THERAPEUTICS FOR SYNGAP HAPLOINSUFFICIENCY
The invention relates to therapeutic compositions for disorders associated with haploinsufficiency. The invention provides antisense oligonucleotides useful for treating neurodevelopmental disorders associated with mutations in the SYNGAP gene. The invention provides compositions that include synthetic antisense oligonucleotides (ASOs) that promote expression of the SynGAP protein by one or any combination of (i) preventing one or more miRNAs from interfering with production of the SynGAP protein; (ii) binding to the 5′-UTR of the SYNGAP1 transcript and augmenting translation of the Syngap protein; and (iii) promoting RNAseH cleavage of antisense long non-coding RNAs that are anticorrelated with SYNGAP expression. When the composition is delivered to a patient with SYNGAP haploinsufficiency, the ASOs promote expression of the SynGAP protein.
1 . A composition comprising:
at least one nucleic acid that promotes expression of a SynGAP protein from a transcript of the SYNGAP gene and has at least 80% sequence similarity to one of SEQ ID Nos: 1-29.
2 . The composition of claim 1 , wherein the nucleic acid has a length between about 10 and about 30 bases.
3 . The composition of claim 2 , wherein the nucleic acid has a region of at least about 10 contiguous bases with a 100% match to a segment within one of SEQ ID Nos: 1-29.
4 . The composition of claim 3 , wherein some of the bases of the nucleic acid have a 2′-O-methoxyethyl-modified ribose.
5 . The composition of claim 4 , wherein a majority of inter-base linkages in the nucleic acid are phosphorothioate bonds.
6 . The composition of claim 5 , wherein at least about half of the bases in the nucleic acid comprise 2′-O-methoxyethyl ribose sugars.
7 . The composition of claim 5 , wherein the nucleic acid has at least 88% sequence similarity to one of SEQ ID Nos: 1-29.
8 . The composition of claim 5 , the nucleic acid has at least 94% sequence similarity to one of SEQ ID Nos: 1-29 and wherein at least about half of the bases in the nucleic acid comprise 2′-O-methoxyethyl ribose sugars.
9 . The composition of claim 8 , wherein at least about 90% of inter-base linkages in the nucleic acid are phosphorothioate bonds.
10 . The composition of claim 1 , wherein: the nucleic acid has 100% sequence similarity to one of SEQ ID Nos: 1-29; at least about half of the bases in the nucleic acid comprise 2′-O-methoxyethyl ribose sugars; all instances of U and C are methylated at position 5 of a nitrogenous base; and wherein all inter-base linkages in the nucleic acid are phosphorothioate bonds.
11 . The composition of one of claims 1-10 , wherein the nucleic acid has a sequence at least 90% similar to one of SEQ ID NO: 11-20 and blocks an miRNA from binding to the transcript.
12 . The composition of claim 11 , wherein the nucleic acid binds within a 3′ untranslated region (UTR) of a SYNGAP1 transcript and prevents binding of the miRNA, wherein the miRNA is a member of the has-miR-29-3p family.
13 . The composition of claim 12 , wherein the miRNA is one selected from the group consisting of hsa-miR-29c-3p, hsa-miR-29b-3p, and hsa-miR-29a-3p and wherein the nucleic acid hybridizes to a location within bases 4520-4526 of the transcript, wherein the transcript is given by NCBI reference sequence NM_006772.3.
14 . The composition of claim 12 , wherein the miRNA is one selected from the group consisting of hsa-miR-1343-3p and hsa-miR-6783-3p and wherein the nucleic acid hybridizes to a location within bases 4479-4485 of the transcript, wherein the transcript is given by NCBI reference sequence NM_006772.3.
15 . The composition of claim 12 , wherein the nucleic acid is a steric blocking oligonucleotide (SBO).
16 . The composition of one of claims 1-10 , wherein the nucleic acid has a sequence at least 90% similar to one of SEQ ID NO: 1-10 and promotes expression by mitigating negative effects of a 5′UTR of the transcript.
17 . The composition of claim 16 , further wherein the composition comprises a plurality of nucleic acids, each having a sequence at least 90% similar to one of SEQ ID Nos: 1-10.
18 . The composition of claim 17 , further comprising at least about 5 of the nucleic acids.
19 . The composition of claim 18 , wherein the 5 nucleic acids hybridize to locations distributed across a 5′ UTR of the transcript.
20 . The composition of claim 19 , further ten nucleic acids described by SEQ ID Nos. 1-10, wherein the 10 nucleic acids tile across substantially all of the 200 nt of the 5′ UTR.
21 . The composition of one of claims 1-10 , wherein the nucleic acid has a sequence at least 90% similar to one of SEQ ID NO: 21-29 and mediates digestion of a long, non-coding RNA antisense to the transcript.
22 . The composition of claim 21 , wherein the composition comprises one or a plurality of nucleic acids, each having a base sequence at least 94% identical to one of SEQ ID NOs: 21-29, wherein each of the nucleic acids has a gapmer structure that comprises a central DNA segment flanked by modified RNA wings.
23 . The composition of claim 21 , wherein the nucleic acids comprises two wings flanking a central region of at least 9 DNA bases.
24 . The composition of claim 21 , wherein at least one end of the nucleic acids comprises modified RNA bases.
25 . The composition of claim 24 , wherein each modified RNA base is 2′-O-methoxyethyl RNA.
26 . The composition of claim 21 , wherein the nucleic acids has a base sequence with at least a 94% match to one of SEQ ID NO: 21-29, in which at least the outer-most inter-base linkages and all linkages involving a DNA base are phosphorothioate, and in which the oligonucleotide further comprises a central 12 DNA bases flanked by a 5′ RNA wing and a 3′ RNA wing, the 5′ wing and the 3′ wing each comprising 4 consecutive 2′ modified RNA bases.
27 . The composition of claim 26 , in which the oligonucleotide has the sequence of one of SEQ ID NO: 21-29 and in which both RNA wings consist of four 2-methoxyethyl-modified RNA bases.
28 . The composition of claim 26 , further comprising a plurality of the nucleic acids, wherein the plurality of nucleic acids tile along the long, non-coding RNA antisense to the transcript.