Treatment of pancreatic developmental gene related diseases by inhibition of natural antisense transcript to a pancreatic developmental gene

• US 8,912,157 B2
• Filed: 01/06/2011
• Issued: 12/16/2014
• Est. Priority Date: 01/06/2010
• 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:
  US13/520,496
• Publication Number:
  US 20120322853A1
• Time in Patent Office: 1,440 Days
• Field of Search: None
• US Class Current: 514/44
• CPC Class Codes: A61K 31/7088 Compounds having three or more nucleosides or nucleotides
• CPC Class Codes: A61P 1/00 Drugs for disorders of the alimentary tract or the digestive system
• CPC Class Codes: A61P 1/04 for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
• CPC Class Codes: A61P 1/14 Prodigestives, e.g. acids, enzymes, appetite stimulants, antidyspeptics, tonics, antiflatulents
• CPC Class Codes: A61P 1/16 for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
• CPC Class Codes: A61P 1/18 for pancreatic disorders, e.g. pancreatic enzymes
• CPC Class Codes: A61P 11/02 Nasal agents, e.g. decongestants
• CPC Class Codes: A61P 13/10 of the bladder
• CPC Class Codes: A61P 13/12 of the kidneys
• CPC Class Codes: A61P 17/06 Antipsoriatics
• 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 21/00 Drugs for disorders of the muscular or neuromuscular system
• CPC Class Codes: A61P 21/02 Muscle relaxants, e.g. for tetanus or cramps
• 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 25/04 Centrally acting analgesics, e.g. opioids
• CPC Class Codes: A61P 25/16 Anti-Parkinson drugs
• 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 27/02 : Ophthalmic agents
• CPC Class Codes: A61P 27/12 : for cataracts
• 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 3/04 : Anorexiants; Antiobesity agents
• CPC Class Codes: A61P 3/06 : Antihyperlipidemics
• 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 31/20 : for DNA viruses
• CPC Class Codes: A61P 31/22 : for herpes viruses
• CPC Class Codes: A61P 35/00 : Antineoplastic agents
• CPC Class Codes: A61P 37/02 : Immunomodulators
• CPC Class Codes: A61P 37/06 : Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: A61P 37/08 : Antiallergic agents antiasthmatic agents A61P11/06; ophthalmic antiallergics A61P27/14
• 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 9/06 : Antiarrhythmics
• 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 15/113 : 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: C12Q 1/6813 : Hybridisation assays

Abstract

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

Claims

1. A method of upregulating a function of and/or the expression of a Pancreatic Developmental 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 19 to 21 nucleotides in length wherein said at least one oligonucleotide has at least 90% sequence identity to a reverse complement of a polynucleotide comprising 19 to 21 consecutive nucleotides within the natural antisense polynucleotide selected from the group consisting of nucleotides 1 to 1235 of SEQ ID SEQ ID NO;

6, 1 to 17,964 of SEQ ID NO;

7, 1 to 1 to 50,003 of SEQ ID SEQ ID NO;

8, 1 to 486 of SEQ ID NO;

9, 1 to 494 of SEQ ID NO;

10, 1 to 1992 of SEQ ID NO;

11, or 1 to 1767 of SEQ ID NO;

12 and wherein said antisense oligonucleotide specifically targets said natural antisense polynucleotide;

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

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

13 to 45.

2. A method of upregulating a function of and/or the expression of a Pancreatic Developmental gene polynucleotide selected from the group comprising SEQ ID NOS:

1-5 in patient cells or tissues in vivo or in vitro comprising;

contacting said cells or tissues with at least one single stranded antisense oligonucleotide 19 to 21 nucleotides in length wherein said at least one antisense oligonucleotide has at least 90% sequence identity to a corresponding 19 to 21 nucleotide region within a reverse complement of a natural antisense polynucleotide of a Pancreatic Developmental gene polynucleotide wherein said antisense oligonucleotide specifically targets said natural antisense polynucleotide;

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

3. A method of upregulating a function of and/or the expression of a Pancreatic Developmental gene polynucleotide in patient cells or tissues in vivo or in vitro comprising:

contacting said cells or tissues with at least one modified single stranded antisense oligonucleotide of 19 to 21 nucleotides in length that specifically targets a complementary region of a natural antisense polynucleotide the Pancreatic Developmental gene;

thereby upregulating a function of and/or the expression of the Pancreatic Developmental gene in patient cells or tissues in vivo or in vitro.

4. The method of claim 3, wherein a function of and/or the expression of Pancreatic Developmental gene is increased 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 selected from the group consisting of SEQ ID NOS:

6-12.

6. The method of claim 3, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide antisense to non-coding nucleic acid sequences of a Pancreatic Developmental gene polynucleotide.

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

8. The method of claim 3, wherein at least one antisense oligonucleotide comprises one or more modifications selected from:

at least one modified sugar moiety, at least one modified internuclcoside 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 internucleoside linkage selected from:

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

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

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

13. A method of upregulating a function of and/or the expression of a Pancreatic Developmental 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 21 nucleotides in length, said at least one siRNA oligonucleotide being specific for a natural antisense polynucleotide of a Pancreatic Developmental gene, wherein said at least one siRNA oligonucleotide has at least 90% sequence complementarity to a sequence of at least about nineteen consecutive nucleic acids of the natural antisense polynucleotide; and

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

14. The method of claim 13, wherein said oligonucleotide has sequence complementarity to a sequence of at least about nineteen consecutive nucleic acids of the natural antisense polynucleotide of the Pancreatic Developmental gene polynucleotide.

15. A method of upregulating a function of and/or the expression of a Pancreatic Developmental gene in mammalian cells or tissues in vitro comprising:

contacting said cells or tissues with at least one single stranded modified antisense oligonucleotide of about 19 to 21 nucleotides in length specific for a natural antisense polynucleotide of a Pancreatic Developmental gene wherein said at least one antisense oligonucleotide has at least 90% sequence identity to a 19 to 21 consecutive nucleotide region of the group consisting of SEQ ID NOS;

1 to 5 or polynucleotides transcribed from the Pancreatic Developmental gene; and

, upregulating the function and/or expression of the Pancreatic Developmental gene in mammalian cells or tissues in vitro.