Treatment of NANOG related diseases by inhibition of natural antisense transcript to NANOG

• US 8,987,225 B2
• Filed: 11/17/2011
• Issued: 03/24/2015
• Est. Priority Date: 11/23/2010
• 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): Chong, Kimberly
• Application Number:
  US13/989,124
• Publication Number:
  US 20130261065A1
• Time in Patent Office: 1,223 Days
• Field of Search: None
• US Class Current: 514/44
• CPC Class Codes: A61K 31/713 Double-stranded nucleic acids or oligonucleotides
• CPC Class Codes: A61P 1/16 for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
• CPC Class Codes: A61P 13/12 of the kidneys
• CPC Class Codes: A61P 17/00 Drugs for dermatological disorders
• 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 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 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/02 Immunomodulators
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: A61P 9/00 Drugs for disorders of the cardiovascular system
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• 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 2310/111 spanning the whole gene, or a large part of it
• CPC Class Codes: C12N 2310/113 : targeting other non-coding nucleic acids, e.g. antagomirs
• CPC Class Codes: C12N 2310/14 : interfering N.A.
• CPC Class Codes: C12N 2310/314 : Phosphoramidates
• CPC Class Codes: C12N 2310/315 : Phosphorothioates
• CPC Class Codes: C12N 2330/10 : naturally occurring
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]

Abstract

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

Claims

1. A method of upregulating a function of and/or the expression of an NANOG polynucleotide having SEQ ID NO:

1 in a mammalian system comprising;

contacting said system with at least one antisense oligonucleotide 10 to 30 nucleotides in length wherein said at least one oligonucleotide has at least 90% sequence identity to a 14 to 30 nucleotide region of a reverse complement of a natural antisense polynucleotide of an NANOG polynucleotide and specifically binds to said natural antisense polynucleotide;

thereby upregulating a function of and/or the expression of the NANOG polynucleotide.

2. A method of upregulating a function of and/or the expression of an NANOG polynucleotide in a mammalian system according to claim 1 comprising:

contacting said mammalian system with at least one antisense oligonucleotide 14 to 30 nucleotides in length wherein said at least one oligonucleotide has at least 80% sequence identity to a 14 to 30 nucleotide region of a reverse complement of a polynucleotide comprising 12 to 30 nucleotides within the natural antisense transcript nucleotides 1 to 548 of SEQ ID NO;

2;

thereby upregulating a function of and/or the expression of the NANOG polynucleotide.

11. The method of claim 1, wherein the at least one oligonucleotide comprises at least one oligonucleotide sequence selected from SEQ ID NOS:

3 to 6.

3. A method of upregutating a function of andlor the expression of an NANOG polynucleotide having SEQ ID NO:

1 in a mammalian system comprising;

contacting said system with at least one antisense oligonucleotide of 16 to 30 nucleotides in length that specifically targets and hybridizes to a region of a natural antisense polynucleotide of the NANOG polynucleotide wherein said natural antisense is selected from a polynucleotide having, SEQ ED NO;

2;

thereby upregulating a function of and/or the expression of the NANOG polynucleotide.

4. The method of claim 3, wherein a function of and/or the expression of the NANOG is increased in vivo or in vitro with respect to a mock-transfected control.

5. The method of claim 3, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide antisense to coding and/or non-coding nucleic acid sequences of an NANOG polynucleotide.

6. The method of claim 3, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide having overlapping and/or non-overlapping sequences of will with the RNA transcribed from the NANOG polynucleotide.

7. The method of claim 3, 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.

8. The method of claim 7, 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.

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

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

10. The method of claim 7, 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.

12. A method of upregulating a function of and/or the expression of an NANOG gene in mammalian cells or tissues in vivo or in vitro comprising:

contacting said cells or tissues with at least one short interfering RNA (siRNA) oligonucleotide 19 to 30 nucleotides in length, said at least one siRNA oligonucleotide being specific for a single strand of a natural antisense polynucleotide of an NANOG polynucleotide, wherein said at least one siRNA oligonucleotide has at least 80% sequence completnemarity to a region of said natural antisense polynucleotide of the NANOG polynucleotide; and

, upregulating a function of and/or the expression of NANOG in mammalian cells or tissues in vivo or in vitro.

13. The method of claim 12, wherein said oligonucleotide has at least 90% sequence complementarity to said region of said natural antisense polvnucleotide of the NANOG polynucleotide.

14. A method of upregulating a function of and/or the expression of NANOG polynucleotidc having SEQ ID NO:

1 in mammalian cells or tissues in vivo or vitro comprising;

contacting said cells or tissues with at least one antisense oligonucleotide of about 12 to 30 nucleotides in length specific for noncoding and/or coding sequences of a natural antisense strand of an NANOG polynucleotide wherein said at least one antisense oligonucleotide has at least 80% sequence identity to a 12 to 30 nucleotide region of at least one nucleic acid sequence set forth within SEQ ID NO;

1 or an RNA transcribed from the NANOG polynucleotide ; and

, upregulating the function and/or expression of the NANOG in mammalian cells or tissues in vivo or in vitro.

15. A method of preventing or treating a disease associated with at least one NANOG 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 10 to 30 nucleotides in length that specifically binds to a natural antisense sequence of said at least one NANOG polynucleotide and upregulates expression of said at least one NANOG polynucleotide;

thereby preventing or treating the disease associated with the at least one NANOG polynucleotide and/or at least one encoded product thereof wherein said disease associated with the at least one NANOG polynucleotide is selected from a disease or disorder associated with loss of a particular cell type or tissue that can be replaced by new cells/tissues regenerated from the pluripotent stem cells.