Treatment of pyrroline-5-carboxylate reductase 1 (PYCR1) related diseases by inhibition of natural antisense transcript to PYCR1

• US 8,962,586 B2
• Filed: 02/21/2011
• Issued: 02/24/2015
• Est. Priority Date: 02/22/2010
• 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): GIBBS, TERRA C
• Application Number:
  US13/580,488
• Publication Number:
  US 20120309814A1
• Time in Patent Office: 1,464 Days
• Field of Search: 514/44, 536/24.5
• US Class Current: 514/44.A
• CPC Class Codes: A61K 31/7088 Compounds having three or more nucleosides or nucleotides
• CPC Class Codes: A61P 1/02 Stomatological preparations, e.g. drugs for caries, aphtae, periodontitis
• 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 1/16 for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
• CPC Class Codes: A61P 11/00 Drugs for disorders of the respiratory system
• CPC Class Codes: A61P 13/02 of urine or of the urinary tract, e.g. urine acidifiers
• CPC Class Codes: A61P 13/08 of the prostate
• CPC Class Codes: A61P 13/10 of the bladder
• CPC Class Codes: A61P 13/12 of the kidneys
• CPC Class Codes: A61P 15/00 Drugs for genital or sexual disorders for disorders of sex hormones A61P5/24; Contraceptives
• CPC Class Codes: A61P 17/00 Drugs for dermatological disorders
• CPC Class Codes: A61P 17/06 Antipsoriatics
• CPC Class Codes: A61P 19/00 Drugs for skeletal disorders
• CPC Class Codes: A61P 19/02 for joint disorders, e.g. arthritis, arthrosis
• CPC Class Codes: A61P 19/06 Antigout agents, e.g. antihyperuricemic or uricosuric agents
• 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 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 25/08 : Antiepileptics; Anticonvulsants
• 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 25/18 : Antipsychotics, i.e. neuroleptics; Drugs for mania or schizophrenia
• 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 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 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 5/00 : Drugs for disorders of the endocrine system
• 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 15/113 : 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 15/1137 : against enzymes viral enzymes C12N15/1131; receptors C12N15/1138
• 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 2310/315 : Phosphorothioates
• CPC Class Codes: C12N 2320/30 : Special therapeutic applications
• CPC Class Codes: C12Q 1/68 : involving nucleic acids
• CPC Class Codes: C12Q 1/6876 : Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2600/136 : Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/158 : Expression markers
• CPC Class Codes: C12Q 2600/178 : miRNA, siRNA or ncRNA
• CPC Class Codes: C12Y 105/01002 : Pyrroline-5-carboxylate reductase (1.5.1.2)

Abstract

The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of Pyrroline-5-carboxylate reductase 1 (PYCR1), in particular, by targeting natural antisense polynucleotides of Pyrroline-5-carboxylate reductase 1 (PYCR1). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of PYCR1.

Claims

1. A method of upregulating function of and/or the expression of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide having SEQ ID NO:

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

contacting said cells or tissues with at least one antisense oligonucleotide 12 to 26 nucleotides in length wherein said at least one oligonucleotide has at least 90% sequence identity to a reverse complement of a polynucleotide comprising 12 to 26 consecutive nucleotides within nucleotides 1 to 380 of SEQ ID NO;

2;

thereby upregulating a function of and/or the expression of the Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide in said 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:

3 to 6.

2. A method of upregulating a function of and/or the expression of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide having SEQ ID NO:

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

contacting said cells or tissues with at least one antisense oligonucleotide 12 to 26 nucleotides in length wherein said at least one oligonucleotide has at least 90% sequence identity to a reverse complement of a natural antisense of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide;

thereby upregulating a function of and/or the expression of the Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide in said cells or tissues in vivo or in vitro.

3. A method of upregulating a function of and/or the expression of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide having SEQ ID NO:

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

contacting said cells or tissues with at least one antisense oligonucleotide 12 to 26 nucleotides in length wherein said oligonucleotide has at least 80% sequence identity to 12 to 26 nucleotides within a sense polynucleotide of the Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide;

thereby upregulating a function of and/or the expression of the Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide in said cells or tissues in vivo or in vitro.

4. A method of upregulating a function of and/or the expression of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide having SEQ ID NO:

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

contacting said cells or tissues with at least one antisense oligonucleotide of 12 to 26 nucleotides in length that targets a region of and specifically hybridizes to a natural antisense oligonucleotide of the Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide having SEQ ID NO;

2;

thereby upregulating a function of and/or the expression of the Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide in said cells or tissues in vivo or in vitro.

5. The method of claim 4, wherein a function of and/or the expression of the Pyrroline-5-carboxylate reductase 1 (PYCR1) is increased in vim or in vitro with respect to a control.

6. The method of claim 4, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide antisense to coding and/or non-coding nucleic acid sequences of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide.

7. A The method of claim 4, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide having overlapping and/or non-overlapping sequences with a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide.

8. The method of claim 4, 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 internucleoside linkage selected from:

a phosphorothioate, 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 one modified nucleotide selected from:

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

13. A method of upregulating a function of and/or the expression of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide having SEQ ID NO:

1 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 Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide selected from SEQ ID NO;

2, and, upregulating a function of and/or the expression of Pyrroline-5-carboxylate reductase 1 (PYCR1) in mammalian cells or tissues in vivo or in vitro.

14. A method of upregulating a function of and/or the expression of Pyrroline-5-carboxylate reductase 1 (PYCR1) having SEQ ID NO:

1 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 12 to 26 nucleotides in length specific for a natural antisense strand of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide wherein said at least one antisense oligonucleotide has at least 80% sequence identity to 12 to 26 nucleotides within at least one nucleic acid sequence set forth as SEQ ID NOS;

1 or a polynucleotide encoded by the PYCR1 gene; and

, upregulating the function and/or expression of the Pyrroline-5-carboxylate reductase 1 (PYCR1) in mammalian cells or tissues in vivo or in vitro.

15. A method of preventing or treating a disease associated with at least one Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide having SEQ ID NO:

1, comprising;

administering to a human patient a therapeutically effective dose of at least one antisense oligonucleotide of 12 to 26 nucleotides in length that specifically hybridizes to a natural antisense sequence of said at least one Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide and upregulates expression of said at least one Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide;

thereby preventing or treating the disease associated with the at least one Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide and/or at least one encoded product thereof.

16. The method of claim 15, wherein a disease associated with the at least one Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide is selected from:

a disease or disorder associated with progeroid changes in connective tissue (e.g., cutis laxa, cutis lax type 1, cutis laxa type 2, Walt Disney dwarfism Autosomal recessive cutis laxa (ACRL), Geroderma osteodysplastica, De Barsy type Progeroid syndrome, Wrinkly skin syndrome, etc.