Treatment of alpha-L-iduronidase (IDUA) related diseases by inhibition of natural antisense transcript to IDUA

• US 9,222,088 B2
• Filed: 10/20/2011
• Issued: 12/29/2015
• Est. Priority Date: 10/22/2010
• Status: Active Grant

• Current Assignee: CURNA, Inc. (Opko Health, Inc.)
• Original Assignee: CURNA, Inc. (Opko Health, Inc.)
• Inventors: Collard, Joseph, Khorkova Sherman, Olga, Coito, Carlos, Shen, Gang
• Primary Examiner(s): WHITEMAN, BRIAN A
• Application Number:
  US13/880,409
• Publication Number:
  US 20130253036A1
• Time in Patent Office: 1,531 Days
• US Class Current: 1/1
• CPC Class Codes: A61K 31/7088 Compounds having three or more nucleosides or nucleotides
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• 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 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C12N 15/1034 Isolating an individual clone by screening libraries
• 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 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2320/50 Methods for regulating/modulating their activity
• CPC Class Codes: C12N 2330/10 naturally occurring
• CPC Class Codes: C12Y 302/01076 L-Iduronidase (3.2.1.76)
• CPC Class Codes: G01N 33/5308 for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites

Abstract

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

Claims

1. A method of upregulating a function of and/or the expression of an Alpha-L-Iduronidase (IDUA) polynucleotide having SEQ ID NO:

1 in a biological system comprising;

contacting said biological system with at least one single stranded antisense oligonucleotide 12 to 30 nucleotides in length wherein said at least one oligonucleotide has at least sequence identity to a reverse complement of a polynucleotide comprising 12 to 30 consecutive nucleotides within the natural antisense transcript nucleotides 1 to 2695 of SEQ ID NO;

2 or 1 to 2082 of SEQ ID NO;

3 or 1 to 2739 of SEQ ID NO;

9;

thereby upregulating a function of and/or the expression of the Alpha-L-Iduronidase (IDUA) polynucleotide.

2. A method of upregulating a function of and/or the expression of an Alpha-L-Iduronidase (IDUA) polynucleotide having SEQ ID NO:

1 in a biological system comprising;

contacting said system with at least one single stranded antisense oligonucleotide of 10 to 30 nucleotides in length that targets and specifically hybridizes to a region of a natural antisense polynucleotide of the Alpha-L-Iduronidase (IDUA) polynucleotide selected from the group consisting of SEQ ID NOS;

2 or 9;

thereby upregulating a function of and/or the expression of the Alpha-L-Iduronidase (IDUA) polynucleotide.

3. The method of claim 2, wherein a function of and/or the expression of the Alpha-L-Iduronidase (IDUA) is increased in vivo or in vitro with respect to a control.

4. The method according to claim 3 wherein the increase in expression relative to control is greater than about fifteen (15) percent.

5. The method according to claim 3 wherein the increase in expression relative to control is greater than about nineteen (19) percent.

6. The method according to claim 3 wherein the increase in expression relative to control is greater than about twenty-five (25) percent.

7. The method of claim 2, wherein the at least one antisense oligonucleotide targets a natural antisense sequence of an Alpha-L-Iduronidase (IDUA) polynucleotide selected from SEQ ID NO:

2.

8. The method of claim 2, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide antisense to coding nucleic acid sequences of an Alpha-L-Iduronidase (IDUA) polynucleotide.

9. The method of claim 2, wherein the at least one antisense oligonucleotide targets a natural antisense polynucleotide having overlapping sequences with an Alpha-L-Iduronidase (IDUA) polynucleotide.

10. The method of claim 2, 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.

14. The method of claim 2, wherein the at least one oligonucleotide comprises at least one oligonucleotide sequences set forth as SEQ ID NOS:

10, 11, 16, 17, 19, 20, 21, 22, 23, 24, 25 and 27.

15. A method of upregulating a function of and/or the expression of an Alpha-L-Iduronidase (IDUA) gene 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 an Alpha-L-Iduronidase (IDUA) polynucleotide selected from the group consisting of SEQ ID NOS;

2, 3 and 9; and

, upregulating a function of and/or the expression of Alpha-L-Iduronidase (IDUA) in mammalian cells or tissues in vivo or in vitro.

16. A method of upregulating a function of and/or the expression of Alpha-L-Iduronidase (IDUA) 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 single stranded antisense oligonucleotide of about 12 to 30 nucleotides in length specific for a natural antisense strand of an Alpha-L-Iduronidase (IDUA) polynucleotide wherein said at least one antisense oligonucleotide has sequence identity to 12 to 30 consecutive nucleotides of at least one nucleic acid sequence set forth as SEQ ID NO;

1; and

, upregulating the function and/or expression of the Alpha-L-Iduronidase (IDUA) in mammalian cells or tissues in vivo or in vitro.

17. A method of increasing expression of an IDUA polynucleotide or expression product thereof in a patient in need of treatment thereof comprising administration of an oligonucleotide that is at least 50% identical to a reverse complement of a natural antisense transcript to said IDUA polynucleotide to said patient and wherein the increase in expression of IDUA relative to a control is greater than about ten (10) percent and said natural antisense transcript is selected from SEQ ID NOS:

2, 3 and 9.