Treatment of colony-stimulating factor 3 (CSF3) related diseases by inhibition of natural antisense transcript to CSF3

• US 8,980,856 B2
• Filed: 04/01/2011
• Issued: 03/17/2015
• Est. Priority Date: 04/02/2010
• 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:
  US13/638,954
• Publication Number:
  US 20130035372A1
• Time in Patent Office: 1,446 Days
• Field of Search: 514/44, 536/24.5
• US Class Current: 514/44.A
• 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 19/00 Drugs for skeletal disorders
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• 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 31/00 Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/00 Drugs for immunological or allergic disorders
• CPC Class Codes: A61P 37/02 Immunomodulators
• CPC Class Codes: A61P 37/06 Immunosuppressants, e.g. drugs for graft rejection
• 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 7/06 Antianaemics
• CPC Class Codes: A61P 9/00 Drugs for disorders of the cardiovascular system
• 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 15/1136 against growth factors, growth regulators, cytokines, lymphokines or hormones
• 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 2310/315 : Phosphorothioates
• CPC Class Codes: C12N 2330/10 : naturally occurring
• 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 2600/178 : miRNA, siRNA or ncRNA
• CPC Class Codes: G01N 25/04 : of melting point; of freezing point; of softening point

Abstract

The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of Colony-stimulating factor 3 (CSF3), in particular, by targeting natural antisense polynucleotides of Colony-stimulating factor 3 (CSF3). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of CSF3.

Claims

1. A method of upregulating a function of and/or the expression of a Colony-stimulating factor 3 (CSF3) 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 30 nucleotides in length wherein said at least one oligonucleotide has at least 80% sequence identity to a reverse complement of a polynucleotide comprising 12 to 30 nucleotides within nucleotides 1 to 742 of SEQ ID NO;

2;

thereby upregulating a function of and/or the expression of the Colony-stimulating factor 3 (CSF3) polynucleotide in mammalian cells or tissues in vivo or in vitro.

13. 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 7.

2. A method of upregulating a function of and/or the expression of a Colony-stimulating factor 3 (CSF3) polynucleotide in mammalian cells or tissues in vivo or in vitro comprising:

contacting said cells or tissues with at least one antisense oligonucleotide 12 to 30 nucleotides in length wherein said at least one oligonucleotide has at least 80% sequence identity to a reverse complement of a natural antisense of a Colony-stimulating factor 3 (CSF3) polynucleotide;

thereby upregulating a function of and/or the expression of the Colony-stimulating factor 3 (CSF3) 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 Colony-stimulating factor 3 (CSF3) polynucleotide in mammalian cells or tissues in viva or in vitro comprising:

contacting said cells or tissues with at least one antisense oligonucleotide 12 to 30 nucleotides in length wherein said oligonucleotide has at least 80% sequence identity to 12 to 30 nucleotides within an antisense oligonucleotide to the Colony-stimulating factor 3 (CSF3) polynucleotide having SEQ ID NO;

1;

thereby upregulating a function of and/or the expression of the Colony-stimulating factor 3 (CSF3) polynucleotide in mammalian cells or tissues in vive or in vitro.

4. A method of upregulating a function of and/or the expression of a Colony-stimulating factor 3 (CSF3) 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 30 nucleotides in length that targets and specifically hybridizes to a region of a natural antisense polynucleotide of the Colony-stimulating factor 3 (CSF3) polynucleotide;

thereby upregulating a function of and/or the expression of the Colony-stimulating factor 3 (CSF3) polynucleotide in mammalian cells or tissues in vivo or in vitro.

5. The method of claim 4, wherein a function of and/or the expression of the Colony-stimulating factor 3 (CSF3) is increased in vivo 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 of a Colony-stimulating factor 3 (CSF3) polynucleotide having SEQ ID NO:

2.

7. 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 Colony-stimulating factor 3 (CSF3) polynucleotide.

8. 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 Colony-stimulating factor 3 (CSF3) polynucleotide.

9. 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.

10. The method of claim 9, 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.

11. The method of claim 9, 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.

12. The method of claim 9, 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.

14. A method of upregulating a function of and/or the expression of a Colony-stimulating factor 3 (CSF3) 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 natural antisense polynucleotide of a Colony-stimulating factor 3 (CSF3) polynucleotide, wherein said at least one siRNA oligonucleotide has at least 80% complementarity to the natural antisense polynucleotide of the Colony-stimulating factor 3 (CSF3) polynucleotide; and

, upregulating a function of and/or the expression of Colony-stimulating factor 3 (CSF3) in mammalian cells or tissues in vivo or in vitro.

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

16. A method of upregulating a function of and/or the expression of Colony-stimulating factor 3 (CSF3) in mammalian cells or tissues in vivo or in vitro comprising:

contacting said cells or tissues with at least one antisense oligonucleotide of about 14 to 28 nucleotides in length specific for noncoding and/or coding sequences of a natural antisense strand of a Colony-stimulating factor 3 (CSF3) 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 NO;

1 or an RNA transcribed from the CSF3 polynucleotide; and

, upregulating the function and/or expression of the Colony-stimulating factor 3 (CSF3) in mammalian cells or tissues in vivo or in vitro.

17. A method of treating a disease associated with at least one Colony-stimulating factor 3 (CSF3) polynucleotide having SEQ ID NO:

1, comprising;

administering to a patient a therapeutically effective dose of at least one antisense oligonucleotide of 10 to 30 nucleotides in length that binds and specifically hybridizes to a natural antisense sequence of said at least one Colony-stimulating factor 3 (CSF3) polynucleotide and upregulates expression of A said at least one Colony-stimulating factor 3 (CSF3) polynucleotide;

thereby treating the disease associated with the at least one Colony-stimulating factor 3 (CSF3) polynucleotide wherein said disease associated with the at least one Colony-stimulating factor 3 (CSF3) polynucleotide is selected from;

a disease or disorder associated with abnormal function and/or expression of CSF3, cancer, neutropenia, neoplasm, Idiopathic Thrombocytopenia Purpura (ITP), a hematological disease or disorder, wound, skin aging, a skin disease or disorder, wrinkles, a skin aberration (e.g., skin injury, scar, skin damaged by disease or sun etc.), a disease or disorder associated with collagen deposition, a disease or disorder associated with impaired neurogenesis, a disease or disorder associated with defective granulocyte formation, a cardiovascular disease or disorder, diabetic peripheral neuropathy, Felty'"'"'s syndrome, systemic lupus erythematosus (SLE), a pathological condition, an immune disease or disorder, an infectious disease or disorder, an autoimmune disease or disorder, an inflammatory disease or disorder, organ transplant support, Graft versus host disease (GVHD), an inflammation, a bone loss disease or disorder, a bone marrow disease or disorder, a proliferative disease or disorder, a neurological disease or disorder and a chronic inflammatory disease or disorder.