Oligonucleotide therapy for leber congenital amaurosis

• US 10,421,963 B2
• Filed: 02/26/2016
• Issued: 09/24/2019
• Est. Priority Date: 02/27/2015
• Status: Active Grant

• Current Assignee: ProQR Therapeutics II B.V
• Original Assignee: ProQR Therapeutics II B.V
• Inventors: Biasutto, Patricia Coromoto, Chan, Hee Lam
• Primary Examiner(s): Poliakova-Georgantas, Ekaterina
• Application Number:
  US15/551,026
• Publication Number:
  US 20180030439A1
• Time in Patent Office: 1,306 Days
• Field of Search: None
• CPC Class Codes: A61K 31/7125 Nucleic acids or oligonucleotides having modified internucleoside linkage, i.e. other than 3'-5' phosphodiesters
• CPC Class Codes: A61P 27/02 Ophthalmic agents
• 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 2310/346 having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2320/33 Alteration of splicing
• CPC Class Codes: C12N 2330/51 Specially adapted vectors

Abstract

Antisense oligonucleotides target the mutation in intron 26 of the CEP290 gene and reduce inclusion of the aberrant exon into the CEP290 mRNA. The oligonucleotides include no more than 3 consecutive guanosines, have no more than 60% guanosine nucleobases, include at most one CpG sequence, and/or do not have the potential to form a hairpin comprising 3 or more consecutive complementary base pairs.

Claims

1. An in vitro and/or in vivo method for modulating splicing of CEP290 pre-mRNA in a cell carrying a c.2991+1655A>

G mutation in intron 26 of the CEP290 gene, the method comprising contacting the cell with an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of SEQ ID NO;

5, 6, and 7.

2. The method of claim 1, wherein the oligonucleotide comprises a modified ribose that is substituted at the 2′

position with a substituent selected from the group consisting of;

(i) OH;

(ii) F;

(iii) substituted or unsubstituted, linear or branched lower (C1-C10) alkyl, alkenyl, alkynyl, alkaryl, allyl, or aralkyl, that may be interrupted by one or more heteroatoms;

(iv) O-, S-, or N-alkyl;

(v) O-, S-, or N-alkenyl;

(vi) O-, S- or N-alkynyl;

(vii) O-, S-, or N-allyl;

(viii) O-alkyl-O-alkyl, -methoxy, or -aminopropoxy;

(ix) methoxyethoxy;

(x) dimethylaminooxyethoxy; and

(xi) dimethylaminoethoxyethoxy.

3. The method of claim 2, wherein the oligonucleotide comprises a 2′

-O-methyl modified ribose.

4. The method of claim 3, wherein each ribose in the oligonucleotide is a 2′

-O-methyl modified ribose.

5. The method of claim 2, wherein the oligonucleotide comprises a 2′

-O-methoxyethyl modified ribose.

6. The method of claim 5, wherein each ribose in the oligonucleotide is a 2′

-O-methoxyethyl modified ribose.

7. The method of claim 1, wherein the oligonucleotide comprises a phosphorothioate backbone.

11. The method of claim 1, wherein the oligonucleotide consists of the nucleotide sequence of SEQ ID NO:

7.

8. An in vitro and/or in vivo method for modulating splicing of CEP290 pre-mRNA in a cell carrying a c.2991+1655A>

G mutation in intron 26 of the CEP290 gene, the method comprising contacting the cell with a viral vector capable of expressing an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of SEQ ID NO;

5, 6, and 7.

12. The method of claim 8, wherein the oligonucleotide consists of the nucleotide sequence of SEQ ID NO:

7.

9. A method for treating Leber Congenital Amaurosis in a human subject carrying a c.2991+1655A>

G mutation in intron 26 of the CEP290 gene, the method comprising administering to the subject an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of SEQ ID NO;

5, 6, and 7.

13. The method of claim 9, wherein the oligonucleotide consists of the nucleotide sequence of SEQ ID NO:

7.

10. A method for treating Leber Congenital Amaurosis in a human subject carrying a c.2991+1655A>

G mutation in intron 26 of the CEP290 gene, the method administering to the subject a viral vector capable of expressing an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of SEQ ID NO;

5, 6 and 7.

14. The method of claim 10, wherein the oligonucleotide consists of the nucleotide sequence of SEQ ID NO:

7.