Treatment of reprogramming factor related diseases by inhibition of natural antisense transcript to a reprogramming factor

• US 8,957,037 B2
• Filed: 05/18/2010
• Issued: 02/17/2015
• Est. Priority Date: 05/18/2009
• 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): GIBBS, TERRA C
• Application Number:
  US13/320,637
• Publication Number:
  US 20120064048A1
• Time in Patent Office: 1,736 Days
• Field of Search: 514/44, 536/24.5
• US Class Current: 514/44.A
• 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 17/06 Antipsoriatics
• CPC Class Codes: A61P 21/04 for myasthenia gravis
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 27/02 Ophthalmic agents
• CPC Class Codes: A61P 27/10 for accommodation disorders, e.g. myopia
• 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 3/04 Anorexiants; Antiobesity agents
• CPC Class Codes: A61P 3/10 for hyperglycaemia, e.g. antidiabetics
• CPC Class Codes: A61P 31/00 Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 31/04 Antibacterial agents
• CPC Class Codes: A61P 31/10 Antimycotics
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 33/00 Antiparasitic agents
• CPC Class Codes: A61P 33/02 Antiprotozoals, e.g. for leishmaniasis, trichomoniasis, toxoplasmosis
• CPC Class Codes: A61P 35/00 : Antineoplastic agents
• CPC Class Codes: A61P 37/00 : Drugs for immunological or allergic disorders
• CPC Class Codes: A61P 37/04 : Immunostimulants
• CPC Class Codes: A61P 37/06 : Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: A61P 9/00 : Drugs for disorders of the cardiovascular system
• 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 15/111 : General methods applicable to biologically active non-coding nucleic acids
• 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 2310/113 : targeting other non-coding nucleic acids, e.g. antagomirs
• CPC Class Codes: C12N 2310/14 : interfering N.A.
• CPC Class Codes: C12N 2310/31 : of the backbone
• CPC Class Codes: C12N 2310/312 : Phosphonates
• CPC Class Codes: C12N 2310/313 : Phosphorodithioates
• CPC Class Codes: C12N 2310/314 : Phosphoramidates
• CPC Class Codes: C12N 2310/315 : Phosphorothioates
• CPC Class Codes: C12N 2310/316 : Phosphonothioates
• CPC Class Codes: C12N 2310/3181 : Peptide nucleic acid, PNA
• CPC Class Codes: C12N 2310/32 : of the sugar
• CPC Class Codes: C12N 2310/321 : 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 : 2'-R Modification
• CPC Class Codes: C12N 2310/3231 : having an additional ring, e.g. LNA, ENA
• CPC Class Codes: C12N 2320/30 : Special therapeutic applications

Abstract

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

Claims

1. A method of upregulating a function of or the expression of a Reprogramming factor polynucleotide selected from SEQ ID NOS:

1,2 or 3 in mammalian cells or tissues in vivo or in vitro comprising;

contacting said cells or tissues with at least one single stranded antisense oligonucleotide 14 to 28 nucleotides in length wherein said at least one oligonucleotide is specific for a natural antisense polynucleotide of said Reprogramming thetor polynucleotide and has at least 90% sequence identity to a reverse complement of said natural antisense polynucleotide comprising 10 to 30 consecutive nucleotides within nucleotides 1 to 993 of SEQ ID NO;

4, 1 to 493 of SEQ ID NO;

5, and 1 to 418 of SEQ ID NO;

6;

thereby upregulating a function of and/or the expression of the Reprogramming factor polynucleotide in mammalian cells or tissues in vivo or in vitro.

12. The method of claim 1, wherein the at least one oligonucleotide comprises at least one oligonueleotide sequences set forth as SEQ ID NOS:

7 to 17.

18. The method of claim 1, wherein the at least one oligonucleotide comprises at least one oligonucleotide sequences set forth as SEQ ID NOS:

7 to 17.

2. A method of upregulating a function of and/or the expression of a Reprogramming factor polynucleotide selected from SOX2, KLF4 or POUF51 in mammalian cells or tissues in vivo or in vitro comprising:

contacting said cells or tissues with at least one single stranded antisense oligonucleotide 14 to 28 nucleotides in length wherein said at least one oligonucleotide is specific for a natural antisense polynucleotide of said Reprogramming Factor polynucleotide and has at least 90% sequence identity to a reverse complement of a natural antisense of a Reprogramming factor polynucleotide;

thereby upregulating a function of and/or the expression of the Reprogramming factor polynucleotide in mammalian cells or tissues in vivo or in vitro.

3. A method of upregulating a function of and/or the expression of a Reprogramming factor polynucleotide selected from SOX1, KLF4 or POU5F1 in mammalian cells or tissues in vivo or in vitro comprising:

contacting said cells or tissues with at least one single stranded antisense oligonucleotide of 12 to 28 nucleotides in length that specifically targets and hybridizes to a region of a natural antisense polynuelcotide of the Reprogramming factor polynuceotide selected from SEQ ID NOS;

4, 5 or 6;

thereby upregulating a function of and/or the expression of the Reprogramming factor polynucleotide in mammalian cells or tissues in vivo or in vitro.

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

5. The method of claim 3, wherein the at least one antisense oligonucleotide targets a natural antisense sequence of a Reprogramming factor polynucleotide having SEQ ID NO:

4.

6. The method of claim 3, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide antisense to coding nucleic acid sequences of a Reprogramming factor polynucleotide.

7. The method of claim 3, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide having overlapping sequences with a Reprogramming factor polynucleotide.

8. 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.

9. The method of claim 8, 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.

10. The method of claim 8, wherein the one or more modifications comprise at least one modified intemucleoside linkage selected from:

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

11. The method of claim 8, 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-nueleic acid (FANA), an analogue, a derivative, and combinations thereof.

13. A method of upregulating a function of and/or the expression of a Reprogramming factor selected from SOX1, KLF41 or POU5F1 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 natural antisense polynucleotide of a Reprogramming factor polynucleotide, wherein one strand of said at least one siRNA oligonucleotide has at least 80% sequence complementarity to at least about 19 nucleotides of said natural antisense polvnucleotide and, upregulating a function of and/or the expression of a Reprogramming factor in mammalian cells or tissues in vivo or in vitro.

14. The method of claim 13, wherein said oligonucleotide has at least 90% sequence complementarity to said natural antisense polynucleotide.

15. A method of upregulating a function of and/or the expression of a Reprogramming factor selected from SOX1, KLF4 or POU5F1 in mammalian cells or tissues in vivo or in vitro comprising:

contacting said cells or tissues with at least one single stranded antisense oligonucleotide of about 16 to 30 nucleotides in length specific for as natural antisense strand of as Reprogramming factor polynucleotide wherein said at least one antisense oligonucleotide has at least 80% sequence identity to at least one nucleic acid sequence set forth as SEQ ID NOS;

1 to 3 or an RNA transcribed from the Reprogramming factor polynucleotide; and

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

16. A method of preventing or treating a disease associated with at least one Reprogramming factor polynucleotide and/or at least one encoded product thereof selected from SOX1, KLF4 or POU5F1, comprising:

administering to a patient a therapeutically effective dose of at least one single stranded antisense oligonucleotide of 10 to 30 nucleotides in length that specifically binds to a natural antisense sequence of said at least one Reprogramming factor polynucleotide selected from SEQ ID NOS;

4, 5 or 6 and upregulates expression of said at least one Reprogramming factor polynucleotide;

thereby preventing or treating the disease associated with the at least one Reprogramming factor polynucleotide and/or at least one encoded product thereof.

17. The method of claim 16, wherein a disease associated with the at least one Reprogramming factor polynucleotide is selected from:

abnormal Reprogramming factor expression and/or function, cancer, a renal disease, a cardiovascular disease or disorder, inflammation, a neurological disease or disorder, scarring, ophthalmic diseases or disorders selected from microphthalmia, coloboma, myopia, anophthalmia/microphthalmia—

esophageal atresia syndrome, Septooptic dysplasia, an autoimmune disease or disorder, diabetes, atherosclerosis, an immunodeficiency disease, a disease caused by infectious agent including, viral, bacterial, fungal, protozoan, a genetic disease selected, from Duchenne muscular dystrophy, a metabolic disease or disorder selected from diabetes, obesity, metabolic syndrome, lysosomal disease, trauma selected from spinal cord injury, burns;

ischemia, a vascular disease, a hepatic disease or disorder, Psoriasis, a disease, a disease or disorder requiring transplantation of cells, tissues, and organs, disorder or condition requiring stem cell therapy and a congenital disease or disorder.