Antisense oligonucleotides for inducing exon skipping and methods of use thereof

• US 9,605,262 B2
• Filed: 06/15/2015
• Issued: 03/28/2017
• Est. Priority Date: 06/28/2004
• Status: Active Grant

• Current Assignee: University of Western Australia
• Original Assignee: University of Western Australia
• Inventors: Wilton, Stephen Donald, Fletcher, Sue, McClorey, Graham
• Primary Examiner(s): Chong, Kimberly
• Application Number:
  US14/740,097
• Publication Number:
  US 20150353931A1
• Time in Patent Office: 652 Days
• US Class Current: 1/1
• CPC Class Codes: A61P 21/00 Drugs for disorders of the muscular or neuromuscular 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 2310/11 Antisense
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/3233 Morpholino-type ring
• CPC Class Codes: C12N 2310/33 of the base
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/3519 Fusion with another nucleic acid
• CPC Class Codes: C12N 2320/30 Special therapeutic applications
• CPC Class Codes: C12N 2320/33 Alteration of splicing

Abstract

An antisense molecule capable of binding to a selected target site to induce exon skipping in the dystrophin gene, as set forth in SEQ ID NO: 1 to 214.

Claims

1. A method for treating a patient with Duchenne muscular dystrophy (DMD) in need thereof who has a mutation of the DMD gene that is amenable to exon 8 skipping, comprising administering to the patient an antisense oligonucleotide selected from the group consisting of:

(i) an antisense oligonucleotide of 24 bases in length 100% complementary to a target region of exon 8 of the human dystrophin pre-mRNA, wherein the target region is annealing site H8A(−

06+18), wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide specifically hybridizes to the annealing site inducing exon 8 skipping;

(ii) an antisense oligonucleotide of 21 bases in length 100% complementary to a target region of exon 8 of the human dystrophin pre-mRNA, wherein the target region is annealing site H8A (−

03+18), wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide specifically hybridizes to the annealing site inducing exon 8 skipping;

(iii) an antisense oligonucleotide of 25 bases in length 100% complementary to a target region of exon 8 of the human dystrophin pre-mRNA, wherein the target region is annealing site H8A(−

07+18), wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide specifically hybridizes to the annealing site inducing exon 8 skipping;

(iv) an antisense oligonucleotide of 20 bases in length 100% complementary to a target region of exon 8 of the human dystrophin pre-mRNA, wherein the target region is annealing site H8A(−

06+14), wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide specifically hybridizes to the annealing site inducing exon 8 skipping;

or a pharmaceutically acceptable salt thereof,

thereby treating the patient.

2. The method of claim 1, wherein the antisense oligonucleotide is chemically linked to one or more moieties or conjugates that enhance the activity, cellular distribution, or cellular uptake of the antisense oligonucleotide.

3. The method of claim 1, wherein the antisense oligonucleotide is chemically linked to a polyethylene glycol chain.

4. The method of claim 1, wherein the antisense oligonucleotide is administered intravenously.

5. A method for treating a patient with Duchenne muscular dystrophy (DMD) in need thereof who has a mutation of the DMD gene that is amenable to exon 8 skipping, comprising administering to the patient an antisense oligonucleotide selected from the group consisting of:

(i) an antisense oligonucleotide of 24 bases comprising the base sequence GAU AGG UGG UAU CAA CAU CUG UAA (SEQ ID NO;

     1), in which the uracil bases are thymine bases and wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide;

(ii) an antisense oligonucleotide of 21 bases comprising the base sequence GAU AGG UGG UAU CAA CAU CUG (SEQ ID NO;

     2), in which the uracil bases are thymine bases and wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide;

(iii) an antisense oligonucleotide of 25 bases comprising the base sequence GAU AGG UGG UAU CAA CAU CUG UAA G (SEQ ID NO;

     3), in which the uracil bases are thymine bases and wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide;

(iv) an antisense oligonucleotide of 20 bases comprising the base sequence GGU GGU AUC AAC AUC UGU AA (SEQ ID NO;

     4), in which the uracil bases are thymine bases and wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide;

or a pharmaceutically acceptable salt thereof,

thereby treating the patient.

6. The method of claim 5, wherein the antisense oligonucleotide is chemically linked to one or more moieties or conjugates that enhance the activity, cellular distribution, or cellular uptake of the antisense oligonucleotide.

7. The method of claim 5, wherein the antisense oligonucleotide is chemically linked to a polyethylene glycol chain.

8. The method of claim 5, wherein the antisense oligonucleotide is administered intravenously.

9. A method for treating a patient with Duchenne muscular dystrophy (DMD) in need thereof who has a mutation of the DMD gene that is amenable to exon 8 skipping, comprising administering to the patient a pharmaceutical composition comprising:

(a) an antisense oligonucleotide selected from the group consisting of;

(i) an antisense oligonucleotide of 24 bases comprising the base sequence GAU AGG UGG UAU CAA CAU CUG UAA (SEQ ID NO;

     1), in which the uracil bases are thymine bases, wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide is chemically linked to a polyethylene glycol chain;

(ii) an antisense oligonucleotide of 21 bases comprising the base sequence GAU AGG UGG UAU CAA CAU CUG (SEQ ID NO;

     2), in which the uracil bases are thymine bases, wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide is chemically linked to a polyethylene glycol chain;

(iii) an antisense oligonucleotide of 25 bases comprising the base sequence GAU AGG UGG UAU CAA CAU CUG UAA G (SEQ ID NO;

     3), in which the uracil bases are thymine bases, wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide is chemically linked to a polyethylene glycol chain;

(iv) an antisense oligonucleotide of 20 bases comprising the base sequence GGU GGU AUC AAC AUC UGU AA (SEQ ID NO;

     4), in which the uracil bases are thymine bases, wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide is chemically linked to a polyethylene glycol chain;

or a pharmaceutically acceptable salt thereof; and

(b) a pharmaceutically acceptable carrier,

thereby treating the patient.

10. The method of claim 9, wherein the antisense oligonucleotide is administered intravenously.

11. A method for restoring an mRNA reading frame to induce dystrophin protein production in a patient with Duchenne muscular dystrophy (DMD) in need thereof who has a mutation of the DMD gene that is amenable to exon 8 skipping, comprising administering to the patient an antisense oligonucleotide selected from the group consisting of:

(i) an antisense oligonucleotide of 24 bases in length 100% complementary to a target region of exon 8 of the human dystrophin pre-mRNA, wherein the target region is annealing site H8A(−

06+18), wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide specifically hybridizes to the annealing site inducing exon 8 skipping;

(ii) an antisense oligonucleotide of 21 bases in length 100% complementary to a target region of exon 8 of the human dystrophin pre-mRNA, wherein the target region is annealing site H8A (−

03+18), wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide specifically hybridizes to the annealing site inducing exon 8 skipping;

(iii) an antisense oligonucleotide of 25 bases in length 100% complementary to a target region of exon 8 of the human dystrophin pre-mRNA, wherein the target region is annealing site H8A(−

07+18), wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide specifically hybridizes to the annealing site inducing exon 8 skipping;

(iv) an antisense oligonucleotide of 20 bases in length 100% complementary to a target region of exon 8 of the human dystrophin pre-mRNA, wherein the target region is annealing site H8A(−

06+14), wherein the antisense oligonucleotide is a morpholino antisense oligonucleotide, and wherein the antisense oligonucleotide specifically hybridizes to the annealing site inducing exon 8 skipping;

or a pharmaceutically acceptable salt thereof,

thereby restoring the mRNA reading frame to induce dystrophin protein production in the patient.

12. The method of claim 11, wherein the antisense oligonucleotide is chemically linked to one or more moieties or conjugates that enhance the activity, cellular distribution, or cellular uptake of the antisense oligonucleotide.

13. The method of claim 11, wherein the antisense oligonucleotide is chemically linked to a polyethylene glycol chain.

14. The method of claim 11, wherein the antisense oligonucleotide is administered intravenously.