.g. chorea, dyskinesia
• CPC Class Codes: A61P 25/16 Anti-Parkinson drugs
• 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 3/00 Drugs for disorders of the metabolism of the blood or the extracellular fluid A61P7/00
• CPC Class Codes: A61P 3/10 for hyperglycaemia, e.g. antidiabetics
• CPC Class Codes: A61P 31/04 Antibacterial agents
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 31/18 for HIV
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 35/02 specific for leukemia
• CPC Class Codes: A61P 37/00 Drugs for immunological or allergic disorders
• CPC Class Codes: A61P 37/02 : Immunomodulators
• CPC Class Codes: A61P 37/06 : Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: A61P 39/02 : Antidotes
• CPC Class Codes: A61P 43/00 : Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: A61P 7/00 : Drugs for disorders of the blood or the extracellular fluid
• CPC Class Codes: A61P 9/00 : Drugs for disorders of the cardiovascular system
• CPC Class Codes: A61P 9/04 : Inotropic agents, i.e. stimulants of cardiac contraction; Drugs for heart failure
• CPC Class Codes: A61P 9/10 : for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
• CPC Class Codes: C12N 15/1135 : against oncogenes or tumor suppressor genes
• CPC Class Codes: C12N 15/1137 : against enzymes viral enzymes C12N15/1131; receptors C12N15/1138
• CPC Class Codes: C12N 2310/11 : Antisense
• CPC Class Codes: C12N 2310/14 : interfering N.A.
• CPC Class Codes: C12N 2310/315 : Phosphorothioates
• CPC Class Codes: C12Q 1/6886 : for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/158 : Expression markers

Abstract

The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of Tumor Suppressor genes, in particular, by targeting natural antisense polynucleotides of Tumor Suppressor genes. The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of Tumor Suppressor genes.

Claims

1. A method of upregulating a function of and/or the expression of a PTEN Tumor Suppressor gene polynucleotide in patient cells or tissues in vivo or in vitro comprising:

contacting said cells or tissues with at least one single-stranded antisense oligonucleotide of 15 to 30 nucleotides in length that targets, is 100% complementary to and specifically hybridizes to a complementary region of a natural antisense polynucleotide of a Tumor Suppressor gene polynucleotide selected from the group consisting of nucleotides 1-189 of SEQ ID NO;

14 and nucleotides 1-467 of SEQ ID NO;

15;

thereby upregulating a function of and/or the expression of the Tumor Suppressor gene polynucleotide in patient cells or tissues in vivo or in vitro.

2. The method of claim 1, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide antisense to coding and/or non-coding nucleic acid sequences of a Tumor Suppressor gene polynucleotide.

3. The method of claim 1, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide having overlapping and/or non-overlapping sequences with a Tumor Suppressor gene polynucleotide.

4. The method of claim 1, wherein the at least one antisense oligonucleotide comprises one or more modifications selected from:

at least one modified sugar moiety, at least one modified internucleoside linkage, at least one modified nucleotide, and combinations thereof.

5. The method of claim 4, wherein the one or more modifications comprise at least one modified sugar moiety selected from:

a 2′

-O-methoxyethyl modified sugar moiety, a 2′

-methoxy modified sugar moiety, a 2′

-O-alkyl modified sugar moiety, a bicyclic sugar moiety, and combinations thereof.

6. The method of claim 4, wherein the one or more modifications comprise at least one modified internucleoside linkage selected from:

a phosphorothioate, alkylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, a carboxymethyl ester, and combinations thereof.

7. The method of claim 4, wherein the one or more modifications comprise at least one modified nucleotide selected from:

a peptide nucleic acid (PNA), a locked nucleic acid (LNA), an arabino-nucleic acid (FANA), and combinations thereof.

8. The method of claim 1, wherein the at least one oligonucleotide comprises at least one of the oligonucleotide sequences set forth as SEQ ID NO:

36.

9. A method of upregulating a function of and/or the expression of a Tumor Suppressor gene in mammalian cells or tissues in vivo or in vitro comprising:

contacting said cells or tissues with at least one antisense oligonucleotide of about 20 to 30 nucleotides in length specifically hybridizing to a natural antisense strand of a PTEN Tumor Suppressor gene polynucleotide wherein said at least one single-stranded antisense oligonucleotide has at least 100% sequence complementarity to 20 to 30 nucleotides within at least one nucleic acid sequence set forth as SEQ ID NO;

14 and, upregulating the function and/or expression of the PTEN Tumor Suppressor gene in mammalian cells or tissues in vivo or in vitro and further wherein the target region includes nucleotides 1-189, 431-789 of SEQ ID NO;

14 and nucleotides 1-467 of SEQ ID NO;

15.

10. A method of preventing or treating a disease associated with at least one Tumor Suppressor gene polynucleotide and/or at least one encoded product thereof, comprising:

administering to a patient a therapeutically effective dose of at least one antisense oligonucleotide of 15 to 30 nucleotides in length that is 100% complementary to and specifically hybridizes to a complementary region of a natural antisense sequence of said at least one Tumor Suppressor gene polynucleotide having nucleotides 1-189 of SEQ ID NO;

14 or nucleotides 1-467 of SEQ ID NO;

15 and upregulates expression of said at least one Tumor Suppressor gene polynucleotide;

thereby preventing or treating the disease associated with the at least one Tumor Suppressor gene polynucleotide and/or at least one encoded product thereof and further wherein the disease is selected from cancer.