Treatment of atonal homolog 1 (ATOH1) related diseases by inhibition of natural antisense transcript to ATOH1

• US 8,895,528 B2
• Filed: 05/25/2011
• Issued: 11/25/2014
• Est. Priority Date: 05/26/2010
• 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): Bowman, Amy
• Application Number:
  US13/699,346
• Publication Number:
  US 20130085112A1
• Time in Patent Office: 1,280 Days
• US Class Current: 514/44
• CPC Class Codes: A61K 31/7125 Nucleic acids or oligonucleotides having modified internucleoside linkage, i.e. other than 3'-5' phosphodiesters
• CPC Class Codes: A61K 31/713 Double-stranded nucleic acids or oligonucleotides
• CPC Class Codes: A61P 1/00 Drugs for disorders of the alimentary tract or the digestive system
• 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 11/00 Drugs for disorders of the respiratory system
• CPC Class Codes: A61P 19/02 for joint disorders, e.g. arthritis, arthrosis
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 27/00 Drugs for disorders of the senses
• CPC Class Codes: A61P 27/16 Otologicals
• 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: C07K 2/00 Peptides of undefined number of amino acids; Derivatives thereof
• 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 2310/312 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 2310/321 : 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 2310/3521 : Methyl
• CPC Class Codes: C12N 2310/3525 : MOE, methoxyethoxy
• CPC Class Codes: C12N 2310/3533 : Halogen
• CPC Class Codes: C12N 2330/10 : naturally occurring
• CPC Class Codes: Y02A 50/30 : Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Abstract

The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of Atonal homolog 1 (ATOH1), in particular, by targeting natural antisense polynucleotides of Atonal homolog 1 (ATOH1). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of ATOH1.

Claims

1. A method of upregulating a function of and/or the expression of an Atonal homolog (ATOH1) polynucleotide selected from SEQ ID NO:

1 in a biological system comprising;

contacting said system with at least one single stranded antisense oligonucleotide 15 to 30 nucleotides in length wherein said at least one oligonucleotide has at least 80% sequence identity to a 15 to 30 nucleotide region of a reverse complement of a natural antisense of said Atonal homolog 1 (ATOH1) polynucleotide;

thereby upregulating a function of and/or the expression of the Atonal homolog 1 (ATOH1) polynucleotide.

2. A method of upregulating a function of and/or the expression of an Atonal homolog 1 (ATOH1) polynucleotide selected from SEQ ID NO:

1 in a biological system according to claim 1 comprising;

contacting said biological system with at least one single stranded antisense oligonucleotide 15 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 15 to 30 consecutive nucleotides within the natural antisense transcript nucleotides 1 to 589 of SEQ ID NO;

2;

thereby upregulating a function of and/or the expression of the Atonal homolog 1 (ATOH1) polynucleotide.

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

3 and 4.

3. A method of upregulating a function of and/or the expression of an Atonal homolog 1 (ATOH1) polynucleotide or encoded product thereof selected from SEQ ID NO:

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

contacting said cells or tissues with at least one single stranded antisense oligonucleotide 15 to 30 nucleotides in length wherein said oligonucleotide has at least 80% sequence identity to a 15 to 30 nucleotide region of an RNA transcribed from the Atonal homolog 1 (ATOH1) polynucleotide;

thereby upregulating a function of and/or the expression of the Atonal homolog 1 (ATOH1) polynucleotide in patient cells or tissues in vivo or in vitro.

4. A method of upregulating a function of and/or the expression of an Atonal homolog 1 (ATOH1) polynucleotide having SEQ ID NO:

1 in patient cells or tissues according to claim 3 comprising;

contacting said biological system with at least one single stranded antisense oligonucleotide 15 to 25 nucleotides in length wherein said at least one oligonucleotide has at least 90% sequence identity to 15 to 25 consecutive nucleotides of an RNA transcribed from a ATOH1 polynucleotide thereby upregulating a function of and/or the expression of the Atonal homolog 1 (ATOH1) polynucleotide.

5. A method of upregulating a function of and/or the expression of an Atonal homolog 1 (ATOH1) polynucleotide having SEQ ID NO:

1 in a biological system comprising;

contacting said system with at least one single stranded antisense oligonucleotide of about 10 to 30 nucleotides in length that is a complement of and specifically targets a region of a natural antisense oligonucleotide of the Atonal homolog 1 (ATOH1) polynucleotide;

thereby binding to said natural antisense oligonucleotide and upregulating a function of and/or the expression of the Atonal homolog 1 (ATOH1) polynucleotide.

6. The method of claim 5, wherein a function of and/or the expression of the Atonal homolog 1 (ATOH1) is increased in vivo or in vitro with respect to a control.

7. The method of claim 5, wherein the at least one antisense oligonucleotide targets a natural antisense sequence of an Atonal homolog 1 (ATOH1) polynucleotide having SEQ ID NO:

2.

8. The method of claim 5, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide antisense to coding and/or non-coding nucleic acid sequences of an Atonal homolog 1 (ATOH1) polynucleotide.

9. The method of claim 5, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide having overlapping and/or non-overlapping sequences with an Atonal homolog 1 (ATOH1) polynucleotide.

10. The method of claim 5, 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.

11. The method of claim 10, 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.

12. The method of claim 10, 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.

13. The method of claim 10, 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.

15. A method of upregulating a function of and/or the expression of Atonal homolog 1 (ATOH1) 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 30 nucleotides in length specific for noncoding sequences of a natural antisense strand of an Atonal homolog 1 (ATOH1) polynucleotide wherein said at least one antisense oligonucleotide has at least 50% sequence identity to at least one nucleic acid sequence set forth as SEQ ID NOS;

1 or a pre-RNA of said SEQ ID NO;

1; and

, upregulating the function and/or expression of the Atonal homolog 1 (ATOH1) in mammalian cells or tissues in vivo or in vitro.