Antisense oligomers for treatment of non-sense mediated rna decay based conditions and diseases

Abstract

Alternative splicing events in genes can lead to non-productive mRNA transcripts which in turn can lead to aberrant protein expression, and therapeutic agents which can target the alternative splicing events in genes can modulate the expression level of functional proteins in patients and/or inhibit aberrant protein expression. Such therapeutic agents can be used to treat a condition or disease caused by protein deficiency.

1 - 69 . (canceled) 
     
     
         70 . A pharmaceutical composition comprising a therapeutic agent or a vector encoding the therapeutic agent, and a pharmaceutically acceptable excipient,
 wherein the therapeutic agent is configured to bind to a targeted portion of a pre-mRNA that that comprises a non-sense mediated mRNA decay-inducing exon (NMD exon) and encodes a target protein in a cell, wherein the therapeutic agent is configured to modulate splicing of the NMD exon from the pre-mRNA, thereby modulating a level of processed mRNA encoding the target protein, and modulating expression of the target protein in the cell, and wherein the target protein is selected from the group consisting of: OPA1, ABCB4, ASS1, ATP8B1, BAG3, CACNAIA, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, and SYNGAP1 proteins.   
     
     
         71 . The pharmaceutical composition of  claim 70 , wherein the target protein comprises OPA1. 
     
     
         72 . The pharmaceutical composition of  claim 70 , wherein the pre-mRNA encoding the target protein is encoded by a genetic sequence with at least about 80% sequence identity to a sequence of SEQ ID NO: 12. 
     
     
         73 . The pharmaceutical composition of  claim 70 , wherein the targeted portion comprises a sequence with at least 80% sequence identity to a region comprising at least 8 contiguous nucleic acids of a sequence of SEQ ID NO: 173. 
     
     
         74 . The pharmaceutical composition of  claim 70 , wherein the NMD exon is defined by a pair of genomic coordinates GRCh38/hg38: chr3 193628509 193628616. 
     
     
         75 . The pharmaceutical composition of  claim 70 , wherein the therapeutic agent promotes exclusion of the NMD exon from the pre-mRNA encoding the target protein, and increases the level of the processed mRNA encoding the target protein in the cell. 
     
     
         76 . The pharmaceutical composition of  claim 75 , wherein the therapeutic agent increases the expression of the target protein in the cell. 
     
     
         77 . The pharmaceutical composition of  claim 70 , wherein the targeted portion is at most about 1500 nucleotides upstream of 5′ end of the NMD exon, or at most about 1500 nucleotides downstream of 3′ end of the NMD exon. 
     
     
         78 . The pharmaceutical composition of  claim 70 , wherein the targeted portion is located in an intronic region between two canonical exonic regions of the pre-mRNA encoding the target protein, and wherein the intronic region contains the NMD exon. 
     
     
         79 . The pharmaceutical composition of  claim 70 , wherein the targeted portion at least partially overlaps with the NMD exon. 
     
     
         80 . The pharmaceutical composition of  claim 70 , wherein the targeted portion comprises 5′ NMD exon-intron junction or 3′ NMD exon-intron junction. 
     
     
         81 . The pharmaceutical composition of  claim 70 , wherein the targeted portion is within the NMD exon. 
     
     
         82 . The pharmaceutical composition of  claim 70 , wherein the targeted portion comprises about 5 or more consecutive nucleotides of the NMD exon. 
     
     
         83 . The pharmaceutical composition of  claim 70 , wherein the target protein produced is a full-length protein or a wild-type protein. 
     
     
         84 . The pharmaceutical composition of  claim 70 , wherein the therapeutic agent is an antisense oligomer (ASO). 
     
     
         85 . The pharmaceutical composition of  claim 84 , wherein the antisense oligomer comprises a backbone modification, a sugar moiety modification, or a combination thereof. 
     
     
         86 . The pharmaceutical composition of  claim 84 , wherein the antisense oligomer comprises a phosphorothioate linkage, a phosphorodiamidate linkage, a phosphorodiamidate morpholino, a locked nucleic acid, a peptide nucleic acid, a 2′-O-methyl, a 2′-Fluoro, or a 2′-O-methoxyethyl moiety. 
     
     
         87 . The pharmaceutical composition of  claim 84 , wherein the antisense oligomer consists of from 8 to 50 nucleobases. 
     
     
         88 . The pharmaceutical composition of  claim 84 , wherein the antisense oligomer is at least 80% complementary to the targeted portion. 
     
     
         89 . A method of treating a disease or condition in a subject in need thereof, comprising contacting a cell of the subject with the therapeutic agent or the vector encoding the therapeutic agent of the pharmaceutical composition of  claim 70 , whereby the therapeutic agent modulates splicing of the NMD exon from the pre-mRNA that encodes the target protein, thereby modulating the level of processed mRNA encoding the target protein, and modulating the expression of the target protein in the cell of the subject. 
     
     
         90 . A method of treating a disease or condition in a subject in need thereof, comprising contacting a cell of the subject with a therapeutic agent, wherein the cell has a pre-mRNA that comprises a non-sense mediated RNA decay-inducing exon (NMD exon) and encodes a target protein, whereby the therapeutic agent binds to a targeted portion of the pre-mRNA and modulates splicing of the NMD exon from the pre-mRNA, thereby modulating a level of processed mRNA encoding the target protein, and modulating expression of the target protein in the cell of the subject, wherein the target protein is selected from the group consisting of: OPA1, ABCB4, ASS1, ATP8B1, BAG3, CACNAIA, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, and SYNGAP1 proteins. 
     
     
         91 . A method of modulating expression of a target protein by a cell having a pre-mRNA that comprises a non-sense mediated RNA decay-inducing exon (NMD exon) and encodes the target protein, the method comprising contacting an agent to the cell, whereby the agent binds to a targeted portion of the pre-mRNA and modulates splicing of the NMD exon from the pre-mRNA, thereby modulating level of processed mRNA encoding the target protein, and modulating the expression of the target protein in the cell, wherein the target protein is selected from the group consisting of: OPA1, ABCB4, ASS1, ATP8B1, BAG3, CACNAIA, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, and SYNGAP1 proteins.