Antisense oligomers for treating conditions and diseases based on non-sense mediated RNA detection

Abstract

A variable splicing event in a gene may result in a non-productive mRNA transcript, which in turn may result in aberrant protein expression, and a therapeutic agent that may target a variable splicing event in a gene may modulate the expression level of a functional protein in a patient, and / or inhibit aberrant protein expression. Such therapeutic agents may be used to treat conditions or diseases caused by protein deficiency.

Description

[0001] This application is a divisional application of a Chinese patent application with an application date of October 23, 2018, an application number of 201880084329.7, and an invention title of "Antisense Oligomers for Treating Conditions and Diseases Based on Nonsense-Mediated RNA Decay" (the application date of the corresponding PCT application is October 23, 2018, and the application number is PCT / US2018 / 057165).

[0002] Cross-reference

[0003] This application claims the benefit of U.S. Provisional Application No. 62 / 575,924, filed on October 23, 2017, and U.S. Provisional Application No. 62 / 667,200, filed on May 4, 2018, each of which is hereby incorporated by reference in its entirety. BACKGROUND OF THE INVENTION

[0004] Alternative splicing events in genes can result in non-productive mRNA transcripts, which in turn can lead to abnormal protein expression, and therapeutic agents that can target alternative splicing events in genes can modulate the expression level of functional proteins in a patient and / or inhibit abnormal protein expression. Such therapeutic agents can be used to treat conditions or diseases caused by protein deficiency. SUMMARY OF THE INVENTION

[0005] In certain embodiments, a method is described herein for modulating the expression of a target protein in a cell having an mRNA that comprises a nonsense-mediated RNA decay-inducing exon (NMD exon) and encodes the target protein, the method comprising contacting the cell with a therapeutic agent, whereby the therapeutic agent modulates splicing of the NMD exon from the mRNA, thereby modulating the level of the 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: AKT3, CACNA1A, CBS, CD46, CFH, CHD2, CLN3, COL11A2, COL4A3, COL4A4, COL4A4, CR1, CRX, CYP2J2, DHDDS, DNAJC8, EIF2AK3, ERN1, GALE, GUCY2F, GUCY2F, HEXA, HEXA, MAPK3, MBD5, MBD5, MBD5, MUT, MYH14, MYO6, NF1, NF2, NIPBL, NR1H4, NSD1, NSD1, NSD1, NSD1, OPA1, OPA1, PCCA, PKP2, PPARA, PRPF3, PRPF3, SCN2A, SCN8A, SCN8A, SCN9A, SEMA3C, SEMA3D, SIRT3, STK11, STK11, SYNGAP1, TOPORS, and VCAN proteins.

[0006] In certain embodiments, described herein is a method of treating a disease or condition in a subject in need thereof by modulating the expression of a target protein in cells of the subject, the method comprising: contacting cells of the subject with a therapeutic agent that modulates splicing of a nonsense-mediated mRNA decay-inducing exon (NMD exon) from an mRNA in the cells, wherein the mRNA comprises the NMD exon and encodes the target protein, thereby modulating the level of the processed mRNA encoding the target protein and modulating the expression of the target protein in cells of the subject, wherein the target protein is selected from the group consisting of: AKT3, CACNA1A, CBS, CD46, CFH, CHD2, CLN3, COL11A2, COL4A3, COL4A4, COL4A4, CR1, CRX, CYP2J2, DHDDS, DNAJC8, EIF2AK3, ERN1, GALE, GUCY2F, GUCY2F, HEXA, HEXA, MAPK3, MBD5, MBD5, MBD5, MUT, MYH14, MYO6, NF1, NF2, NIPBL, NR1H4, NSD1, NSD1, NSD1, NSD1, OPA1, OPA1, PCCA, PKP2, PPARA, PRPF3, PRPF3, SCN2A, SCN8A, SCN8A, SCN9A, SEMA3C, SEMA3D, SIRT3, STK11, STK11, SYNGAP1, TOPORS, and VCAN proteins.

[0007] In some embodiments, the therapeutic agent: (a) binds to a targeting portion of the mRNA encoding the target protein; (b) modulates the binding of factors involved in splicing of the NMD exon; or (c) a combination of (a) and (b).

[0008] In some embodiments, the therapeutic agent interferes with the binding of a factor involved in splicing of the NMD exon to a region of the targeting moiety. In some embodiments, the targeting moiety is adjacent to the NMD exon. In some embodiments, the targeting moiety is up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides upstream of the 5' end of the NMD exon. In some embodiments, the targeting moiety is at least about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides, about 40 nucleotides, about 30 nucleotides, about 20 nucleotides, about 10 nucleotides, about 5 nucleotides, about 4 nucleotides, about 2 nucleotides, about 1 nucleotide upstream of the 5' end of the NMD exon. In some embodiments, the targeting moiety is up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides downstream of the 3' end of the NMD exon. In some embodiments, the targeting moiety is at least about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides, about 40 nucleotides, about 30 nucleotides, about 20 nucleotides, about 10 nucleotides, about 5 nucleotides, about 4 nucleotides, about 2 nucleotides, about 1 nucleotide downstream of the 3' end of the NMD exon.

[0009] In some embodiments, the targeting moiety is located upstream of a genomic locus selected from the group consisting of up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides: GRCh38 / hg38:chr1 243564388; GRCh38 / hg38:chr19 13236618; GRCh38 / hg38:chr21 43060012; GRCh38 / hg38:chr1 207775610; GRCh38 / hg38:chr1 196675450; GRCh38 / hg38:chr15 92998149; GRCh38 / hg38:chr16 28479765; GRCh38 / hg38:chr6 33183698; GRCh38 / hg38:chr2 227296487; GRCh38 / hg38:chr22 27144833; GRCh38 / hg38:chr2 227015360; GRCh38 / hg38:chr1 207637688; GRCh38 / hg38:chr19 47835403; GRCh38 / hg38:chr1 59904516; GRCh38 / hg38:chr1 26442335; GRCh38 / hg38:chr1 28230252; GRCh38 / hg38:chr2 88582824; GRCh38 / hg38:chr17 64102804; GRCh38 / hg38:chr1 23798484; GRCh38 / hg38:chrX 109383446; GRCh38 / hg38:chrX 109439175; GRCh38 / hg38:chr15 72362466; GRCh38 / hg38:chr15 72345776; GRCh38 / hg38:chr16 30115645; GRCh38 / hg38:chr2 148460219; GRCh38 / hg38:chr2 148490695; GRCh38 / hg38:chr2 148505761; GRCh38 / hg38:chr6 49436597; GRCh38 / hg38:chr19 50230825; GRCh38 / hg38:chr6 75867431; GRCh38 / hg38:chr17 31249955;GRCh38 / hg38: chr22 29628658; GRCh38 / hg38: chr5 37048127; GRCh38 / hg38: chr12 100499841; GRCh38 / hg38: chr5 177169394; GRCh38 / hg38: chr5 177200761; GRCh38 / hg38: chr5 177247924; GRCh38 / hg38: chr5 177275947; GRCh38 / hg38: chr3 193628509; GRCh38 / hg38: chr3 193603500; GRCh38 / hg38: chr13 100305751; GRCh38 / hg38: chr12 32894778; GRCh38 / hg38: chr22 46203575; GRCh38 / hg38: chr1 150327557; GRCh38 / hg38: chr1 150330401; GRCh38 / hg38: chr2 165327155; GRCh38 / hg38: chr12 51688758; GRCh38 / hg38: chr12 51780202; GRCh38 / hg38: chr2 166304329; GRCh38 / hg38: chr7 80794957; GRCh38 / hg38: chr7 85059541; GRCh38 / hg38: chr11 226081; GRCh38 / hg38: chr19 1216268; GRCh38 / hg38: chr19 1221621; GRCh38 / hg38: chr6 33448789; GRCh38 / hg38: chr9 32551469; and GRCh38 / hg38: chr5 83544965.;

[0010] In some embodiments, the targeting moiety is upstream of a genomic locus selected from the group consisting of about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides: GRCh38 / hg38:chr1 243564388; GRCh38 / hg38:chr19 13236618; GRCh38 / hg38:chr21 43060012; GRCh38 / hg38:chr1 207775610; GRCh38 / hg38:chr1 196675450; GRCh38 / hg38:chr15 92998149; GRCh38 / hg38:chr16 28479765; GRCh38 / hg38:chr6 33183698; GRCh38 / hg38:chr2 227296487; GRCh38 / hg38:chr2 227144833; GRCh38 / hg38:chr2 227015360; GRCh38 / hg38:chr1 207637688; GRCh38 / hg38:chr19 47835403; GRCh38 / hg38:chr1 59904516; GRCh38 / hg38:chr1 26442335; GRCh38 / hg38:chr1 28230252; GRCh38 / hg38:chr2 88582824; GRCh38 / hg38:chr17 64102804; GRCh38 / hg38:chr1 23798484; GRCh38 / hg38:chrX 109383446; GRCh38 / hg38:chrX 109439175; GRCh38 / hg38:chr15 72362466; GRCh38 / hg38:chr15 72345776; GRCh38 / hg38:chr16 30115645; GRCh38 / hg38:chr2 148460219; GRCh38 / hg38:chr2 148490695; GRCh38 / hg38:chr2 148505761; GRCh38 / hg38:chr6 49436597; GRCh38 / hg38:chr19 50230825; GRCh38 / hg38:chr6 75867431; GRCh38 / hg38:chr17 31249955;GRCh38 / hg38: chr22 29628658; GRCh38 / hg38: chr5 37048127; GRCh38 / hg38: chr12 100499841; GRCh38 / hg38: chr5 177169394; GRCh38 / hg38: chr5 177200761; GRCh38 / hg38: chr5 177247924; GRCh38 / hg38: chr5 177275947; GRCh38 / hg38: chr3 193628509; GRCh38 / hg38: chr3 193603500; GRCh38 / hg38: chr13 100305751; GRCh38 / hg38: chr12 32894778; GRCh38 / hg38: chr22 46203575; GRCh38 / hg38: chr1 150327557; GRCh38 / hg38: chr1 150330401; GRCh38 / hg38: chr2 165327155; GRCh38 / hg38: chr12 51688758; GRCh38 / hg38: chr12 51780202; GRCh38 / hg38: chr2 166304329; GRCh38 / hg38: chr7 80794957; GRCh38 / hg38: chr7 85059541; GRCh38 / hg38: chr11 226081; GRCh38 / hg38: chr19 1216268; GRCh38 / hg38: chr19 1221621; GRCh38 / hg38: chr6 33448789; GRCh38 / hg38: chr9 32551469; and GRCh38 / hg38: chr5 83544965.;

[0011] In some embodiments, the targeting moiety is downstream of a genomic locus selected from the group consisting of at most about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides: GRCh38 / hg38:chr1 243564285; GRCh38 / hg38:chr19 13236449; GRCh38 / hg38:chr21 43059730; GRCh38 / hg38:chr1 207775745; GRCh38 / hg38:chr1 196675529; GRCh38 / hg38:chr15 92998261; GRCh38 / hg38:chr16 28479644; GRCh38 / hg38:chr6 33183634; GRCh38 / hg38:chr2 227296526; GRCh38 / hg38:chr22 27144653; GRCh38 / hg38:chr2 227015283; GRCh38 / hg38:chr1 207637848; GRCh38 / hg38:chr19 47835579; GRCh38 / hg38:chr1 59904366; GRCh38 / hg38:chr1 26442372; GRCh38 / hg38:chr1 28230131; GRCh38 / hg38:chr2 88582755; GRCh38 / hg38:chr17 64102673; GRCh38 / hg38:chr1 23798311; GRCh38 / hg38:chrX 109383365; GRCh38 / hg38:chrX 109439038; GRCh38 / hg38:chr15 72362376; GRCh38 / hg38:chr15 72345677; GRCh38 / hg38:chr16 30115595; GRCh38 / hg38:chr2 148460304; GRCh38 / hg38:chr2 148490787; GRCh38 / hg38:chr2 148505830; GRCh38 / hg38:chr6 49436522; GRCh38 / hg38:chr19 50230999; GRCh38 / hg38:chr6 75867523; GRCh38 / hg38:chr17 31250125;GRCh38 / hg38: chr22 29628773; GRCh38 / hg38: chr5 37048354; GRCh38 / hg38: chr12 100500024; GRCh38 / hg38: chr5 177169559; GRCh38 / hg38: chr5 177200783; GRCh38 / hg38: chr5 177248079; GRCh38 / hg38: chr5 177276101; GRCh38 / hg38: chr3 193628616; GRCh38 / hg38: chr3 193603557; GRCh38 / hg38: chr13 100305834; GRCh38 / hg38: chr12 32894516; GRCh38 / hg38: chr22 46203752; GRCh38 / hg38: chr1 150327652; GRCh38 / hg38: chr1 150330498; GRCh38 / hg38: chr2 165327202; GRCh38 / hg38: chr12 51688849; GRCh38 / hg38: chr12 51780271; GRCh38 / hg38: chr2 166304238; GRCh38 / hg38: chr7 80794854; GRCh38 / hg38: chr7 85059498; GRCh38 / hg38: chr11 225673; GRCh38 / hg38: chr19 1216398; GRCh38 / hg38: chr19 1221846; GRCh38 / hg38: chr6 33448868; GRCh38 / hg38: chr9 32551365; and GRCh38 / hg38: chr5 83545070.;

[0012] In some embodiments, the targeting moiety is downstream of a genomic locus selected from the group consisting of about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides: GRCh38 / hg38:chr1 243564285; GRCh38 / hg38:chr19 13236449; GRCh38 / hg38:chr21 43059730; GRCh38 / hg38:chr1 207775745; GRCh38 / hg38:chr1 196675529; GRCh38 / hg38:chr15 92998261; GRCh38 / hg38:chr16 28479644; GRCh38 / hg38:chr6 33183634; GRCh38 / hg38:chr2 227296526; GRCh38 / hg38:chr2 227144653; GRCh38 / hg38:chr2 227015283; GRCh38 / hg38:chr1 207637848; GRCh38 / hg38:chr19 47835579; GRCh38 / hg38:chr1 59904366; GRCh38 / hg38:chr1 26442372; GRCh38 / hg38:chr1 28230131; GRCh38 / hg38:chr2 88582755; GRCh38 / hg38:chr17 64102673; GRCh38 / hg38:chr1 23798311; GRCh38 / hg38:chrX 109383365; GRCh38 / hg38:chrX 109439038; GRCh38 / hg38:chr15 72362376; GRCh38 / hg38:chr15 72345677; GRCh38 / hg38:chr16 30115595; GRCh38 / hg38:chr2 148460304; GRCh38 / hg38:chr2 148490787; GRCh38 / hg38:chr2 148505830; GRCh38 / hg38:chr6 49436522; GRCh38 / hg38:chr19 50230999; GRCh38 / hg38:chr6 75867523; GRCh38 / hg38:chr17 31250125;GRCh38 / hg38: chr22 29628773; GRCh38 / hg38: chr5 37048354; GRCh38 / hg38: chr12 100500024; GRCh38 / hg38: chr5 177169559; GRCh38 / hg38: chr5 177200783; GRCh38 / hg38: chr5 177248079; GRCh38 / hg38: chr5 177276101; GRCh38 / hg38: chr3 193628616; GRCh38 / hg38: chr3 193603557; GRCh38 / hg38: chr13 100305834; GRCh38 / hg38: chr12 32894516; GRCh38 / hg38: chr22 46203752; GRCh38 / hg38: chr1 150327652; GRCh38 / hg38: chr1 150330498; GRCh38 / hg38: chr2 165327202; GRCh38 / hg38: chr12 51688849; GRCh38 / hg38: chr12 51780271; GRCh38 / hg38: chr2 166304238; GRCh38 / hg38: chr7 80794854; GRCh38 / hg38: chr7 85059498; GRCh38 / hg38: chr11 225673; GRCh38 / hg38: chr19 1216398; GRCh38 / hg38: chr19 1221846; GRCh38 / hg38: chr6 33448868; GRCh38 / hg38: chr9 32551365; and GRCh38 / hg38: chr5 83545070.;

[0013] In some embodiments, the targeting moiety is located in an intron region between two canonical exon regions of the mRNA encoding the target protein, and wherein the intron region contains the NMD exon. In some embodiments, the targeting moiety at least partially overlaps with the NMD exon. In some embodiments, the targeting moiety at least partially overlaps with an intron upstream or downstream of the NMD exon. In some embodiments, the targeting moiety comprises a 5' NMD exon-intron junction or a 3' NMD exon-intron junction. In some embodiments, the targeting moiety is within the NMD exon. In some embodiments, the targeting moiety comprises about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more consecutive nucleotides of the NMD exon.

[0014] In some embodiments, the mRNA encoding the target protein comprises a sequence having at least about 80%, 85%, 90%, 95%, 97% or 100% sequence identity to a sequence selected from SEQ ID NOs: 135-191. In some embodiments, the mRNA encoding the target protein is encoded by a gene sequence having at least about 80%, 85%, 90%, 95%, 97% or 100% sequence identity to a sequence selected from SEQ ID NOs: 1-5, 12, 19-21, 25, 26, 28, 30, 33, 35, 38, 40, 41, 44, 45, 51, 53, 55-57 and 192-211. In some embodiments, the targeting moiety of the mRNA comprises a sequence having at least 80%, 85%, 90%, 95%, 97% or 100% sequence identity to a region containing at least 8 consecutive nucleic acids selected from SEQ ID NOs: 135-191. In some embodiments, the agent is an antisense oligomer (ASO), and wherein the ASO comprises a sequence that is at least about 80%, 85%, 90%, 95%, 97% or 100% complementary to at least 8 consecutive nucleic acids of a sequence selected from SEQ ID NOs: 135-191.

[0015] In some embodiments, the targeting portion of the mRNA is within a nonsense-mediated RNA decay-inducing exon selected from the group consisting of: GRCh38 / hg38: chr1 243564285 243564388; GRCh38 / hg38: chr19 13236449 13236618; GRCh38 / hg38: chr21 43059730 43060012; GRCh38 / hg38: chr1 207775610 207775745; GRCh38 / hg38: chr11 96675450 196675529; GRCh38 / hg38: chr15 92998149 92998261; GRCh38 / hg38: chr16 28479644 28479765; GRCh38 / hg38: chr6 33183634 33183698; GRCh38 / hg38: chr2 227296487 227296526; GRCh38 / hg38: chr22 27144653 227144833; GRCh38 / hg38: chr2 227015283 227015360; GRCh38 / hg38: chr1 207637688 207637848; GRCh38 / hg38: chr19 47835403 47835579; GRCh38 / hg38: chr15 9904366 59904516; GRCh38 / hg38: chr1 26442335 26442372; GRCh38 / hg38: chr1 28230131 28230252; GRCh38 / hg38: chr2 88582755 88582824; GRCh38 / hg38: chr17 64102673 64102804; GRCh38 / hg38: chr1 23798311 23798484; GRCh38 / hg38: chrX 109383365 109383446; GRCh38 / hg38: chrX 109439038 109439175; GRCh38 / hg38: chr15 72362376 72362466; GRCh38 / hg38: chr15 72345677 72345776; GRCh38 / hg38: chr16 30115595 30115645; GRCh38 / hg38: chr21 48460219 148460304; GRCh38 / hg38: chr2 148490695 148490787; GRCh38 / hg38: chr2 148505761 148505830;GRCh38 / hg38: chr6 49436522 - 49436597; GRCh38 / hg38: chr19 50230825 - 50230999; GRCh38 / hg38: chr6 75867431 - 75867523; GRCh38 / hg38: chr17 31249955 - 31250125; GRCh38 / hg38: chr22 29628658 - 29628773; GRCh38 / hg38: chr5 37048127 - 37048354; GRCh38 / hg38: chr12 100499841 - 100500024; GRCh38 / hg38: chr5 177169394 - 177169559; GRCh38 / hg38: chr5 177200761 - 177200783; GRCh38 / hg38: chr5 177247924 - 177248079; GRCh38 / hg38: chr5 177275947 - 177276101; GRCh38 / hg38: chr3 193628509 - 193628616; GRCh38 / hg38: chr3 193603500 - 193603557; GRCh38 / hg38: chr13 100305751 - 100305834; GRCh38 / hg38: chr12 32894516 - 32894778; GRCh38 / hg38: chr22 46203575 - 46203752; GRCh38 / hg38: chr11 50327557 - 50327652; GRCh38 / hg38: chr1 150330401 - 150330498; GRCh38 / hg38: chr2 165327155 - 165327202; GRCh38 / hg38: chr12 51688758 - 51688849; GRCh38 / hg38: chr12 51780202 - 51780271; GRCh38 / hg38: chr2 166304238 - 166304329; GRCh38 / hg38: chr7 80794854 - 80794957; GRCh38 / hg38: chr7 85059498 - 85059541; GRCh38 / hg38: chr11 2256732 - 2256732 + 6081; GRCh38 / hg38: chr19 1216268 - 1216398; GRCh38 / hg38: chr19 1221621 - 1221846; GRCh38 / hg38: chr6 33448789 - 33448868;GRCh38 / hg38: chr9 32551365 32551469; and GRCh38 / hg38: chr5 83544965 83545070.;

[0016] In some embodiments, the targeting portion of the mRNA is upstream or downstream of a nonsense-mediated RNA decay-inducing exon selected from the group consisting of: GRCh38 / hg38:chr1 243564285 243564388; GRCh38 / hg38:chr19 13236449 13236618; GRCh38 / hg38:chr21 43059730 43060012; GRCh38 / hg38:chr1 207775610 207775745; GRCh38 / hg38:chr1 196675450 196675529; GRCh38 / hg38:chr15 92998149 92998261; GRCh38 / hg38:chr16 28479644 28479765; GRCh38 / hg38:chr6 33183634 33183698; GRCh38 / hg38:chr2 227296487 227296526; GRCh38 / hg38:chr22 27144653 227144833; GRCh38 / hg38:chr22 27015283 227015360; GRCh38 / hg38:chr1 207637688 207637848; GRCh38 / hg38:chr19 47835403 47835579; GRCh38 / hg38:chr15 9904366 9904516; GRCh38 / hg38:chr1 26442335 26442372; GRCh38 / hg38:chr1 28230131 28230252; GRCh38 / hg38:chr2 88582755 88582824; GRCh38 / hg38:chr17 64102673 64102804; GRCh38 / hg38:chr1 23798311 23798484; GRCh38 / hg38:chrX 109383365 109383446; GRCh38 / hg38:chrX 109439038 109439175; GRCh38 / hg38:chr15 72362376 72362466; GRCh38 / hg38:chr15 72345677 72345776; GRCh38 / hg38:chr16 30115595 30115645; GRCh38 / hg38:chr2 148460219 148460304; GRCh38 / hg38:chr2 148490695 148490787;GRCh38 / hg38: chr2 148505761 148505830; GRCh38 / hg38: chr6 49436522 49436597; GRCh38 / hg38: chr19 50230825 50230999; GRCh38 / hg38: chr6 75867431 75867523; GRCh38 / hg38: chr17 31249955 31250125; GRCh38 / hg38: chr22 29628658 29628773; GRCh38 / hg38: chr5 37048127 37048354; GRCh38 / hg38: chr12 10049984 1100500024; GRCh38 / hg38: chr5 177169394 177169559; GRCh38 / hg38: chr5 177200761 177200783; GRCh38 / hg38: chr5 177247924 177248079; GRCh38 / hg38: chr5 177275947 177276101; GRCh38 / hg38: chr3 193628509 193628616; GRCh38 / hg38: chr3 193603500 193603557; GRCh38 / hg38: chr13 100305751 100305834; GRCh38 / hg38: chr12 32894516 32894778; GRCh38 / hg38: chr22 46203575 46203752; GRCh38 / hg38: chr11 50327557 150327652; GRCh38 / hg38: chr1 150330401 150330498; GRCh38 / hg38: chr21 65327155 165327202; GRCh38 / hg38: chr12 51688758 51688849; GRCh38 / hg38: chr12 51780202 51780271; GRCh38 / hg38: chr2 166304238 166304329; GRCh38 / hg38: chr7 80794854 80794957; GRCh38 / hg38: chr7 85059498 85059541; GRCh38 / hg38: chr11 22567322 6081; GRCh38 / hg38: chr19 1216268 1216398; GRCh38 / hg38: chr19 1221621 1221846;GRCh38 / hg38: chr6 33448789 33448868; GRCh38 / hg38: chr9 32551365 32551469; and GRCh38 / hg38: chr5 83544965 83545070.;

[0017] In some embodiments, the targeting portion of the mRNA comprises exon-intron junctions of exons selected from the group consisting of: GRCh38 / hg38:chr1 243564285 243564388; GRCh38 / hg38:chr19 132364491 3236618; GRCh38 / hg38:chr21 43059730 43060012; GRCh38 / hg38:chr1 207775610 207775745; GRCh38 / hg38:chr11 96675450 196675529; GRCh38 / hg38:chr15 92998149 92998261; GRCh38 / hg38:chr16 28479644 28479765; GRCh38 / hg38:chr6 33183634 33183698; GRCh38 / hg38:chr2 227296487 227296526; GRCh38 / hg38:chr22 27144653 227144833; GRCh38 / hg38:chr2 227015283 227015360; GRCh38 / hg38:chr1 207637688 207637848; GRCh38 / hg38:chr19 47835403 47835579; GRCh38 / hg38:chr15 9904366 59904516; GRCh38 / hg38:chr1 26442335 26442372; GRCh38 / hg38:chr1 28230131 28230252; GRCh38 / hg38:chr2 88582755 88582824; GRCh38 / hg38:chr17 64102673 64102804; GRCh38 / hg38:chr1 23798311 23798484; GRCh38 / hg38:chrX 109383365 109383446; GRCh38 / hg38:chrX 109439038 109439175; GRCh38 / hg38:chr15 72362376 72362466; GRCh38 / hg38:chr15 72345677 72345776; GRCh38 / hg38:chr16 30115595 30115645; GRCh38 / hg38:chr21 48460219 148460304; GRCh38 / hg38:chr2 148490695 148490787; GRCh38 / hg38:chr2 148505761 148505830;GRCh38 / hg38: chr6 49436522 - 49436597; GRCh38 / hg38: chr19 50230825 - 50230999; GRCh38 / hg38: chr6 75867431 - 75867523; GRCh38 / hg38: chr17 31249955 - 31250125; GRCh38 / hg38: chr22 29628658 - 29628773; GRCh38 / hg38: chr5 37048127 - 37048354; GRCh38 / hg38: chr12 100499841 - 100500024; GRCh38 / hg38: chr5 177169394 - 177169559; GRCh38 / hg38: chr5 177200761 - 177200783; GRCh38 / hg38: chr5 177247924 - 177248079; GRCh38 / hg38: chr5 177275947 - 177276101; GRCh38 / hg38: chr3 193628509 - 193628616; GRCh38 / hg38: chr3 193603500 - 193603557; GRCh38 / hg38: chr13 100305751 - 100305834; GRCh38 / hg38: chr12 32894516 - 32894778; GRCh38 / hg38: chr22 46203575 - 46203752; GRCh38 / hg38: chr11 503275571 - 50327652; GRCh38 / hg38: chr1 150330401 - 150330498; GRCh38 / hg38: chr2 165327155 - 165327202; GRCh38 / hg38: chr12 51688758 - 51688849; GRCh38 / hg38: chr12 51780202 - 51780271; GRCh38 / hg38: chr2 166304238 - 166304329; GRCh38 / hg38: chr7 80794854 - 80794957; GRCh38 / hg38: chr7 85059498 - 85059541; GRCh38 / hg38: chr11 225673226 - 081; GRCh38 / hg38: chr19 1216268 - 1216398; GRCh38 / hg38: chr19 1221621 - 1221846; GRCh38 / hg38: chr6 33448789 - 33448868;GRCh38 / hg38: chr9 32551365 32551469; and GRCh38 / hg38: chr5 83544965 83545070.;

[0018] In some embodiments, the resulting target protein is a full-length protein or a wild-type protein.

[0019] In some embodiments, the therapeutic agent promotes the exclusion of the NMD exon from the processed mRNA encoding the target protein. In some embodiments, compared to the exclusion of the NMD exon from the processed mRNA encoding the target protein in control cells, the exclusion of the NMD exon from the processed mRNA encoding the target protein in cells contacted with the therapeutic agent is increased by about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8-fold, about 1.1 to about 9-fold, about 2 to about 5-fold, about 2 to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold or at least about 10-fold. In some embodiments, the therapeutic agent increases the level of the processed mRNA encoding the target protein in the cells. In some embodiments, compared to the level of the processed mRNA encoding the target protein in control cells, the level of the processed mRNA encoding the target protein produced in cells contacted with the therapeutic agent is increased by about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8-fold, about 1.1 to about 9-fold, about 2 to about 5-fold, about 2 to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold or at least about 10-fold. In some embodiments, the therapeutic agent increases the expression of the target protein in the cells.In some embodiments, the level of the target protein produced in the cells contacted with the therapeutic agent is increased by about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8-fold, about 1.1 to about 9-fold, about 2 to about 5-fold, about 2 to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold or at least about 10-fold, compared to the level of the target protein produced in control cells.

[0020] In some embodiments, the disease or condition is induced by a loss-of-function mutation in the target protein.

[0021] In some embodiments, the disease or condition is associated with haploinsufficiency of the gene encoding the target protein, and wherein the subject has a first allele encoding a functional target protein and a second allele that does not produce or produces the target protein at a reduced level, or a second allele encoding a non-functional or partially functional target protein. In some embodiments, the disease or condition is selected from: Sotos syndrome 1; Beckwith-Wiedemann syndrome; familial hemiplegic migraine 1; episodic ataxia type 2; childhood-onset epileptic encephalopathy; Wagner syndrome 1; optic atrophy type 1; Alport syndrome; arrhythmogenic right ventricular dysplasia 9; neurofibromatosis type 1; early infantile epileptic encephalopathy 11; benign familial infantile convulsions 3; cognitive impairment with or without cerebellar ataxia; early infantile epileptic encephalopathy 13; benign familial infantile convulsions 5; pathway (CNS); 16p11.2 deletion syndrome?; autosomal dominant mental retardation 1; retinitis pigmentosa 18; retinitis pigmentosa 31; autosomal dominant deafness 13; cone-rod dystrophy-2; autosomal dominant deafness 4A; peripheral neuropathy, myopathy, hoarseness and hearing loss; autosomal dominant deafness 22; neurofibromatosis type 2; autosomal dominant mental retardation 5; generalized epilepsy with febrile seizures plus type 7; and familial febrile seizures 3B.

[0022] In some embodiments, the disease or condition is associated with an autosomal recessive mutation in a gene encoding a target protein, wherein the subject has a first coding allele by which (i) no target protein is produced or the target protein is produced at a reduced level compared to the wild-type allele; or (ii) the target protein produced is non-functional or partially functional compared to the wild-type allele; and a second allele by which: (iii) the target protein is produced at a reduced level compared to the wild-type allele and the target protein produced is at least partially functional compared to the wild-type allele; or (iv) the target protein produced is partially functional compared to the wild-type allele. In some embodiments, the disease or condition is selected from: Alport syndrome; neuronal ceroid lipofuscinosis 3; galactose epimerase deficiency; B6-responsive and non-responsive homocystinuria; methylmalonic aciduria; propionic academia; retinitis pigmentosa 59; Tay-Sachs disease; congenital insensitivity to pain; and autosomal recessive HSAN2D.

[0023] In some embodiments, the therapeutic agent promotes the exclusion of the NMD exon from the processed mRNA encoding the target protein and increases the expression of the target protein in the cell. In some embodiments, the therapeutic agent inhibits the exclusion of the NMD exon from the processed mRNA encoding the target protein. In some embodiments, compared to the exclusion of the NMD exon from the processed mRNA encoding the target protein in control cells, the exclusion of the NMD exon from the processed mRNA encoding the target protein in cells contacted with the therapeutic agent is reduced by about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8-fold, about 1.1 to about 9-fold, about 2 to about 5-fold, about 2 to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold or at least about 10-fold. In some embodiments, the therapeutic agent reduces the level of the processed mRNA encoding the target protein in the cell. In some embodiments, compared to the level of the processed mRNA encoding the target protein in control cells, the level of the processed mRNA encoding the target protein in cells contacted with the therapeutic agent is reduced by about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8-fold, about 1.1 to about 9-fold, about 2 to about 5-fold, about 2 to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold or at least about 10-fold.

[0024] In some embodiments, the therapeutic agent reduces the expression of a target protein in the cell. In some embodiments, the level of the target protein produced in the cells contacted with the therapeutic agent is reduced by about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8-fold, about 1.1 to about 9-fold, about 2 to about 5-fold, about 2 to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold or at least about 10-fold compared to the level of the target protein produced in control cells.

[0025] In some embodiments, the disease or condition is induced by a gain-of-function mutation in the target protein. In some embodiments, the subject has an allele that produces the target protein at elevated levels, or an allele that encodes a mutant target protein that exhibits increased activity in the cell.

[0026] In some embodiments, the therapeutic agent inhibits the exclusion of the NMD exon from the processed mRNA encoding the target protein and reduces the expression of the target protein in the cell. In some embodiments, the target protein includes SCN8A. In some embodiments, the disease or condition includes a central nervous system disease. In some embodiments, the disease or condition includes epilepsy. In some embodiments, the disease or condition includes Dravet syndrome.

[0027] In some embodiments, the therapeutic agent is an antisense oligomer (ASO), and wherein the antisense oligomer comprises a backbone modification that comprises a phosphorothioate bond or a diaminophosphate bond. In some embodiments, the therapeutic agent is an antisense oligomer (ASO), and wherein the antisense oligomer comprises a diaminophosphate morpholino, locked nucleic acid, peptide nucleic acid, 2'-O-methyl, 2'-fluoro or 2'-O-methoxyethyl moiety.

[0028] In some embodiments, the therapeutic agent is an antisense oligomer (ASO), and wherein the antisense oligomer comprises at least one modified sugar moiety. In some embodiments, each sugar moiety is a modified sugar moiety.

[0029] In some embodiments, the therapeutic agent is an antisense oligomer (ASO), and wherein the antisense oligomer consists of 8 to 50 nucleobases, 8 to 40 nucleobases, 8 to 35 nucleobases, 8 to 30 nucleobases, 8 to 25 nucleobases, 8 to 20 nucleobases, 8 to 15 nucleobases, 9 to 50 nucleobases, 9 to 40 nucleobases, 9 to 35 nucleobases, 9 to 30 nucleobases, 9 to 25 nucleobases, 9 to 20 nucleobases, 9 to 15 nucleobases, 10 to 50 nucleobases, 10 to 40 nucleobases, 10 to 35 nucleobases, 10 to 30 nucleobases, 10 to 25 nucleobases, 10 to 20 nucleobases, 10 to 15 nucleobases, 11 to 50 nucleobases, 11 to 40 nucleobases, 11 to 35 nucleobases, 11 to 30 nucleobases, 11 to 25 nucleobases, 11 to 20 nucleobases, 11 to 15 nucleobases, 12 to 50 nucleobases, 12 to 40 nucleobases, 12 to 35 nucleobases, 12 to 30 nucleobases, 12 to 25 nucleobases, 12 to 20 nucleobases or 12 to 15 nucleobases.

[0030] In some embodiments, the therapeutic agent is an antisense oligomer (ASO), and wherein the antisense oligomer is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99% or 100% complementary to the target portion of the mRNA.

[0031] In some embodiments, the method further comprises assessing the mRNA level or expression level of the target protein.

[0032] In some embodiments, the subject is a human. In some embodiments, the subject is a non-human animal. In some embodiments, the subject is a fetus, embryo or child. In some embodiments, the cells are ex vivo. In some embodiments, the therapeutic agent is administered by intrathecal injection, intracerebroventricular injection, intraperitoneal injection, intramuscular injection, subcutaneous injection, intravitreal or intravenous injection of the subject. In some embodiments, the method further comprises administering a second therapeutic agent to the subject.

[0033] In some embodiments, the second therapeutic agent is a small molecule. In some embodiments, the second therapeutic agent is an antisense oligomer. In some embodiments, the second therapeutic agent corrects intron retention.

[0034] In some embodiments, the disease or condition is selected from: 16p11.2 deletion syndrome; Alport syndrome; arrhythmogenic right ventricular dysplasia 9; neuronal ceroid lipofuscinosis 3; cognitive impairment with or without cerebellar ataxia; early infantile epileptic encephalopathy 13; benign familial infantile convulsions 5; cone-rod dystrophy-2; Cornelia de Lange; autosomal dominant deafness 13; autosomal dominant deafness 4A; peripheral neuropathy, myopathy, hoarseness and hearing loss; generalized epilepsy with febrile seizures plus type 7; familial febrile seizures 3B; congenital insensitivity to pain; autosomal recessive HSAN2D; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; benign familial infantile convulsions 3; galactose epimerase deficiency; B6-responsive and non-responsive homocystinuria; autosomal dominant mental retardation 1; autosomal dominant mental retardation 5; methylmalonic aciduria; familial hemiplegic migraine 1; episodic ataxia type 2; NASH; neurofibromatosis type 1; neurofibromatosis type 2; optic atrophy type 1; propionic academia; retinitis pigmentosa 18; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Tay-Sachs disease; and Wagner syndrome 1.

[0035] Incorporation by reference

[0036] All publications, patents, and patent applications mentioned in this specification are hereby incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. BRIEF DESCRIPTION OF THE DRAWINGS

[0037] The novel features of the present disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained from the following detailed description of illustrative embodiments that explain the principles of the present disclosure, along with the accompanying drawings, in which:

[0038] Figure 1A and Figure 1B A schematic diagram depicting a target mRNA containing a nonsense-mediated mRNA decay-inducing exon (NMD exon mRNA) and the exclusion of the nonsense-mediated mRNA decay-inducing exon by a therapeutic agent to increase full-length target protein or functional RNA expression. Figure 1AShows a cell divided into nuclear and cytoplasmic compartments. In the nucleus, the pre-mRNA transcript of the target gene undergoes splicing to generate mRNA, and this mRNA is exported to the cytoplasm and translated into the target protein. For this target gene, some portions of the mRNA contain nonsense-mediated mRNA decay-inducing exons (NMD exon mRNA) that are degraded in the cytoplasm, thus resulting in no target protein production.

[0039] Figure 1B Shows an example of the same cell divided into nuclear and cytoplasmic compartments. Treatment with a therapeutic agent such as an antisense oligomer (ASO) promotes the exclusion of nonsense-mediated mRNA decay-inducing exons and results in an increase in mRNA, which in turn is translated into higher levels of the target protein.

[0040] Figure 2 Depicts the identification of an exemplary nonsense-mediated mRNA decay (NMD)-inducing exon in the CD46 gene. Shows the identification of the NMD-inducing exon in the CD46 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the CD46 gene. The peak corresponding to the RNA sequencing reads was identified in intron GRCh38 / hg38:chr12 07770363 207783291 and is shown in the middle panel. Bioinformatics analysis identified an exon-like sequence flanked by 3' and 5' splice sites (the sequence highlighted in uppercase letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0041] Figure 3 Depicts the identification of an exemplary nonsense-mediated mRNA decay (NMD)-inducing exon in the COL11A2 gene. Shows the identification of the NMD-inducing exon in the COL11A2 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the COL11A2 gene. The peak corresponding to the RNA sequencing reads was identified in intron GRCh38 / hg38:chr6 33181172 33184144 and is shown in the middle panel. Bioinformatics analysis identified an exon-like sequence flanked by 3' and 5' splice sites (the sequence highlighted in uppercase letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0042] Figure 4Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the CR1 gene. Shows the identification of NMD-inducing exons in the CR1 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the CR1 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr12:076306222-07639396, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0043] Figure 5 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the CRX gene. Shows the identification of NMD-inducing exons in the CRX gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the CRX gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr19:47834545-47836242, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0044] Figure 6 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the DNAJC8 gene. Shows the identification of NMD-inducing exons in the DNAJC8 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the DNAJC8 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr1:28229025-28232920, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0045] Figure 7Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the MYH14 gene. Shows the identification of NMD-inducing exons in the MYH14 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the MYH14 gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr19 50230625 50231929, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower panel). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0046] Figure 8 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the SEMA3C gene. Shows the identification of NMD-inducing exons in the SEMA3C gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the SEMA3C gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr7 80789529 80798091, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower panel). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0047] Figure 9 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the VCAN gene. Shows the identification of NMD-inducing exons in the VCAN gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the VCAN gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr5 83542270 83545536, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower panel). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0048] Figure 10Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the OPAI gene. The identification of NMD-inducing exons in the OPAI gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the OPAI gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr3 193626204 193631611 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0049] Figure 11 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the COL4A3 gene. The identification of NMD-inducing exons in the COL4A3 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the COL4A3 gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr2 227295318 227297673 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0050] Figure 12 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the DHDDS gene. The identification of NMD-inducing exons in the DHDDS gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the DHDDS gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr12 6438286 26442730 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0051] Figure 13Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the CFH gene. The identification of NMD-inducing exons in the CFH gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the CFH gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr11 96673964 196675988 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0052] Figure 14 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the AKT3 gene. The identification of NMD-inducing exons in the AKT3 gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the AKT3 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr12 43563849 243572925 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0053] Figure 15 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the TOPORS gene. The identification of NMD-inducing exons in the TOPORS gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the TOPORS gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr9 32550970 32552433 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0054] Figure 16Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the PRPF3 gene. The identification of NMD-inducing exons in the PRPF3 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper panel shows a diagram of the PRPF3 gene to scale. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr11:50325883-150328319, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower panel). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0055] Figure 17 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the PRPF3 gene. The identification of NMD-inducing exons in the PRPF3 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper panel shows a diagram of the PRPF3 gene to scale. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr11:50328468-150332683, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower panel). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0056] Figure 18 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the NIPBL gene. The identification of NMD-inducing exons in the NIPBL gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper panel shows a diagram of the NIPBL gene to scale. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr5:37046201-37048501, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower panel). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0057] Figure 19Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the CBS gene. The identification of NMD-inducing exons in the CBS gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the CBS gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr21 4305930543060440, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0058] Figure 20 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the PKP2 gene. The identification of NMD-inducing exons in the PKP2 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the PKP2 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr12 32879034 32896508, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0059] Figure 21 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the COL4A4 gene. The identification of NMD-inducing exons in the COL4A4 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the COL4A4 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr2 227144560 227147412, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0060] Figure 22Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the COL4A4 gene. The identification of NMD-inducing exons in the COL4A4 gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the COL4A4 gene. The peak corresponding to the RNA sequencing reads was identified in intron GRCh38 / hg38:chr2 227012299 227022047 and is shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0061] Figure 23 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the CYP2J2 gene. The identification of NMD-inducing exons in the CYP2J2 gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the CYP2J2 gene. The peak corresponding to the RNA sequencing reads was identified in intron GRCh38 / hg38:chr1 59901104 59904870 and is shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0062] Figure 24 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the PPARA gene. The identification of NMD-inducing exons in the PPARA gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the PPARA gene. The peak corresponding to the RNA sequencing reads was identified in intron GRCh38 / hg38:chr22 46198592 46215172 and is shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0063] Figure 25Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the SEMA3D gene. The identification of NMD-inducing exons in the SEMA3D gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the SEMA3D gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr7 85055860 85065423, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0064] Figure 26 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the ERN1 gene. The identification of NMD-inducing exons in the ERN1 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the ERN1 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr17 64098242 64129975, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0065] Figure 27 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the GUCY2F gene. The identification of NMD-inducing exons in the GUCY2F gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the GUCY2F gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chrX 109382213 109385183, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0066] Figure 28Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the GUCY2F gene. The identification of NMD-inducing exons in the GUCY2F gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the GUCY2F gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chrx 109430397 109441350 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0067] Figure 29 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the SCN2A gene. The identification of NMD-inducing exons in the SCN2A gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the SCN2A gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr21 65326986 165331329 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0068] Figure 30 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the SCN8A gene. The identification of NMD-inducing exons in the SCN8A gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the SCN8A gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr12 51687221 51689004 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0069] Figure 31Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the SCN8A gene. Shows the identification of NMD-inducing exons in the SCN8A gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the SCN8A gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr12 51774364-51786541, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0070] Figure 32 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the SCN9A gene. Shows the identification of NMD-inducing exons in the SCN9A gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the SCN9A gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr21 166304123-166305791, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0071] Figure 33 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the CLN3 gene. Shows the identification of NMD-inducing exons in the CLN3 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the CLN3 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr16 28477879-28482104, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0072] Figure 34Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the MAPK3 gene. The identification of NMD-inducing exons in the MAPK3 gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the MAPK3 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr16:30114710-30116635 and are shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0073] Figure 35 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the NF1 gene. The identification of NMD-inducing exons in the NF1 gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the NF1 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr17:312491203-1252937 and are shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0074] Figure 36 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the MBD5 gene. The identification of NMD-inducing exons in the MBD5 gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the MBD5 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr21:48502511-148510059 and are shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0075] Figure 37Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the MBD5 gene. The identification of NMD-inducing exons in the MBD5 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the MBD5 gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr21 48458873 148462581 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature stop codon, making the transcript a target for NMD.

[0076] Figure 38 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the MBD5 gene. The identification of NMD-inducing exons in the MBD5 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the MBD5 gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr21 48490596 148502435 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature stop codon, making the transcript a target for NMD.

[0077] Figure 39 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the NF2 gene. The identification of NMD-inducing exons in the NF2 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the NF2 gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr22 29604114 29636750 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature stop codon, making the transcript a target for NMD.

[0078] Figure 40Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the MYO6 gene. Shows the identification of NMD-inducing exons in the MYO6 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the MYO6 gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr6:75867107-75870646, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0079] Figure 41 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the SYNGAP1 gene. Shows the identification of NMD-inducing exons in the SYNGAP1 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the SYNGAP1 gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr6:33447935-33451759, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0080] Figure 42 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the SIRT3 gene. Shows the identification of NMD-inducing exons in the SIRT3 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper panel shows a scaled diagram of the SIRT3 gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr11:224241-230451, shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower panel). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0081] Figure 43Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the CACNA1A gene. The identification of NMD-inducing exons in the CACNA1A gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the CACNA1A gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr19 13235732 13241520 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0082] Figure 44 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the CHD2 gene. The identification of NMD-inducing exons in the CHD2 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the CHD2 gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr15 92997404 92998498 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0083] Figure 45 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the NSD1 gene. The identification of NMD-inducing exons in the NSD1 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the NSD1 gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr5 177136032 177191883 and are shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0084] Figure 46Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the NSD1 gene. Shows the identification of NMD-inducing exons in the NSD1 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the NSD1 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr5:177192021-177204119, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0085] Figure 47 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the NSD1 gene. Shows the identification of NMD-inducing exons in the NSD1 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the NSD1 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr5:177246798-177248180, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0086] Figure 48 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the NSD1 gene. Shows the identification of NMD-inducing exons in the NSD1 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the NSD1 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr5:177273786-177280564, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature termination codon, making the transcript a target for NMD.

[0087] Figure 49Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the EIF2AK3 gene. The identification of NMD-inducing exons in the EIF2AK3 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the EIF2AK3 gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr2:88579641-88583429, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0088] Figure 50 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the GALE gene. The identification of NMD-inducing exons in the GALE gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the GALE gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr12:3798232-23798614, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0089] Figure 51 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the HEXA gene. The identification of NMD-inducing exons in the HEXA gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the HEXA gene. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr15:72356652-72375719, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0090] Figure 52Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the HEXA gene. The identification of NMD-inducing exons in the HEXA gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the HEXA gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr15:72345552-72346234, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0091] Figure 53 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the NR1H4 gene. The identification of NMD-inducing exons in the NR1H4 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the NR1H4 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr12:100493403-100505574, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0092] Figure 54 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the STK11 gene. The identification of NMD-inducing exons in the STK11 gene using RNA sequencing is shown, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the STK11 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr19:1207204-1218416, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD.

[0093] Figure 55Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the STK11 gene. Shows the identification of NMD-inducing exons in the STK11 gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the STK11 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr19:1221341-1221948, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0094] Figure 56 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the PCCA gene. Shows the identification of NMD-inducing exons in the PCCA gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the PCCA gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr13:100302999-100307191, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0095] Figure 57 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the MUT gene. Shows the identification of NMD-inducing exons in the MUT gene using RNA sequencing, visualized in the UCSC Genome Browser. The upper figure shows a scaled diagram of the MUT gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr6:49435625-49440205, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in capital letters in the lower figure). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0096] Figure 58Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-inducing exons in the OPA1 gene. The identification of NMD-inducing exons in the OPA1 gene using RNA sequencing is shown and visualized in the UCSC Genome Browser. The upper panel shows a schematic representation of the OPA1 gene to scale. Peaks corresponding to RNA-seq reads were identified in intron GRCh38 / hg38:chr3 193593374 193614710 and are shown in the middle panel. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (sequences highlighted in uppercase letters in the lower panel). Inclusion of this exon leads to the introduction of a premature termination codon, making the transcript a target for NMD.

[0097] Figure 59 Depicts the confirmation of NMD-inducing exons by puromycin or cycloheximide treatment in various cell lines. RT-PCR analysis using total RNA from cells treated with water, DMSO, puromycin, or cycloheximide confirmed the presence of a band corresponding to the NMD-inducing exon 8x of the AKT3 gene (GRCh38 / hg38:chr1 243564285 243564388).

[0098] Figure 60 Depicts an exemplary ASO walk around the AKT3 exon 8x (GRCh38 / hg38:chr1 243564285 243564388) region. A schematic of the ASO walk targeting sequences around the AKT3 exon 8x (GRCh38 / hg38:chr1 243564285 243564388) region upstream of the 3' splice site, within the 3' splice site, exon 8x, within the 5' splice site, and downstream of the 5' splice site is shown. The ASOs were designed to cover these regions by shifting 5 nucleotides at a time.

[0099] Figure 61 Depicts the ASO walk around the AKT3 exon 8x (GRCh38 / hg38:chr1 243564285 243564388) region evaluated by reverse transcription Taqman-qPCR. A plot of the fold change in AKT3 productive mRNA product relative to Sham is shown.

[0100] Figure 62 Depicts the confirmation of NMD-inducing exons by cycloheximide treatment in various cell lines. RT-PCR analysis using total RNA from cells treated with DMSO or cycloheximide confirmed the presence of a band corresponding to the NMD-inducing exon 14x of the PCCA gene (GRCh38 / hg38:chr13 100305751 100305834).

[0101] Figure 63 Depicts exemplary ASO walking around the PCCA exon 14x (GRCh38 / hg38: chr13 100305751-100305834) region. Illustrations of ASO walking conducted around the targeting sequences of the PCCA exon 14x (GRCh38 / hg38: chr13 100305751-100305834) region upstream of the 3' splice site, within the 3' splice site, exon 14x, within the 5' splice site, and downstream of the 5' splice site are shown. The ASOs were designed to cover these regions by shifting 5 nucleotides at a time.

[0102] Figure 64 Depicts ASO walking of the PCCA exon 14x (GRCh38 / hg38: chr13 100305751-100305834) region evaluated by reverse transcription Taqman-qPCR and RT-PCR. Plots of the fold change of PCCA productive mRNA products relative to Sham (gray) and the percentage change in NMD exon inclusion (black) are shown.

[0103] Figure 65 Depicts confirmation of NMD-induced exons by puromycin or cycloheximide treatment in various cell lines, as well as confirmation of NMD-induced exons in brain and retina samples. RT-PCR analysis using total RNA from water-treated, DMSO-treated, puromycin-treated, or cycloheximide-treated cells confirmed the presence of bands corresponding to the NMD-induced exon 7x (GRCh38 / hg38: chr3 193628509-193628616) of the OPA1 gene.

[0104] Figure 66 Depicts exemplary ASO walking around the OPA1 exon 7x (GRCh38 / hg38: chr3 193628509-193628616) region. Illustrations of ASO walking conducted around the targeting sequences of the OPA1 exon 7x (GRCh38 / hg38: chr3 193628509-193628616) region upstream of the 3' splice site, within the 3' splice site, exon 7x, within the 5' splice site, and downstream of the 5' splice site are shown. The ASOs were designed to cover these regions by shifting 5 nucleotides at a time or 3 nucleotides across the splice site region.

[0105] Figure 67 and 68Depicts ASO walking of the OPA1 exon 7x (GRCh38 / hg38: chr3 193628509-193628616) region evaluated by Taqman RT-qPCR. A graph of the fold change of the OPA1 productive mRNA product relative to Sham is plotted.

[0106] Figure 69 Depicts confirmation of NMD-inducing exons by cycloheximide treatment and by the presence of NMD-inducing exon mRNA (NF1) in human and monkey cortex in ReNCell VM. RT-PCR analysis using total RNA from DMSO-treated or cycloheximide-treated cells confirmed the presence of bands corresponding to the NMD-inducing exon 31x (GRCh38 / hg38: chr17 31249955-31250125) of the NF1 gene.

[0107] Figure 70 Depicts exemplary ASO walking around the NF1 exon 31x (GRCh38 / hg38: chr17 31249955-31250125) region. Diagrams of ASO walking performed around the targeting sequences of the NF1 exon 31x (GRCh38 / hg38: chr17 31249955-31250125) region upstream of the 3' splice site, in the 3' splice site, exon 31x, in the 5' splice site, and downstream of the 5' splice site are shown. The ASOs were designed to cover these regions by shifting 5 nucleotides at a time.

[0108] Figure 71 Depicts ASO walking of the NF1 exon 31x (GRCh38 / hg38: chr17 31249955-31250125) region evaluated by RT-PCR (upper panel) and RT-Taqman-qPCR (lower panel). A graph of the fold change of the NF1 productive mRNA product relative to Sham is shown.

[0109] Figure 72 Depicts confirmation of NMD-inducing exons by puromycin or cycloheximide treatment in various cell lines. RT-PCR analysis using total RNA from water-treated, DMSO-treated, puromycin-treated, or cycloheximide-treated cells confirmed the presence of bands corresponding to the NMD-inducing exon 18x (GRCh38 / hg38: chr6 33448789-33448868) of the SYNGAP1 gene.

[0110] Figure 73Depicts an exemplary ASO walk around the SYNGAP1 exon 18x (GRCh38 / hg38: chr6 334487893 33448868) region. Illustrations of ASO walks around the targeting sequences for the regions upstream of the 3' splice site, within the 3' splice site, exon 18x, within the 5' splice site, and downstream of the 5' splice site of the SYNGAP1 exon 18x (GRCh38 / hg38: chr6 33448789 33448868) region are shown. The ASOs were designed to cover these regions by shifting 5 nucleotides at a time.

[0111] Figure 74 Depicts an ASO walk of the SYNGAP1 exon 18x (GRCh38 / hg38: chr6 33448789 33448868) region evaluated by RT-PCR (upper panel) and Taqman-qPCR (lower panel). Plots of % exon 18x inclusion and fold change of SYNGAP1 productive mRNA products relative to Sham are shown (upper and lower panels, respectively).

[0112] Figure 75 Depicts confirmation of NMD-induced exons by cycloheximide treatment. RT-PCR analysis using total RNA from DMSO-treated or cycloheximide-treated cells confirmed the presence of a band corresponding to the NMD-induced exon 30x (GRCh38 / hg38: chr15 92998149 92998261) of the CHD2 gene. Also shown is RT-PCR analysis demonstrating the presence of mRNA containing the NMD-induced exon 30x in cortical samples from mouse, non-human primate, and human.

[0113] Figure 76 Depicts an exemplary ASO walk around the CHD2 exon 30x (GRCh38 / hg38: chr15 92998149 92998261) region. Illustrations of ASO walks around the targeting sequences for the regions upstream of the 3' splice site, within the 3' splice site, exon 30x, within the 5' splice site, and downstream of the 5' splice site of the CHD2 exon 30x (GRCh38 / hg38: chr15 92998149 92998261) region are shown. The ASOs were designed to cover these regions by shifting 5 nucleotides at a time.

[0114] Figure 77Depicts ASO walking in the CHD2 exon 30x (GRCh38 / hg38: chr15 92998149-92998261) region as evaluated by RT-PCR. The RT-PCR results are shown, which display the change in the amount of mRNA containing the NMD-inducing exon 30x.

[0115] Figure 78 Depicts the changes in CHD2 non-productive exon (exon 30x (GRCh38 / hg38: chr15 92998149-92998261)) and CHD2 productive mRNA levels induced by different ASOs. Detailed Description

[0116] Alternative splicing events in the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 genes can result in non-productive mRNA transcripts, which in turn can lead to abnormal protein expression and can target therapeutic agents for alternative splicing events in the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 genes can regulate the expression levels of functional proteins in DS patients and / or inhibit abnormal protein expression.Such therapeutic agents can be used to treat conditions caused by deficiencies in the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins.

[0117] One of the alternative splicing events that can lead to nonproductive mRNA transcripts is the inclusion of additional exons in the mRNA transcript, which can induce nonsense-mediated mRNA decay.The present disclosure provides compositions and methods for modulating the alternative splicing of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 to increase the mature mRNA encoding the protein and thus the amount of the translated functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein produced.These compositions and methods include antisense oligomers (ASOs) that can cause exon skipping, such as pseudoexon skipping, and promote constitutive splicing of pre-mRNAs of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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, or SYNGAP1.In multiple embodiments, the methods of the present disclosure can be used to increase functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins to treat conditions caused by deficiencies in ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins.

[0118] Splicing and nonsense-mediated mRNA decay

[0119] Intervening sequences, or introns, are removed by a large and highly dynamic RNA–protein complex called the spliceosome, which coordinates complex interactions between the primary transcript, small nuclear RNAs (snRNAs), and a large number of proteins. The spliceosome assembles specifically on each intron in an ordered manner, beginning with the recognition of the 5′ splice site (5′ss) by U1 snRNA or the recognition of the 3′ splice site (3′ss) by the U2 pathway, which involves the binding of U2 auxiliary factor (U2AF) to the 3′ss region to facilitate the binding of U2 to the branch point sequence (BPS). U2AF is a stable heterodimer composed of a 65-kD subunit (U2AF65) encoded by U2AF2 that binds to the polypyrimidine tract (PPT) and a 35-kD subunit (U2AF35) encoded by U2AF1 that interacts with the highly conserved AG dinucleotide at the 3′ss and stabilizes the binding of U2AF65. In addition to the BPS / PPT unit and the 3′ss / 5′ss, accurate splicing requires auxiliary sequences or structures that activate or repress splice site recognition, which are called intronic or exonic splicing enhancers or silencers. These elements allow the true splice sites to be recognized among the large excess of cryptic or pseudo-sites in the genomes of higher eukaryotes, which have the same sequence but are one order of magnitude more numerous than the true sites. Although they generally have regulatory functions, little is known about the exact mechanisms of their activation or repression.

[0120] The decision of whether to splice can generally be modeled as a stochastic rather than a deterministic process, such that even the most unambiguous splicing signals may sometimes be spliced incorrectly. However, under normal conditions, pre-mRNA splicing occurs with surprisingly high fidelity. This is partly attributed to the activities of adjacent cis-acting auxiliary exonic and intronic splicing regulatory elements (ESR or ISR). Generally, these functional elements are classified as exonic or intronic splicing enhancers (ESE or ISE) or silencers (ESS or ISS), respectively, according to their ability to stimulate or inhibit splicing. Although there is now evidence that some auxiliary cis-acting elements may act by influencing the kinetics of spliceosome assembly, such as the alignment of the complex between U1 snRNP and the 5'ss, it seems likely that many elements act in concert with trans-acting RNA-binding proteins (RBPs). For example, the family of serine- and arginine-rich RBPs (SR proteins) is a conserved family of proteins that have a key role in defining exons. SR proteins promote exon recognition by recruiting components of the prespliceosome to adjacent splice sites or by antagonizing the action of nearby ESSs. The inhibitory action of ESSs can be mediated by members of the heterogeneous nuclear ribonucleoprotein (hnRNP) family and can alter the recruitment of core splicing factors to adjacent splice sites. In addition to its role in splicing regulation, a silencer element has also been proposed to play a role in the repression of pseudoexons, which are arrays of decoy intronic splicing sites with typical exon spacing but no functional open reading frame. ESEs and ESSs, in concert with their cognate trans-acting RBPs, represent an important component in a set of splicing controls that specify how, where, and when mRNAs are assembled from their precursors.

[0121] The sequences marking exon-intron boundaries are degenerate signals of different strengths that can occur at high frequencies within human genes. In multi-exon genes, different pairs of splice sites can be joined together in many different combinations, creating a diverse array of transcripts from a single gene. This is generally referred to as alternative pre-mRNA splicing. Although most mRNA isoforms generated by alternative splicing can be exported from the nucleus and translated into functional polypeptides, different mRNA isoforms from a single gene may vary widely in their translation efficiency. Those mRNA isoforms that have a premature termination codon (PTC) at least 50 bp upstream of the exon junction complex may be targeted for degradation by the nonsense-mediated mRNA decay (NMD) pathway. Mutations in conventional (BPS / PPT / 3’ss / 5’ss) and auxiliary splicing motifs can lead to aberrant splicing, such as exon skipping or the inclusion of cryptic (or pseudo) exons or the activation of splice sites, and significantly contribute to human morbidity and mortality. Both aberrant and alternative splicing patterns can be affected by natural DNA variations in exons and introns.

[0122] Given that exon-intron boundaries can occur at any of the three positions of a codon, it is clear that only a fraction of alternative splicing events can maintain a canonical open reading frame. For example, only exons that are divisible by 3 can be skipped or included in the mRNA without any reading frame alteration. Splicing events without a compatible phase will induce a frameshift. Unless reversed by downstream events, a frameshift will surely result in one or more PTCs, potentially leading to subsequent degradation by NMD. NMD is a translation-coupled mechanism that eliminates mRNAs containing PTCs. NMD can function as a surveillance pathway present in all eukaryotes. NMD can reduce errors in gene expression by eliminating mRNA transcripts containing premature termination codons. In some cases, the translation of these abnormal mRNAs can lead to a harmful gain-of-function or dominant-negative activity of the resulting protein. NMD not only targets transcripts with PTCs but also a large number of mRNA isoforms expressed from many endogenous genes, suggesting that NMD is a major regulator driving both fine-tuning and coarse-tuning of steady-state RNA levels in cells.

[0123] Exons that induce NMD (NIEs) are exons or pseudoexons that are regions within an intron and, if included in the mature RNA transcript, can activate the NMD pathway. In constitutive splicing events, introns containing NIEs are typically spliced out, but the intron or a portion thereof (e.g., the NIE) can be retained during alternative or aberrant splicing events. Mature mRNA transcripts containing such NIEs may be non-productive due to the frameshift that induces the NMD pathway. Inclusion of an NIE in the mature RNA transcript can downregulate gene expression. In the present disclosure, an mRNA transcript containing an NIE can be referred to as an "NIE-containing mRNA" or an "NMD exon mRNA".

[0124] Cryptic (or pseudo-splice sites) have the same splicing recognition sequences as authentic splice sites but are not used in the splicing reaction. Their number is an order of magnitude greater than that of authentic splice sites in the human genome and they are generally repressed by molecular mechanisms that have not been fully understood to date. Cryptic 5' splice sites have a consensus of NNN / GUNNNN or NNN / GCNNNN, where N is any nucleotide and / is the exon-intron boundary. Cryptic 3' splice sites have a consensus of NAG / N. Their activation is positively influenced by surrounding nucleotides that make them more similar to the optimal consensus sequences of authentic splice sites, which are MAG / GURAGU and YAG / G, respectively, where M is C or A, R is G or A, and Y is C or U.

[0125] A skilled person can readily identify splice sites and their regulatory sequences using suitable algorithms that are publicly available, such as those listed in Kralovicova, J. and Vorechovsky, I. (2007) Global control of aberrant splice site activation by auxiliary splicing sequences: evidence for a gradient in exon and intron definition. Nucleic Acids Res., 35, 6399 - 6413 (http: / / www.ncbi.nlm.nih.gov / pmc / articles / PMC2095810 / pdf / gkm680.pdf).

[0126] Cryptic splice sites or splice regulatory sequences can compete with the splice sites of the NIE for RNA - binding proteins, such as U2AF. In some embodiments, an agent can bind to a cryptic splice site or a splice regulatory sequence to prevent the binding of the RNA - binding protein, thereby facilitating the binding of the RNA - binding protein to the NIE splice site.

[0127] In some embodiments, a cryptic splice site may not contain the 5' or 3' splice site of the NIE. In some embodiments, a cryptic splice site can be at least 10 nucleotides, at least 20 nucleotides, at least 50 nucleotides, at least 100 nucleotides, or at least 200 nucleotides upstream of the NIE 5' splice site. In some embodiments, a cryptic splice site can be at least 10 nucleotides, at least 20 nucleotides, at least 50 nucleotides, at least 100 nucleotides, at least 200 nucleotides downstream of the NIE 3' splice site.

[0128] Target transcript

[0129] In some embodiments, the methods of the present disclosure utilize the presence of NIEs in pre-mRNAs transcribed from the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 genes. Therapeutic agents such as ASOs that stimulate exon skipping of NIEs can be used to induce splicing of the identified ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 NIE pre-mRNA species,To generate functional mature ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 mRNA. Induction of exon spanning can lead to inhibition of the NMD pathway. The resulting mature ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 mRNA can be normally translated without activating the NMD pathway,Thus, increasing the amount of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins in patient cells, and alleviating the symptoms of conditions or diseases associated with deficiencies in ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1.Such as Alport syndrome; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia 9; autism spectrum disorder; dilated cardiomyopathy, 1HH; myofibrillar myopathy 6; neuronal ceroid lipofuscinosis 3; intrahepatic cholestasis of pregnancy 3; progressive familial intrahepatic cholestasis 1; type II citrullinemia; type I citrullinemia; cognitive impairment with or without cerebral ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epileptic aphasia spectrum; generalized epilepsy with febrile seizures plus type 7; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; episodic ataxia type 2; familial focal epilepsy; familial febrile seizures 3B; Friedreich ataxia; Friedreich ataxia with retained reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; autosomal recessive HSAN2D; congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; myoclonic migraine; familial hemiplegic epilepsy 1; neurofibromatosis type 1; opioid addiction; optic atrophy type 1; Phelan-McDermid syndrome; propionic acidemia; primary open-angle glaucoma; propionic academia; retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile convulsions 3; benign familial infantile convulsions 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis; type I tyrosinemia; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant deafness 13; cone-rod dystrophy-2; autosomal dominant deafness 4A; peripheral neuropathy, myopathy, hoarseness and hearing loss; autosomal dominant deafness 22; neurofibromatosis type 2; NASH; or autosomal dominant mental retardation 5.,

[0130] In some embodiments, the diseases or conditions treatable or improvable by the methods or compositions disclosed herein are not directly related to the target protein (gene) targeted by a therapeutic agent. In some embodiments, the therapeutic agents provided herein may target a protein (gene) not directly related to the disease or condition, but modulation of the expression of the target protein (gene) can treat or improve the disease or condition. For example, targeting genes such as CD46, CFH, CR1, DNAJC8, EIF2AK3, ERN1, GUCY2F, GUCY2F, SEMA3C, SEMA3D, SIRT3, or AKT3 by the therapeutic agents provided herein can treat or improve ocular diseases or conditions. In some embodiments, targeting the genes CD46, CFH, CR1, DNAJC8, EIF2AK3, ERN1, GUCY2F, GUCY2F, SEMA3C, SEMA3D, SIRT3, or AKT3 is considered to indicate a pathway (eye). In some embodiments, targeting a gene such as SCN8A can treat or improve central nervous system diseases, e.g., epilepsy, e.g., Dravet syndrome. In some embodiments, such target genes as SCN8A are considered to indicate a pathway (central nervous system) or a pathway (central nervous system, epilepsy).

[0131] In multiple embodiments, the present disclosure provides a therapeutic agent that can target ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 mRNA transcripts to modulate splicing or protein expression levels. The therapeutic agent can be a small molecule, polynucleotide or polypeptide. In some embodiments, the therapeutic agent is an ASO.Individual regions or sequences on the pre-mRNAs of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 can be targeted by therapeutic agents such as ASOs. In some embodiments, the ASO targets the pre-mRNA transcripts of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 containing NIEs.In some embodiments, the ASO targets a sequence within the NIE of the pre-mRNA transcript of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1. In some embodiments, the ASO targets a sequence upstream (or 5') of the 5' end of the NIE (3'ss) of the pre-mRNA transcript of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1.In some embodiments, the ASO targets a sequence downstream (or 3') of the 3' end of the NIE (5'ss) of the pre-mRNA transcript of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1. In some embodiments, the ASO targets a sequence within an intron flanking the 5' end of the NIE of the pre-mRNA transcript of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1.In some embodiments, the ASO targets a sequence within an intron that flanks the 3' end of the NIE of the pre-mRNA transcript of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1. In some embodiments, the ASO targets a sequence at the NIE-intron boundary of the pre-mRNA transcript of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1.The NIE-intron boundary can refer to the junction of the intron sequence and the NIE region. The intron sequence can flank the 5'-end or the 3'-end of the NIE. In some embodiments, the ASO targets a sequence within an exon of the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA transcript.In some embodiments, the ASO targets a sequence within an intron of an ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA transcript. In some embodiments, the ASO targets a sequence that includes a portion of an intron of an ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA transcript and also includes a portion of its exon.

[0132] In some embodiments, the ASO targets a sequence located about 4 to about 300 nucleotides upstream (or 5') of the 5'-end of the NIE. In some embodiments, the ASO targets a sequence located about 1 to about 20 nucleotides, about 20 to about 50 nucleotides, about 50 to about 100 nucleotides, about 100 to about 150 nucleotides, about 150 to about 200 nucleotides, about 200 to about 250 nucleotides, or about 250 to about 300 nucleotides upstream (or 5') of the 5'-end of the NIE region. In some embodiments, the ASO can target a sequence located more than 300 nucleotides upstream of the 5'-end of the NIE. In some embodiments, the ASO targets a sequence located about 4 to about 300 nucleotides downstream (or 3') of the 3'-end of the NIE. In some embodiments, the ASO targets a sequence located about 1 to about 20 nucleotides, about 20 to about 50 nucleotides, about 50 to about 100 nucleotides, about 100 to about 150 nucleotides, about 150 to about 200 nucleotides, about 200 to about 250 nucleotides, or about 250 to about 300 nucleotides downstream of the 3'-end of the NIE. In some embodiments, the ASO targets a sequence located more than 300 nucleotides downstream of the 3'-end of the NIE.

[0133] In some embodiments, the pre-mRNA transcript of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 NIE is encoded by a gene sequence having at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with any one of SEQ ID NOs. 1-59 or 192-211.In some embodiments, the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 NIE pre-mRNA transcript comprises a sequence having at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to any one of SEQ ID NOs: 60 - 191.

[0134] In some embodiments, the pre-mRNA transcript (or NMD exon mRNA) containing ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 NIE contains a sequence having at least about 80%, 85%, 90%, 95%, 97% or 100% sequence identity to any one of SEQ ID NOs: 60-191.In some embodiments, the pre-mRNA transcript (or NMD exon mRNA) of NIE containing ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 is encoded by a sequence having at least about 80%, 85%, 90%, 95%, 97% or 100% sequence identity to any one of SEQ ID NOs: 60 - 191. In some embodiments, the targeted portion of the NMD exon mRNA comprises a sequence having at least 80%, 85%, 90%, 95%, 97% or 100% sequence identity to a region comprising at least 8 contiguous nucleic acids of any one of SEQ ID NOs: 60 - 191.

[0135] In some embodiments, the ASO targets exon 8x of the ABCB4 NIE-containing pre-mRNA comprising NIE exon 8, exon 9x of the ASS1 NIE-containing pre-mRNA comprising NIE exon 9, exon 16x of the ATP8B1 NIE-containing pre-mRNA comprising NIE exon 16, exon 1x of the BAG3 NIE-containing pre-mRNA comprising NIE exon 1, exon 31x of the CACNA1A NIE-containing pre-mRNA comprising NIE exon 31, exon 36x of the CACNA1A NIE-containing pre-mRNA comprising NIE exon 36, exon 37x of the CACNA1A NIE-containing pre-mRNA comprising NIE exon 37, exon 3x of the CBS NIE-containing pre-mRNA comprising NIE exon 3, exon 12x of the CBS NIE-containing pre-mRNA comprising NIE exon 12, exon 1x of the CD55 NIE-containing pre-mRNA comprising NIE exon 1, exon 16x of the CDKL5 NIE-containing pre-mRNA comprising NIE exon 16, exon 3x of the CFH NIE-containing pre-mRNA comprising NIE exon 3, exon 30x of the CHD2 NIE-containing pre-mRNA comprising NIE exon 30, exon 4x of the CHRNA7 NIE-containing pre-mRNA comprising NIE exon 4, exon 1x of the CISD2 NIE-containing pre-mRNA comprising NIE exon 1, exon 15x of the CLN3 NIE-containing pre-mRNA comprising NIE exon 15, exon 11x of the COL4A3 NIE-containing pre-mRNA comprising NIE exon 11, exon 41x of the COL4A3 NIE-containing pre-mRNA comprising NIE exon 41, exon 22x of the COL4A4 NIE-containing pre-mRNA comprising NIE exon 22, exon 44x of the COL4A4 NIE-containing pre-mRNA comprising NIE exon 44, exon 20x of the DEPDC5 NIE-containing pre-mRNA comprising NIE exon 20, exon 2x of the DHDDS NIE-containing pre-mRNA comprising NIE exon 2, exon 3x of the ELOVL4 NIE-containing pre-mRNA comprising NIE exon 3, exon 5x of the FAH NIE-containing pre-mRNA comprising NIE exon 5, exon 4x of the FXN NIE-containing pre-mRNA comprising NIE exon 4, exon 4x of the GALE NIE-containing pre-mRNA comprising NIE exon 4, exon 3x of the GBE1 NIE-containing pre-mRNA comprising NIE exon 3, exon 11x of the GRIN2A NIE-containing pre-mRNA comprising NIE exon 11, exon 1x of the GRNExon 1x of the NIE pre-mRNA, exon 2x of the HEXA NIE pre-mRNA containing NIE exon 2, exon 2x of the KANSL1 NIE pre-mRNA containing NIE exon 2, exon 1x of the KCNQ2 NIE pre-mRNA containing NIE exon 1, exon 50x of the KMT2D NIE pre-mRNA containing NIE exon 50, exon 8x of the MAPK3 NIE pre-mRNA containing NIE exon 8, exon 13x of the MBD5 NIE pre-mRNA containing NIE exon 13, exon 2x of the MECP2 NIE pre-mRNA containing NIE exon 2, exon 11x of the MUT NIE pre-mRNA containing NIE exon 11, exon 31x of the NF1 NIE pre-mRNA containing NIE exon 31, exon 7x of the NIPBL NIE pre-mRNA containing NIE exon 7, exon 38x of the NIPBL NIE pre-mRNA containing NIE exon 38, exon 11x of the NSD1 NIE pre-mRNA containing NIE exon 11, exon 6x of the OPA1 NIE pre-mRNA containing NIE exon 6, exon 28x of the OPA1 NIE pre-mRNA containing NIE exon 28, exon 1x of the OPTN NIE pre-mRNA containing NIE exon 1, exon 1x of the PCCA NIE pre-mRNA containing NIE exon 1, exon 5x of the PCCB NIE pre-mRNA containing NIE exon 5, exon 6x of the PCCB NIE pre-mRNA containing NIE exon 6, exon 4x of the PKP2 NIE pre-mRNA containing NIE exon 4, exon 23x of the PLCB1 NIE pre-mRNA containing NIE exon 23, exon 3x of the PRPF3 NIE pre-mRNA containing NIE exon 3, exon 9x of the PRPF31 NIE pre-mRNA containing NIE exon 9, exon 1x of the RAI1 NIE pre-mRNA containing NIE exon 1, exon 5x of the RBFOX2 NIE pre-mRNA containing NIE exon 5, exon 13x of the SCN2A NIE pre-mRNA containing NIE exon 13, exon 6x of the SCN3A NIE pre-mRNA containing NIE exon 6, exon 7x of the SCN3A NIE pre-mRNA containing NIE exon 7, exon 4x of the SCN8A NIE pre-mRNA containing NIE exon 4, exon 6 of the SCN8A NIE pre-mRNA containing NIE exon 6Exon 6x of the NIE pre-mRNA, exon 20x of the SCN8A NIE-containing pre-mRNA including NIE exon 20, exon 6x of the SCN9A NIE-containing pre-mRNA including NIE exon 6, exon 24x of the SHANK3 NIE-containing pre-mRNA including NIE exon 24, exon 3x of the SLC25A13 NIE-containing pre-mRNA including NIE exon 3, exon 6x of the SLC25A13 NIE-containing pre-mRNA including NIE exon 6, exon 9x of the SLC25A13 NIE-containing pre-mRNA including NIE exon 9, exon 11x of the SLC25A13 NIE-containing pre-mRNA including NIE exon 11, exon 13x of the SLC25A13 NIE-containing pre-mRNA including NIE exon 13, exon 1x of the SLC6A1 NIE-containing pre-mRNA including NIE exon 1, exon 12x of the SPTAN1 NIE-containing pre-mRNA including NIE exon 12, exon 10x of the TEK NIE-containing pre-mRNA including NIE exon 10, exon 15x of the TEK NIE-containing pre-mRNA including NIE exon 15, exon 1x of the TOPORS NIE-containing pre-mRNA including NIE exon 1, exon 11x of the TSC2 NIE-containing pre-mRNA including NIE exon 11, exon 30x of the TSC2 NIE-containing pre-mRNA including NIE exon 30, exon 1x of the UBE3A NIE-containing pre-mRNA including NIE exon 1 or exon 7x of the VCAN NIE-containing pre-mRNA including NIE exon 7. In some embodiments, the ASO targets an exon of AKT3 (GRCh38 / hg38: chr1 243564285 243564388); an exon of CACNA1A (GRCh38 / hg38: chr19 13236449 13236618); an exon of CBS (GRCh38 / hg38: chr21 43059730 43060012); an exon of CD46 (GRCh38 / hg38: chr1 207775610 207775745); an exon of CFH (GRCh38 / hg38: chr1 196675450 196675529); an exon of CHD2 (GRCh38 / hg38: chr15 92998149 92998261); an exon of CLN3 (GRCh38 / hg38: chr16 28479644 28479765); an exon of COL11A2 (GRCh38 / hg38: chr6 3318363433183698); Exons of COL4A3 (GRCh38 / hg38: chr2 227296487 227296526); Exons of COL4A4 (GRCh38 / hg38: chr2 227144653 227144833); Exons of COL4A4 (GRCh38 / hg38: chr2 227015283 227015360); Exons of CR1 (GRCh38 / hg38: chr1 207637688 207637848); Exons of CRX (GRCh38 / hg38: chr19 47835403 47835579); Exons of CYP2J2 (GRCh38 / hg38: chr1 59904366 59904516); Exons of DHDDS (GRCh38 / hg38: chr1 26442335 26442372); Exons of DNAJC8 (GRCh38 / hg38: chr1 28230131 28230252); Exons of EIF2AK3 (GRCh38 / hg38: chr2 88582755 88582824); Exons of ERN1 (GRCh38 / hg38: chr17 64102673 64102804); Exons of GALE (GRCh38 / hg38: chr1 23798311 23798484); Exons of GUCY2F (GRCh38 / hg38: chrX 109383365 109383446); Exons of GUCY2F (GRCh38 / hg38: chrX 109439038 109439175); Exons of HEXA (GRCh38 / hg38: chr15 72362376 72362466); Exons of HEXA (GRCh38 / hg38: chr15 72345677 72345776); Exons of MAPK3 (GRCh38 / hg38: chr16 30115595 30115645); Exons of MBD5 (GRCh38 / hg38: chr2 148460219 148460304); Exons of MBD5 (GRCh38 / hg38: chr2 148490695 148490787); Exons of MBD5 (GRCh38 / hg38: chr2 148505761 148505830); Exons of MUT (GRCh38 / hg38: chr6 49436522 49436597); Exons of MYH14 (GRCh38 / hg38: chr195023082550230999); Exons of MYO6 (GRCh38 / hg38: chr6 75867431 75867523); Exons of NF1 (GRCh38 / hg38: chr17 31249955 31250125); Exons of NF2 (GRCh38 / hg38: chr22 29628658 29628773); Exons of NIPBL (GRCh38 / hg38: chr5 37048127 37048354); Exons of NR1H4 (GRCh38 / hg38: chr12 100499841 100500024); Exons of NSD1 (GRCh38 / hg38: chr5 177169394 177169559); Exons of NSD1 (GRCh38 / hg38: chr5 177200761 177200783); Exons of NSD1 (GRCh38 / hg38: chr5 177247924 177248079); Exons of NSD1 (GRCh38 / hg38: chr5 177275947 177276101); Exons of OPA1 (GRCh38 / hg38: chr3 193628509 193628616); Exons of OPA1 (GRCh38 / hg38: chr3 193603500 193603557); Exons of PCCA (GRCh38 / hg38: chr13 100305751 100305834); Exons of PKP2 (GRCh38 / hg38: chr12 32894516 32894778); Exons of PPARA (GRCh38 / hg38: chr22 46203575 46203752); Exons of PRPF3 (GRCh38 / hg38: chr1 150327557 150327652); Exons of PRPF3 (GRCh38 / hg38: chr1 150330401 150330498); Exons of SCN2A (GRCh38 / hg38: chr2 165327155 165327202); Exons of SCN8A (GRCh38 / hg38: chr12 51688758 51688849); Exons of SCN8A (GRCh38 / hg38: chr12 51780202 51780271); Exons of SCN9A (GRCh38 / hg38: chr2 166304238 166304329); Exons of SEMA3C (GRCh38 / hg38: chr7 80794854Exons of SEMA3D (GRCh38 / hg38: chr7 85059498 - 85059541); exons of SIRT3 (GRCh38 / hg38: chr11 225673 - 226081); exons of STK11 (GRCh38 / hg38: chr19 1216268 - 1216398); exons of STK11 (GRCh38 / hg38: chr19 1221621 - 1221846); exons of SYNGAP1 (GRCh38 / hg38: chr6 33448789 - 33448868); exons of TOPORS (GRCh38 / hg38: chr9 32551365 - 32551469); exons of VCAN (GRCh38 / hg38: chr5 83544965 - 83545070).

[0136] In some embodiments, the ASO targets the 5' end (or 5') upstream of approximately 1,500 nucleotides, approximately 1,000 nucleotides, approximately 800 nucleotides, approximately 700 nucleotides of exon 8x of ABCB4, exon 9x of ASS1, exon 16x of ATP8B1, exon 1x of BAG3, exon 31x of CACNA1A, exon 36x of CACNA1A, exon 37x of CACNA1A, exon 3x of CBS, exon 12x of CBS, exon 1x of CD55, exon 16x of CDKL5, exon 3x of CFH, exon 30x of CHD2, exon 4x of CHRNA7, exon 1x of CISD2, exon 15x of CLN3, exon 11x of COL4A3, exon 41x of COL4A3, exon 22x of COL4A4, exon 44x of COL4A4, exon 20x of DEPDC5, exon 2x of DHDDS, exon 3x of ELOVL4, exon 5x of FAH, exon 4x of FXN, exon 4x of GALE, exon 3x of GBE1, exon 11x of GRIN2A, exon 1x of GRN, exon 2x of HEXA, exon 2x of KANSL1, exon 1x of KCNQ2, exon 50x of KMT2D, exon 8x of MAPK3, exon 13x of MBD5, exon 2x of MECP2, exon 11x of MUT, exon 31x of NF1, exon 7x of NIPBL, exon 38x of NIPBL, exon 11x of NSD1, exon 6x of OPA1, exon 28x of OPA1, exon 1x of OPTN, exon 1x of PCCA, exon 5x of PCCB, exon 6x of PCCB, exon 4x of PKP2, exon 23x of PLCB1, exon 3x of PRPF3, exon 9x of PRPF31, exon 1x of RAI1, exon 5x of RBFOX2, exon 13x of SCN2A, exon 6x of SCN3A, exon 7x of SCN3A, exon 4x of SCN8A, exon 6x of SCN8A, exon 20x of SCN8A, exon 6x of SCN9A, exon 24x of SHANK3, exon 3x of SLC25A13, exon 6x of SLC25A13, exon 9x of SLC25A13, exon 11x of SLC25A13, exon 13x of SLC25A13, exon 1x of SLC6A1, exon 12x of SPTAN1, exon 10x of TEK, exon 15x of TEK, exon 1x of TOPORS, exon 11x of TSC2, exon 30x of TSC2, exon 1x of UBE3A, or exon 7x of VCAN.Sequences at approximately 600 nucleotides, approximately 500 nucleotides, approximately 400 nucleotides, approximately 300 nucleotides, approximately 200 nucleotides, approximately 100 nucleotides, approximately 80 nucleotides, approximately 70 nucleotides, approximately 60 nucleotides, approximately 50 nucleotides. In some embodiments, the ASO targets GRCh38 / hg38:chr12 43564388 of AKT3, GRCh38 / hg38:chr19 13236618 of CACNA1A, GRCh38 / hg38:chr21 43060012 of CBS, GRCh38 / hg38:chr1 207775610 of CD46, GRCh38 / hg38:chr11 96675450 of CFH, GRCh38 / hg38:chr15 92998149 of CHD2, GRCh38 / hg38:chr16 28479765 of CLN3, GRCh38 / hg38:chr6 33183698 of COL11A2, GRCh38 / hg38:chr2 227296487 of COL4A3, GRCh38 / hg38:chr2 227144833 of COL4A4, GRCh38 / hg38:chr2 227015360 of COL4A4, GRCh38 / hg38:chr1 207637688 of CR1, GRCh38 / hg38:chr19 47835403 of CRX, GRCh38 / hg38:chr15 9904516 of CYP2J2, GRCh38 / hg38:chr1 26442335 of DHDDS, GRCh38 / hg38:chr12 8230252 of DNAJC8, GRCh38 / hg38:chr2 88582824 of EIF2AK3, GRCh38 / hg38:chr17 64102804 of ERN1, GRCh38 / hg38:chr1 23798484 of GALE, GRCh38 / hg38:chrX 109383446 of GUCY2F, GRCh38 / hg38:chrX 109439175 of GUCY2F, GRCh38 / hg38:chr15 72362466 of HEXA, GRCh38 / hg38:chr15 72345776 of HEXA, GRCh38 / hg38:chr16 30115645 of MAPK3, GRCh38 / hg38:chr2 148460219 of MBD5, GRCh38 / hg38:chr2 148490695 of MBD5, GRCh38 / hg38:chr2 148505761 of MBD5,Upstream (or 5') of approximately 1,500 nucleotides, approximately 1,000 nucleotides, approximately 800 nucleotides of MUT at GRCh38 / hg38:chr6 49436597, MYH14 at GRCh38 / hg38:chr19 50230825, MYO6 at GRCh38 / hg38:chr6 75867431, NF1 at GRCh38 / hg38:chr17 31249955, NF2 at GRCh38 / hg38:chr22 29628658, NIPBL at GRCh38 / hg38:chr5 37048127, NR1H4 at GRCh38 / hg38:chr12 100499841, NSD1 at GRCh38 / hg38:chr5 177169394, NSD1 at GRCh38 / hg38:chr5 177200761, NSD1 at GRCh38 / hg38:chr5 177247924, NSD1 at GRCh38 / hg38:chr5 177275947, OPA1 at GRCh38 / hg38:chr3 193628509, OPA1 at GRCh38 / hg38:chr3 193603500, PCCA at GRCh38 / hg38:chr13 100305751, PKP2 at GRCh38 / hg38:chr12 32894778, PPARA at GRCh38 / hg38:chr22 46203575, PRPF3 at GRCh38 / hg38:chr1 150327557, PRPF3 at GRCh38 / hg38:chr1 150330401, SCN2A at GRCh38 / hg38:chr2 165327155, SCN8A at GRCh38 / hg38:chr12 51688758, SCN8A at GRCh38 / hg38:chr12 51780202, SCN9A at GRCh38 / hg38:chr2 166304329, SEMA3C at GRCh38 / hg38:chr7 80794957, SEMA3D at GRCh38 / hg38:chr7 85059541, SIRT3 at GRCh38 / hg38:chr11 226081, STK11 at GRCh38 / hg38:chr19 1216268, STK11 at GRCh38 / hg38:chr19 1221621, SYNGAP1 at GRCh38 / hg38:chr6 33448789, TOPORS at GRCh38 / hg38:chr9 32551469 or VCAN at GRCh38 / hg38:chr5 83544965,Sequences at approximately 700 nucleotides, approximately 600 nucleotides, approximately 500 nucleotides, approximately 400 nucleotides, approximately 300 nucleotides, approximately 200 nucleotides, approximately 100 nucleotides, approximately 80 nucleotides, approximately 70 nucleotides, approximately 60 nucleotides, approximately 50 nucleotides.

[0137] In some embodiments, the ASO targets the 5' end (or 5') upstream of up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides of exon 8x of ABCB4, exon 9x of ASS1, exon 16x of ATP8B1, exon 1x of BAG3, exon 31x of CACNA1A, exon 36x of CACNA1A, exon 37x of CACNA1A, exon 3x of CBS, exon 12x of CBS, exon 1x of CD55, exon 16x of CDKL5, exon 3x of CFH, exon 30x of CHD2, exon 4x of CHRNA7, exon 1x of CISD2, exon 15x of CLN3, exon 11x of COL4A3, exon 41x of COL4A3, exon 22x of COL4A4, exon 44x of COL4A4, exon 20x of DEPDC5, exon 2x of DHDDS, exon 3x of ELOVL4, exon 5x of FAH, exon 4x of FXN, exon 4x of GALE, exon 3x of GBE1, exon 11x of GRIN2A, exon 1x of GRN, exon 2x of HEXA, exon 2x of KANSL1, exon 1x of KCNQ2, exon 50x of KMT2D, exon 8x of MAPK3, exon 13x of MBD5, exon 2x of MECP2, exon 11x of MUT, exon 31x of NF1, exon 7x of NIPBL, exon 38x of NIPBL, exon 11x of NSD1, exon 6x of OPA1, exon 28x of OPA1, exon 1x of OPTN, exon 1x of PCCA, exon 5x of PCCB, exon 6x of PCCB, exon 4x of PKP2, exon 23x of PLCB1, exon 3x of PRPF3, exon 9x of PRPF31, exon 1x of RAI1, exon 5x of RBFOX2, exon 13x of SCN2A, exon 6x of SCN3A, exon 7x of SCN3A, exon 4x of SCN8A, exon 6x of SCN8A, exon 20x of SCN8A, exon 6x of SCN9A, exon 24x of SHANK3, exon 3x of SLC25A13, exon 6x of SLC25A13, exon 9x of SLC25A13, exon 11x of SLC25A13, exon 13x of SLC25A13, exon 1x of SLC6A1, exon 12x of SPTAN1, exon 10x of TEK, exon 15x of TEK, exon 1x of TOPORS, exon 11x of TSC2, exon 30x of TSC2, exon 1x of UBE3A or exon 7x of VCAN.Sequences at approximately 600 nucleotides, approximately 500 nucleotides, approximately 400 nucleotides, approximately 300 nucleotides, approximately 200 nucleotides, approximately 100 nucleotides, approximately 80 nucleotides, approximately 70 nucleotides, approximately 60 nucleotides, approximately 50 nucleotides. In some embodiments, the ASO targets GRCh38 / hg38:chr1 243564388 of AKT3, GRCh38 / hg38:chr19 13236618 of CACNA1A, GRCh38 / hg38:chr21 43060012 of CBS, GRCh38 / hg38:chr1 207775610 of CD46, GRCh38 / hg38:chr11 96675450 of CFH, GRCh38 / hg38:chr15 92998149 of CHD2, GRCh38 / hg38:chr16 28479765 of CLN3, GRCh38 / hg38:chr6 33183698 of COL11A2, GRCh38 / hg38:chr2 227296487 of COL4A3, GRCh38 / hg38:chr2 227144833 of COL4A4, GRCh38 / hg38:chr2 227015360 of COL4A4, GRCh38 / hg38:chr1 207637688 of CR1, GRCh38 / hg38:chr19 47835403 of CRX, GRCh38 / hg38:chr15 9904516 of CYP2J2, GRCh38 / hg38:chr1 26442335 of DHDDS, GRCh38 / hg38:chr12 8230252 of DNAJC8, GRCh38 / hg38:chr2 88582824 of EIF2AK3, GRCh38 / hg38:chr17 64102804 of ERN1, GRCh38 / hg38:chr1 23798484 of GALE, GRCh38 / hg38:chrX 109383446 of GUCY2F, GRCh38 / hg38:chrX 109439175 of GUCY2F, GRCh38 / hg38:chr15 72362466 of HEXA, GRCh38 / hg38:chr15 72345776 of HEXA, GRCh38 / hg38:chr16 30115645 of MAPK3, GRCh38 / hg38:chr2 148460219 of MBD5, GRCh38 / hg38:chr2 148490695 of MBD5, GRCh38 / hg38:chr2 148505761 of MBD5,Upstream (or 5') of MUT at GRCh38 / hg38:chr6 49436597, MYH14 at GRCh38 / hg38:chr19 50230825, MYO6 at GRCh38 / hg38:chr6 75867431, NF1 at GRCh38 / hg38:chr17 31249955, NF2 at GRCh38 / hg38:chr22 29628658, NIPBL at GRCh38 / hg38:chr5 37048127, NR1H4 at GRCh38 / hg38:chr12 100499841, NSD1 at GRCh38 / hg38:chr5 177169394, NSD1 at GRCh38 / hg38:chr5 177200761, NSD1 at GRCh38 / hg38:chr5 177247924, NSD1 at GRCh38 / hg38:chr5 177275947, OPA1 at GRCh38 / hg38:chr3 193628509, OPA1 at GRCh38 / hg38:chr3 193603500, PCCA at GRCh38 / hg38:chr13 100305751, PKP2 at GRCh38 / hg38:chr12 32894778, PPARA at GRCh38 / hg38:chr22 46203575, PRPF3 at GRCh38 / hg38:chr1 150327557, PRPF3 at GRCh38 / hg38:chr1 150330401, SCN2A at GRCh38 / hg38:chr2 165327155, SCN8A at GRCh38 / hg38:chr12 51688758, SCN8A at GRCh38 / hg38:chr12 51780202, SCN9A at GRCh38 / hg38:chr2 166304329, SEMA3C at GRCh38 / hg38:chr7 80794957, SEMA3D at GRCh38 / hg38:chr7 85059541, SIRT3 at GRCh38 / hg38:chr11 226081, STK11 at GRCh38 / hg38:chr19 1216268, STK11 at GRCh38 / hg38:chr19 1221621, SYNGAP1 at GRCh38 / hg38:chr6 33448789, TOPORS at GRCh38 / hg38:chr9 32551469 or VCAN at GRCh38 / hg38:chr5 83544965 by up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides,Sequences at approximately 700 nucleotides, approximately 600 nucleotides, approximately 500 nucleotides, approximately 400 nucleotides, approximately 300 nucleotides, approximately 200 nucleotides, approximately 100 nucleotides, approximately 80 nucleotides, approximately 70 nucleotides, approximately 60 nucleotides, approximately 50 nucleotides.

[0138] In some embodiments, the ASO targets the 3' end downstream (or 3') of approximately 1500 nucleotides, approximately 1000 nucleotides, approximately 800 nucleotides, approximately 700 nucleotides of exon 8x of ABCB4, exon 9x of ASS1, exon 16x of ATP8B1, exon 1x of BAG3, exon 31x of CACNA1A, exon 36x of CACNA1A, exon 37x of CACNA1A, exon 3x of CBS, exon 12x of CBS, exon 1x of CD55, exon 16x of CDKL5, exon 3x of CFH, exon 30x of CHD2, exon 4x of CHRNA7, exon 1x of CISD2, exon 15x of CLN3, exon 11x of COL4A3, exon 41x of COL4A3, exon 22x of COL4A4, exon 44x of COL4A4, exon 20x of DEPDC5, exon 2x of DHDDS, exon 3x of ELOVL4, exon 5x of FAH, exon 4x of FXN, exon 4x of GALE, exon 3x of GBE1, exon 11x of GRIN2A, exon 1x of GRN, exon 2x of HEXA, exon 2x of KANSL1, exon 1x of KCNQ2, exon 50x of KMT2D, exon 8x of MAPK3, exon 13x of MBD5, exon 2x of MECP2, exon 11x of MUT, exon 31x of NF1, exon 7x of NIPBL, exon 38x of NIPBL, exon 11x of NSD1, exon 6x of OPA1, exon 28x of OPA1, exon 1x of OPTN, exon 1x of PCCA, exon 5x of PCCB, exon 6x of PCCB, exon 4x of PKP2, exon 23x of PLCB1, exon 3x of PRPF3, exon 9x of PRPF31, exon 1x of RAI1, exon 5x of RBFOX2, exon 13x of SCN2A, exon 6x of SCN3A, exon 7x of SCN3A, exon 4x of SCN8A, exon 6x of SCN8A, exon 20x of SCN8A, exon 6x of SCN9A, exon 24x of SHANK3, exon 3x of SLC25A13, exon 6x of SLC25A13, exon 9x of SLC25A13, exon 11x of SLC25A13, exon 13x of SLC25A13, exon 1x of SLC6A1, exon 12x of SPTAN1, exon 10x of TEK, exon 15x of TEK, exon 1x of TOPORS, exon 11x of TSC2, exon 30x of TSC2, exon 1x of UBE3A or exon 7x of VCAN.Sequences at approximately 600 nucleotides, approximately 500 nucleotides, approximately 400 nucleotides, approximately 300 nucleotides, approximately 200 nucleotides, approximately 100 nucleotides, approximately 80 nucleotides, approximately 70 nucleotides, approximately 60 nucleotides, approximately 50 nucleotides. In some embodiments, the ASO targets GRCh38 / hg38:chr12 43564285 of AKT3, GRCh38 / hg38:chr19 13236449 of CACNA1A, GRCh38 / hg38:chr21 43059730 of CBS, GRCh38 / hg38:chr1 207775745 of CD46, GRCh38 / hg38:chr11 96675529 of CFH, GRCh38 / hg38:chr15 92998261 of CHD2, GRCh38 / hg38:chr16 28479644 of CLN3, GRCh38 / hg38:chr6 33183634 of COL11A2, GRCh38 / hg38:chr2 227296526 of COL4A3, GRCh38 / hg38:chr2 227144653 of COL4A4, GRCh38 / hg38:chr2 227015283 of COL4A4, GRCh38 / hg38:chr1 207637848 of CR1, GRCh38 / hg38:chr19 47835579 of CRX, GRCh38 / hg38:chr15 9904366 of CYP2J2, GRCh38 / hg38:chr1 26442372 of DHDDS, GRCh38 / hg38:chr12 8230131 of DNAJC8, GRCh38 / hg38:chr2 88582755 of EIF2AK3, GRCh38 / hg38:chr17 64102673 of ERN1, GRCh38 / hg38:chr1 23798311 of GALE, GRCh38 / hg38:chrX 109383365 of GUCY2F, GRCh38 / hg38:chrX 109439038 of GUCY2F, GRCh38 / hg38:chr15 72362376 of HEXA, GRCh38 / hg38:chr15 72345677 of HEXA, GRCh38 / hg38:chr16 30115595 of MAPK3, GRCh38 / hg38:chr2 148460304 of MBD5, GRCh38 / hg38:chr2 148490787 of MBD5, GRCh38 / hg38:chr2 148505830 of MBD5,Downstream (or 3') of approximately 1500 nucleotides, approximately 1000 nucleotides, approximately 800 nucleotides of MUT at GRCh38 / hg38:chr6 49436522, MYH14 at GRCh38 / hg38:chr19 50230999, MYO6 at GRCh38 / hg38:chr6 75867523, NF1 at GRCh38 / hg38:chr17 31250125, NF2 at GRCh38 / hg38:chr22 29628773, NIPBL at GRCh38 / hg38:chr5 37048354, NR1H4 at GRCh38 / hg38:chr12 100500024, NSD1 at GRCh38 / hg38:chr5 177169559, NSD1 at GRCh38 / hg38:chr5 177200783, NSD1 at GRCh38 / hg38:chr5 177248079, NSD1 at GRCh38 / hg38:chr5 177276101, OPA1 at GRCh38 / hg38:chr3 193628616, OPA1 at GRCh38 / hg38:chr3 193603557, PCCA at GRCh38 / hg38:chr13 100305834, PKP2 at GRCh38 / hg38:chr12 32894516, PPARA at GRCh38 / hg38:chr22 46203752, PRPF3 at GRCh38 / hg38:chr1 150327652, PRPF3 at GRCh38 / hg38:chr1 150330498, SCN2A at GRCh38 / hg38:chr2 165327202, SCN8A at GRCh38 / hg38:chr12 51688849, SCN8A at GRCh38 / hg38:chr12 51780271, SCN9A at GRCh38 / hg38:chr2 166304238, SEMA3C at GRCh38 / hg38:chr7 80794854, SEMA3D at GRCh38 / hg38:chr7 85059498, SIRT3 at GRCh38 / hg38:chr11 225673, STK11 at GRCh38 / hg38:chr19 1216398, STK11 at GRCh38 / hg38:chr19 1221846, SYNGAP1 at GRCh38 / hg38:chr6 33448868, TOPORS at GRCh38 / hg38:chr9 32551365 or VCAN at GRCh38 / hg38:chr5 83545070Sequences at approximately 700 nucleotides, approximately 600 nucleotides, approximately 500 nucleotides, approximately 400 nucleotides, approximately 300 nucleotides, approximately 200 nucleotides, approximately 100 nucleotides, approximately 80 nucleotides, approximately 70 nucleotides, approximately 60 nucleotides, approximately 50 nucleotides.

[0139] In some embodiments, the ASO targets the 3' end downstream (or 3') of up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides of exon 8x of ABCB4, exon 9x of ASS1, exon 16x of ATP8B1, exon 1x of BAG3, exon 31x of CACNA1A, exon 36x of CACNA1A, exon 37x of CACNA1A, exon 3x of CBS, exon 12x of CBS, exon 1x of CD55, exon 16x of CDKL5, exon 3x of CFH, exon 30x of CHD2, exon 4x of CHRNA7, exon 1x of CISD2, exon 15x of CLN3, exon 11x of COL4A3, exon 41x of COL4A3, exon 22x of COL4A4, exon 44x of COL4A4, exon 20x of DEPDC5, exon 2x of DHDDS, exon 3x of ELOVL4, exon 5x of FAH, exon 4x of FXN, exon 4x of GALE, exon 3x of GBE1, exon 11x of GRIN2A, exon 1x of GRN, exon 2x of HEXA, exon 2x of KANSL1, exon 1x of KCNQ2, exon 50x of KMT2D, exon 8x of MAPK3, exon 13x of MBD5, exon 2x of MECP2, exon 11x of MUT, exon 31x of NF1, exon 7x of NIPBL, exon 38x of NIPBL, exon 11x of NSD1, exon 6x of OPA1, exon 28x of OPA1, exon 1x of OPTN, exon 1x of PCCA, exon 5x of PCCB, exon 6x of PCCB, exon 4x of PKP2, exon 23x of PLCB1, exon 3x of PRPF3, exon 9x of PRPF31, exon 1x of RAI1, exon 5x of RBFOX2, exon 13x of SCN2A, exon 6x of SCN3A, exon 7x of SCN3A, exon 4x of SCN8A, exon 6x of SCN8A, exon 20x of SCN8A, exon 6x of SCN9A, exon 24x of SHANK3, exon 3x of SLC25A13, exon 6x of SLC25A13, exon 9x of SLC25A13, exon 11x of SLC25A13, exon 13x of SLC25A13, exon 1x of SLC6A1, exon 12x of SPTAN1, exon 10x of TEK, exon 15x of TEK, exon 1x of TOPORS, exon 11x of TSC2, exon 30x of TSC2, exon 1x of UBE3A or exon 7x of VCAN.Sequences at approximately 600 nucleotides, approximately 500 nucleotides, approximately 400 nucleotides, approximately 300 nucleotides, approximately 200 nucleotides, approximately 100 nucleotides, approximately 80 nucleotides, approximately 70 nucleotides, approximately 60 nucleotides, and approximately 50 nucleotides. In some embodiments, the ASO targets AKT3 at GRCh38 / hg38:chr1 243564285, CACNA1A at GRCh38 / hg38:chr19 13236449, CBS at GRCh38 / hg38:chr21 43059730, CD46 at GRCh38 / hg38:chr12 07775745, CFH at GRCh38 / hg38:chr1 196675529, CHD2 at GRCh38 / hg38:chr15 92998261, CLN3 at GRCh38 / hg38:chr16 28479644, COL11A2 at GRCh38 / hg38:chr6 33183634, COL4A3 at GRCh38 / hg38:chr22 27296526, COL4A4 at GRCh38 / hg38:chr2 227144653, COL4A4 at GRCh38 / hg38:chr22 27015283, CR1 at GRCh38 / hg38:chr1 207637848, CRX at GRCh38 / hg38:chr19 47835579, CYP2J2 at GRCh38 / hg38:chr15 9904366, DHDDS at GRCh38 / hg38:chr1 26442372, DNAJC8 at GRCh38 / hg38:chr1 28230131, EIF2AK3 at GRCh38 / hg38:chr2 88582755, ERN1 at GRCh38 / hg38:chr17 64102673, GALE at GRCh38 / hg38:chr1 23798311, GUCY2F at GRCh38 / hg38:chrX 109383365, GUCY2F at GRCh38 / hg38:chrX 109439038, HEXA at GRCh38 / hg38:chr15 72362376, HEXA at GRCh38 / hg38:chr15 72345677, MAPK3 at GRCh38 / hg38:chr16 30115595, MBD5 at GRCh38 / hg38:chr2 148460304, MBD5 at GRCh38 / hg38:chr2 148490787, MBD5 at GRCh38 / hg38:chr2 148505830,Downstream (or 3') of MUT at GRCh38 / hg38:chr6 49436522, MYH14 at GRCh38 / hg38:chr19 50230999, MYO6 at GRCh38 / hg38:chr6 75867523, NF1 at GRCh38 / hg38:chr17 31250125, NF2 at GRCh38 / hg38:chr22 29628773, NIPBL at GRCh38 / hg38:chr5 37048354, NR1H4 at GRCh38 / hg38:chr12 100500024, NSD1 at GRCh38 / hg38:chr5 177169559, NSD1 at GRCh38 / hg38:chr5 177200783, NSD1 at GRCh38 / hg38:chr5 177248079, NSD1 at GRCh38 / hg38:chr5 177276101, OPA1 at GRCh38 / hg38:chr3 193628616, OPA1 at GRCh38 / hg38:chr3 193603557, PCCA at GRCh38 / hg38:chr13 100305834, PKP2 at GRCh38 / hg38:chr12 32894516, PPARA at GRCh38 / hg38:chr22 46203752, PRPF3 at GRCh38 / hg38:chr1 150327652, PRPF3 at GRCh38 / hg38:chr1 150330498, SCN2A at GRCh38 / hg38:chr2 165327202, SCN8A at GRCh38 / hg38:chr12 51688849, SCN8A at GRCh38 / hg38:chr12 51780271, SCN9A at GRCh38 / hg38:chr2 166304238, SEMA3C at GRCh38 / hg38:chr7 80794854, SEMA3D at GRCh38 / hg38:chr7 85059498, SIRT3 at GRCh38 / hg38:chr11 225673, STK11 at GRCh38 / hg38:chr19 1216398, STK11 at GRCh38 / hg38:chr19 1221846, SYNGAP1 at GRCh38 / hg38:chr6 33448868, TOPORS at GRCh38 / hg38:chr9 32551365 or VCAN at GRCh38 / hg38:chr5 83545070 by up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides,Sequences at approximately 700 nucleotides, approximately 600 nucleotides, approximately 500 nucleotides, approximately 400 nucleotides, approximately 300 nucleotides, approximately 200 nucleotides, approximately 100 nucleotides, approximately 80 nucleotides, approximately 70 nucleotides, approximately 60 nucleotides, approximately 50 nucleotides.

[0140] In some embodiments, the ASO has a sequence complementary to the targeting portion of the NMD exon mRNA according to any one of SEQ ID NOs: 60 - 191.

[0141] In some embodiments, the ASO targets a sequence upstream of the 5' end of the NIE. For example, an ASO targeting a sequence upstream of the 5’ end of the NIE (such as exon 8x of ABCB4, exon 9x of ASS1, exon 16x of ATP8B1, exon 1x of BAG3, exon 31x of CACNA1A, exon 36x of CACNA1A, exon 37x of CACNA1A, exon 3x of CBS, exon 12x of CBS, exon 1x of CD55, exon 16x of CDKL5, exon 3x of CFH, exon 30x of CHD2, exon 4x of CHRNA7, exon 1x of CISD2, exon 15x of CLN3, exon 11x of COL4A3, exon 41x of COL4A3, exon 22x of COL4A4, exon 44x of COL4A4, exon 20x of DEPDC5, exon 2x of DHDDS, exon 3x of ELOVL4, exon 5x of FAH, exon 4x of FXN, exon 4x of GALE, exon 3x of GBE1, exon 11x of GRIN2A, exon 1x of GRN, exon 2x of HEXA, exon 2x of KANSL1, exon 1x of KCNQ2, exon 50x of KMT2D, exon 8x of MAPK3, exon 13x of MBD5, exon 2x of MECP2, exon 11x of MUT, exon 31x of NF1, exon 7x of NIPBL, exon 38x of NIPBL, exon 11x of NSD1, exon 6x of OPA1, exon 28x of OPA1, exon 1x of OPTN, exon 1x of PCCA, exon 5x of PCCB, exon 6x of PCCB, exon 4x of PKP2, exon 23x of PLCB1, exon 3x of PRPF3, exon 9x of PRPF31, exon 1x of RAI1, exon 5x of RBFOX2, exon 13x of SCN2A, exon 6x of SCN3A, exon 7x of SCN3A, exon 4x of SCN8A, exon 6x of SCN8A, exon 20x of SCN8A, exon 6x of SCN9A, exon 24x of SHANK3, exon 3x of SLC25A13, exon 6x of SLC25A13, exon 9x of SLC25A13, exon 11x of SLC25A13, exon 13x of SLC25A13, exon 1x of SLC6A1, exon 12x of SPTAN1, exon 10x of TEK, exon 15x of TEK, exon 1x of TOPORS, exon 11x of TSC2, exon 30x of TSC2, exon 1x of UBE3A or exon 7x of VCAN) comprises a sequence that is identical to SEQ IDSequences that are at least about 80%, 85%, 90%, 95%, 97% or 100% complementary to at least 8 consecutive nucleic acids of any one of NO:60-134. For example, sequences targeting the upstream sequence of the 5' end of NIE (e.g., exons of AKT3 (GRCh38 / hg38: chr1 243564285 243564388); exons of CACNA1A (GRCh38 / hg38: chr19 13236449 13236618); exons of CBS (GRCh38 / hg38: chr2 143059730 43060012); exons of CD46 (GRCh38 / hg38: chr1 207775610 207775745); exons of CFH (GRCh38 / hg38: chr1 196675450 196675529); exons of CHD2 (GRCh38 / hg38: chr15 92998149 92998261); exons of CLN3 (GRCh38 / hg38: chr16 28479644 28479765); exons of COL11A2 (GRCh38 / hg38: chr6 33183634 33183698); exons of COL4A3 (GRCh38 / hg38: chr22 27296487 227296526); exons of COL4A4 (GRCh38 / hg38: chr2 227144653 227144833); exons of COL4A4 (GRCh38 / hg38: chr22 27015283 227015360); exons of CR1 (GRCh38 / hg38: chr1 207637688 207637848); exons of CRX (GRCh38 / hg38: chr19 47835403 47835579); exons of CYP2J2 (GRCh38 / hg38: chr1 59904366 59904516); exons of DHDDS (GRCh38 / hg38: chr1 26442335 26442372); exons of DNAJC8 (GRCh38 / hg38: chr1 28230131 28230252); exons of EIF2AK3 (GRCh38 / hg38: chr2 88582755 88582824); exons of ERN1 (GRCh38 / hg38: chr17 64102673 64102804); exons of GALE (GRCh38 / hg38: chr12 3798311 23798484); exons of GUCY2F (GRCh38 / hg38: chrXExons of GUCY2F (GRCh38 / hg38:chrX 109383365 109383446); Exons of HEXA (GRCh38 / hg38:chr15 72362376 72362466); Exons of HEXA (GRCh38 / hg38:chr15 72345677 72345776); Exons of MAPK3 (GRCh38 / hg38:chr16 30115595 30115645); Exons of MBD5 (GRCh38 / hg38:chr2 148460219 148460304); Exons of MBD5 (GRCh38 / hg38:chr2 148490695 148490787); Exons of MBD5 (GRCh38 / hg38:chr2 148505761 148505830); Exons of MUT (GRCh38 / hg38:chr6 49436522 49436597); Exons of MYH14 (GRCh38 / hg38:chr19 50230825 50230999); Exons of MYO6 (GRCh38 / hg38:chr6 75867431 75867523); Exons of NF1 (GRCh38 / hg38:chr17 31249955 31250125); Exons of NF2 (GRCh38 / hg38:chr22 29628658 29628773); Exons of NIPBL (GRCh38 / hg38:chr5 37048127 37048354); Exons of NR1H4 (GRCh38 / hg38:chr12 100499841 100500024); Exons of NSD1 (GRCh38 / hg38:chr5 177169394 177169559); Exons of NSD1 (GRCh38 / hg38:chr5 177200761 177200783); Exons of NSD1 (GRCh38 / hg38:chr5 177247924 177248079); Exons of NSD1 (GRCh38 / hg38:chr5 177275947 177276101); Exons of OPA1 (GRCh38 / hg38:chr3 193628509 193628616); Exons of OPA1 (GRCh38 / hg38:chr3 193603500 193603557); Exons of PCCA (GRCh38 / hg38:chr13Exons of PKP2 (GRCh38 / hg38: chr12 32894516 32894778); exons of PPARA (GRCh38 / hg38: chr22 46203575 46203752); exons of PRPF3 (GRCh38 / hg38: chr1 150327557 150327652); exons of PRPF3 (GRCh38 / hg38: chr1 150330401 150330498); exons of SCN2A (GRCh38 / hg38: chr2 165327155 165327202); exons of SCN8A (GRCh38 / hg38: chr12 51688758 51688849); exons of SCN8A (GRCh38 / hg38: chr12 51780202 51780271); exons of SCN9A (GRCh38 / hg38: chr2 166304238 166304329); exons of SEMA3C (GRCh38 / hg38: chr7 80794854 80794957); exons of SEMA3D (GRCh38 / hg38: chr7 85059498 85059541); exons of SIRT3 (GRCh38 / hg38: chr11 225673 226081); exons of STK11 (GRCh38 / hg38: chr19 1216268 1216398); exons of STK11 (GRCh38 / hg38: chr19 1221621 1221846); exons of SYNGAP1 (GRCh38 / hg38: chr6 33448789 33448868); exons of TOPORS (GRCh38 / hg38: chr9 32551365 32551469); exons of VCAN (GRCh38 / hg38: chr5 83544965 83545070) ASO may contain a sequence having at least 80%, 85%, 90%, 95%, 97% or 100% sequence identity with any one of SEQ ID NO: 135 - 191.

[0142]

[0143] In some embodiments, the ASO targets exon 8x of the ABCB4 NIE-containing pre-mRNA comprising NIE exon 8, exon 9x of the ASS1 NIE-containing pre-mRNA comprising NIE exon 9, exon 16x of the ATP8B1 NIE-containing pre-mRNA comprising NIE exon 16, exon 1x of the BAG3 NIE-containing pre-mRNA comprising NIE exon 1, exon 31x of the CACNA1A NIE-containing pre-mRNA comprising NIE exon 31, exon 36x of the CACNA1A NIE-containing pre-mRNA comprising NIE exon 36, exon 37x of the CACNA1A NIE-containing pre-mRNA comprising NIE exon 37, exon 3x of the CBS NIE-containing pre-mRNA comprising NIE exon 3, exon 12x of the CBS NIE-containing pre-mRNA comprising NIE exon 12, exon 1x of the CD55 NIE-containing pre-mRNA comprising NIE exon 1, exon 16x of the CDKL5 NIE-containing pre-mRNA comprising NIE exon 16, exon 3x of the CFH NIE-containing pre-mRNA comprising NIE exon 3, exon 30x of the CHD2 NIE-containing pre-mRNA comprising NIE exon 30, exon 4x of the CHRNA7 NIE-containing pre-mRNA comprising NIE exon 4, exon 1x of the CISD2 NIE-containing pre-mRNA comprising NIE exon 1, exon 15x of the CLN3 NIE-containing pre-mRNA comprising NIE exon 15, exon 11x of the COL4A3 NIE-containing pre-mRNA comprising NIE exon 11, exon 41x of the COL4A3 NIE-containing pre-mRNA comprising NIE exon 41, exon 22x of the COL4A4 NIE-containing pre-mRNA comprising NIE exon 22, exon 44x of the COL4A4 NIE-containing pre-mRNA comprising NIE exon 44, exon 20x of the DEPDC5 NIE-containing pre-mRNA comprising NIE exon 20, exon 2x of the DHDDS NIE-containing pre-mRNA comprising NIE exon 2, exon 3x of the ELOVL4 NIE-containing pre-mRNA comprising NIE exon 3, exon 5x of the FAH NIE-containing pre-mRNA comprising NIE exon 5, exon 4x of the FXN NIE-containing pre-mRNA comprising NIE exon 4, exon 4x of the GALE NIE-containing pre-mRNA comprising NIE exon 4, exon 3x of the GBE1 NIE-containing pre-mRNA comprising NIE exon 3, exon 11x of the GRIN2A NIE-containing pre-mRNA comprising NIE exon 11, exon 1x of the GRN NIE-containing pre-mRNA comprising NIE exon 1,Exon 2x of the HEXA NIE-containing pre-mRNA containing NIE exon 2, exon 2x of the KANSL1 NIE-containing pre-mRNA containing NIE exon 2, exon 1x of the KCNQ2 NIE-containing pre-mRNA containing NIE exon 1, exon 50x of the KMT2D NIE-containing pre-mRNA containing NIE exon 50, exon 8x of the MAPK3 NIE-containing pre-mRNA containing NIE exon 8, exon 13x of the MBD5 NIE-containing pre-mRNA containing NIE exon 13, exon 2x of the MECP2 NIE-containing pre-mRNA containing NIE exon 2, exon 11x of the MUT NIE-containing pre-mRNA containing NIE exon 11, exon 31x of the NF1 NIE-containing pre-mRNA containing NIE exon 31, exon 7x of the NIPBL NIE-containing pre-mRNA containing NIE exon 7, exon 38x of the NIPBL NIE-containing pre-mRNA containing NIE exon 38, exon 11x of the NSD1 NIE-containing pre-mRNA containing NIE exon 11, exon 6x of the OPA1 NIE-containing pre-mRNA containing NIE exon 6, exon 28x of the OPA1 NIE-containing pre-mRNA containing NIE exon 28, exon 1x of the OPTN NIE-containing pre-mRNA containing NIE exon 1, exon 1x of the PCCA NIE-containing pre-mRNA containing NIE exon 1, exon 5x of the PCCB NIE-containing pre-mRNA containing NIE exon 5, exon 6x of the PCCB NIE-containing pre-mRNA containing NIE exon 6, exon 4x of the PKP2 NIE-containing pre-mRNA containing NIE exon 4, exon 23x of the PLCB1 NIE-containing pre-mRNA containing NIE exon 23, exon 3x of the PRPF3 NIE-containing pre-mRNA containing NIE exon 3, exon 9x of the PRPF31 NIE-containing pre-mRNA containing NIE exon 9, exon 1x of the RAI1 NIE-containing pre-mRNA containing NIE exon 1, exon 5x of the RBFOX2 NIE-containing pre-mRNA containing NIE exon 5, exon 13x of the SCN2A NIE-containing pre-mRNA containing NIE exon 13, exon 6x of the SCN3A NIE-containing pre-mRNA containing NIE exon 6, exon 7x of the SCN3A NIE-containing pre-mRNA containing NIE exon 7, exon 4x of the SCN8A NIE-containing pre-mRNA containing NIE exon 4, exon 6x of the SCN8A NIE-containing pre-mRNA containing NIE exon 6, exon 20x of the SCN8A NIE-containing pre-mRNA containing NIE exon 20Exon 6x of the SCN9A NIE-containing pre-mRNA containing NIE exon 6, exon 24x of the SHANK3 NIE-containing pre-mRNA containing NIE exon 24, exon 3x of the SLC25A13 NIE-containing pre-mRNA containing NIE exon 3, exon 6x of the SLC25A13 NIE-containing pre-mRNA containing NIE exon 6, exon 9x of the SLC25A13 NIE-containing pre-mRNA containing NIE exon 9, exon 11x of the SLC25A13 NIE-containing pre-mRNA containing NIE exon 11, exon 13x of the SLC25A13 NIE-containing pre-mRNA containing NIE exon 13, exon 1x of the SLC6A1 NIE-containing pre-mRNA containing NIE exon 1, exon 12x of the SPTAN1 NIE-containing pre-mRNA containing NIE exon 12, exon 10x of the TEK NIE-containing pre-mRNA containing NIE exon 10, exon 15x of the TEK NIE-containing pre-mRNA containing NIE exon 15, exon 1x of the TOPORS NIE-containing pre-mRNA containing NIE exon 1, exon 11x of the TSC2 NIE-containing pre-mRNA containing NIE exon 11, exon 30x of the TSC2 NIE-containing pre-mRNA containing NIE exon 30, exon 1x of the UBE3A NIE-containing pre-mRNA containing NIE exon 1 or exon 7x of the VCAN NIE-containing pre-mRNA containing NIE exon 7. In some embodiments, the ASO targets exon 8x of ABCB4, exon 9x of ASS1, exon 16x of ATP8B1, exon 1x of BAG3, exon 31x of CACNA1A, exon 36x of CACNA1A, exon 37x of CACNA1A, exon 3x of CBS, exon 12x of CBS, exon 1x of CD55, exon 16x of CDKL5, exon 3x of CFH, exon 30x of CHD2, exon 4x of CHRNA7, exon 1x of CISD2, exon 15x of CLN3, exon 11x of COL4A3, exon 41x of COL4A3, exon 22x of COL4A4, exon 44x of COL4A4, exon 20x of DEPDC5, exon 2x of DHDDS, exon 3x of ELOVL4, exon 5x of FAH, exon 4x of FXN, exon 4x of GALE, exon 3x of GBE1, exon 11x of GRIN2A, exon 1x of GRN, exon 2x of HEXA, exon 2x of KANSL1, exon 1x of KCNQ2, exon 50x of KMT2D, exon 8x of MAPK3, exon 13x of MBD5,Sequences downstream (or 3') of the 5' end of the pre-mRNAs of exon 2x of MECP2, exon 11x of MUT, exon 31x of NF1, exon 7x of NIPBL, exon 38x of NIPBL, exon 11x of NSD1, exon 6x of OPA1, exon 28x of OPA1, exon 1x of OPTN, exon 1x of PCCA, exon 5x of PCCB, exon 6x of PCCB, exon 4x of PKP2, exon 23x of PLCB1, exon 3x of PRPF3, exon 9x of PRPF31, exon 1x of RAI1, exon 5x of RBFOX2, exon 13x of SCN2A, exon 6x of SCN3A, exon 7x of SCN3A, exon 4x of SCN8A, exon 6x of SCN8A, exon 20x of SCN8A, exon 6x of SCN9A, exon 24x of SHANK3, exon 3x of SLC25A13, exon 6x of SLC25A13, exon 9x of SLC25A13, exon 11x of SLC25A13, exon 13x of SLC25A13, exon 1x of SLC6A1, exon 12x of SPTAN1, exon 10x of TEK, exon 15x of TEK, exon 1x of TOPORS, exon 11x of TSC2, exon 30x of TSC2, exon 1x of UBE3A or exon 7x of VCAN. In some embodiments, the ASO targets exon 8x of ABCB4, exon 9x of ASS1, exon 16x of ATP8B1, exon 1x of BAG3, exon 31x of CACNA1A, exon 36x of CACNA1A, exon 37x of CACNA1A, exon 3x of CBS, exon 12x of CBS, exon 1x of CD55, exon 16x of CDKL5, exon 3x of CFH, exon 30x of CHD2, exon 4x of CHRNA7, exon 1x of CISD2, exon 15x of CLN3, exon 11x of COL4A3, exon 41x of COL4A3, exon 22x of COL4A4, exon 44x of COL4A4, exon 20x of DEPDC5, exon 2x of DHDDS, exon 3x of ELOVL4, exon 5x of FAH, exon 4x of FXN, exon 4x of GALE, exon 3x of GBE1, exon 11x of GRIN2A, exon 1x of GRN, exon 2x of HEXA, exon 2x of KANSL1, exon 1x of KCNQ2, exon 50x of KMT2D, exon 8x of MAPK3, exon 13x of MBD5, exon 2x of MECP2, exon 11x of MUT, exon 31x of NF1,Exon 20x sequence upstream (or 5') of the 3' end of the pre-mRNA of exon 7x of NIPBL, exon 38x of NIPBL, exon 11x of NSD1, exon 6x of OPA1, exon 28x of OPA1, exon 1x of OPTN, exon 1x of PCCA, exon 5x of PCCB, exon 6x of PCCB, exon 4x of PKP2, exon 23x of PLCB1, exon 3x of PRPF3, exon 9x of PRPF31, exon 1x of RAI1, exon 5x of RBFOX2, exon 13x of SCN2A, exon 6x of SCN3A, exon 7x of SCN3A, exon 4x of SCN8A, exon 6x of SCN8A, exon 20x of SCN8A, exon 6x of SCN9A, exon 24x of SHANK3, exon 3x of SLC25A13, exon 6x of SLC25A13, exon 9x of SLC25A13, exon 11x of SLC25A13, exon 13x of SLC25A13, exon 1x of SLC6A1, exon 12x of SPTAN1, exon 10x of TEK, exon 15x of TEK, exon 1x of TOPORS, exon 11x of TSC2, exon 30x of TSC2, exon 1x of UBE3A or exon 7x of VCAN.

[0144]

[0145]

[0146] Protein expression

[0147] In some embodiments, the methods described herein are used to increase the production of functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein or RNA. As used herein, the term "functional" refers to the amount of activity or function of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein or RNA that is necessary to eliminate any one or more symptoms of the treated condition or disease.The condition or disease is, for example, Alport syndrome; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia 9; autism spectrum disorder; dilated cardiomyopathy, 1HH; myofibrillar myopathy 6; neuronal ceroid lipofuscinosis 3; intrahepatic cholestasis of pregnancy 3; progressive familial intrahepatic cholestasis 1; type II citrullinemia; type 1 citrullinemia; cognitive impairment with or without cerebral ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epileptic aphasia spectrum; generalized epilepsy with febrile seizures plus type 7; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; episodic ataxia type 2; familial focal epilepsy; familial febrile seizures 3B; Friedreich ataxia; Friedreich ataxia with retained reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; autosomal recessive HSAN2D; congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; myoclonic migraine; familial hemiplegic epilepsy 1; neurofibromatosis type 1; opioid addiction; optic atrophy type 1; Phelan-McDermid syndrome; propionic academia; primary open-angle glaucoma; propionic academia; retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile convulsions 3; benign familial infantile convulsions 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis; type I tyrosinemia; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant deafness 13; cone-rod dystrophy-2; autosomal dominant deafness 4A; peripheral neuropathy, myopathy, hoarseness and hearing loss; autosomal dominant deafness 22; neurofibromatosis type 2; NASH; or autosomal dominant mental retardation 5. In some embodiments,The method is used to increase the production amount of partial functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein or RNA. As used herein,The term "partially functional" refers to any amount of activity or function of the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein or RNA that is less than the amount of activity or function required to eliminate or prevent any one or more symptoms of a disease or condition. In some embodiments, the partially functional protein or RNA will have at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% or at least 95% less activity than the fully functional protein or RNA.,

[0148] In some embodiments, the method is a method of increasing the expression of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein in a subject cell containing NIE pre-mRNA encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein,wherein the subject has Alport syndrome; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia 9; autism spectrum disorder; dilated cardiomyopathy, 1HH; myofibrillar myopathy 6; neuronal ceroid lipofuscinosis 3; intrahepatic cholestasis of pregnancy 3; progressive familial intrahepatic cholestasis 1; type II citrullinemia; type I citrullinemia; cognitive impairment with or without cerebella ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epileptic aphasia spectrum; generalized epilepsy with febrile seizures plus type 7; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; episodic ataxia type 2; familial focal epilepsy; familial febrile seizures 3B; Friedreich ataxia; Friedreich ataxia with retained reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; autosomal recessive HSAN2D; congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; myoclonic migraine; familial hemiplegic epilepsy 1; neurofibromatosis type 1; opioid addiction; optic atrophy type 1; Phelan-McDermid syndrome; propionic academia; primary open-angle glaucoma; propionic academia; retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile seizures 3; benign familial infantile seizures 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis; type I tyrosinemia; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant deafness 13; cone-rod dystrophy-2; autosomal dominant deafness 4A; peripheral neuropathy, myopathy, hoarseness and hearing loss; autosomal dominant deafness 22; neurofibromatosis type 2; NASH; or autosomal dominant mental retardation 5,The above-mentioned diseases are caused by insufficient amounts of active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins.And wherein the insufficient amount of the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein is caused by haploinsufficiency of the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein. In such embodiments,The subject has a first allele encoding a functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein and a second allele that does not produce the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein. In another such embodiment,The subject has a first allele encoding a functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein and a second allele encoding a non-functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein. In another such embodiment,The subject has a first allele encoding a functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein and a second allele encoding a partially functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein. In any of these embodiments, the antisense oligomer binds to a targeted portion of the pre-mRNA containing the NIE transcribed from the second allele,Thereby inducing the skipping of pseudo-exons from the exons of the pre-mRNA, and causing an increase in the level of mature mRNA encoding functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein, and an increase in the expression of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein in the cells of the subject.,

[0149] In some embodiments, the method is a method of increasing the expression of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein in a subject's cells, wherein the subject's cells have an NIE-containing pre-mRNA encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein, and wherein the subject has Alport syndrome; amyotrophic lateral sclerosis (ALS);Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia 9; autism spectrum disorder; dilated cardiomyopathy, 1HH; myofibrillar myopathy 6; neuronal ceroid lipofuscinosis 3; intrahepatic cholestasis of pregnancy 3; progressive familial intrahepatic cholestasis 1; type II citrullinemia; type I citrullinemia; cognitive impairment with or without cerebellar ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epileptic aphasia spectrum; generalized epilepsy with febrile seizures plus, type 7; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; episodic ataxia type 2; familial focal epilepsy; familial febrile seizures 3B; Friedreich ataxia; Friedreich ataxia with retained reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; autosomal recessive HSAN2D; congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; myoclonic migraine; familial hemiplegic epilepsy 1; neurofibromatosis type 1; opioid addiction; optic atrophy type 1; Phelan-McDermid syndrome; propionic academia; primary open-angle glaucoma; propionic academia; retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile seizures 3; benign familial infantile seizures 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis; type I tyrosinemia; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant deafness 13; cone-rod dystrophy-2; autosomal dominant deafness 4A; peripheral neuropathy, myopathy, hoarseness and hearing loss; autosomal dominant deafness 22; neurofibromatosis type 2; NASH;Or autosomal dominant mental retardation 5, the above diseases are caused by insufficient amounts of active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins, and wherein the insufficient amounts of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins are caused by autosomal recessive inheritance.;

[0150] In some embodiments, the method is a method of increasing the expression of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein in a subject's cells, the subject's cells having a NIE-containing pre-mRNA encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein, wherein the subject has Alport syndrome; amyotrophic lateral sclerosis (ALS);Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia 9; autism spectrum disorder; dilated cardiomyopathy, 1HH; myofibrillar myopathy 6; neuronal ceroid lipofuscinosis 3; intrahepatic cholestasis of pregnancy 3; progressive familial intrahepatic cholestasis 1; type II citrullinemia; type I citrullinemia; cognitive impairment with or without cerebral ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epileptic aphasia spectrum; generalized epilepsy with febrile seizures plus type 7; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; episodic ataxia type 2; familial focal epilepsy; familial febrile seizures 3B; Friedreich ataxia; Friedreich ataxia with retained reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; autosomal recessive HSAN2D; congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; myoclonic migraine; familial hemiplegic epilepsy 1; neurofibromatosis type 1; opioid addiction; optic atrophy type 1; Phelan-McDermid syndrome; propionic academia; primary open-angle glaucoma; propionic academia; retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile seizures 3; benign familial infantile seizures 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis; type I tyrosinemia; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant deafness 13; cone-rod dystrophy-2; autosomal dominant deafness 4A; peripheral neuropathy, myopathy, hoarseness and hearing loss; autosomal dominant deafness 22; neurofibromatosis type 2; NASH;Or autosomal dominant mental retardation 5, the above diseases are caused by insufficient amounts of active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins, and wherein the insufficient amounts of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins are caused by autosomal dominant inheritance.;

[0151] In some embodiments, the method is a method of increasing the expression of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein in a subject's cells, wherein the subject's cells have an NIE-containing pre-mRNA encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein, and wherein the subject has Alport syndrome; amyotrophic lateral sclerosis (ALS);Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia 9; autism spectrum disorder; dilated cardiomyopathy, 1HH; myofibrillar myopathy 6; neuronal ceroid lipofuscinosis 3; intrahepatic cholestasis of pregnancy 3; progressive familial intrahepatic cholestasis 1; citrullinemia type II; citrullinemia type I; cognitive impairment with or without cerebral ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epileptic aphasia spectrum; generalized epilepsy with febrile seizures plus type 7; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; episodic ataxia type 2; familial focal epilepsy; familial febrile seizures 3B; Friedreich ataxia; Friedreich ataxia with retained reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; autosomal recessive HSAN2D; congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; myoclonic migraine; familial hemiplegic epilepsy 1; neurofibromatosis type 1; opioid addiction; optic atrophy type 1; Phelan-McDermid syndrome; propionic academia; primary open-angle glaucoma; propionic academia; retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile seizures 3; benign familial infantile seizures 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis; tyrosinemia type I; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant deafness 13; cone-rod dystrophy-2; autosomal dominant deafness 4A; peripheral neuropathy, myopathy, hoarseness and hearing loss; autosomal dominant deafness 22; neurofibromatosis type 2; NASH;Or autosomal dominant mental retardation 5, the above diseases are caused by insufficient amounts of active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins, and wherein the insufficient amounts of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins are caused by X-linked dominant inheritance.;

[0152] In related embodiments, the method is a method of increasing the expression of a protein or functional RNA using an ASO. In some embodiments, the ASO can be used to increase the expression of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein in a subject's cells, the subject's cells having an NIE-containing pre-mRNA encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein.in which the subject has deficiencies in the amount or function of proteins such as ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1; for example, Alport syndrome; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia 9; autism spectrum disorder; dilated cardiomyopathy, 1HH; myofibrillar myopathy 6; neuronal ceroid lipofuscinosis 3; intrahepatic cholestasis of pregnancy 3; progressive familial intrahepatic cholestasis 1; type II citrullinemia; type I citrullinemia; cognitive impairment with or without cerebral ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epileptic aphasia spectrum; generalized epilepsy with febrile seizures plus type 7; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; episodic ataxia type 2; familial focal epilepsy; familial febrile seizures 3B; Friedreich ataxia; Friedreich ataxia with retained reflexes; galactose epimerase deficiency; primary congenital glaucoma 3,E; Glycogen storage disease type IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; Autosomal recessive HSAN2D; Congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries syndrome; Autosomal dominant mental retardation 1; Methylmalonic aciduria; Myoclonic migraine; Familial hemiplegic migraine type 1; Neurofibromatosis type 1; Opioid addiction; Optic atrophy type 1; Phelan-McDermid syndrome; Propionic academia; Primary open-angle glaucoma; Propionic academia; Retinitis pigmentosa 11; Retinitis pigmentosa 18; Retinitis pigmentosa 31; Retinitis pigmentosa 59; Rett syndrome; Benign familial infantile seizures 3; Benign familial infantile seizures 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; Tuberous sclerosis; Tyrosinemia type I; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; Autosomal dominant deafness 13; Cone-rod dystrophy-2; Autosomal dominant deafness 4A; Peripheral neuropathy, myopathy, hoarseness and hearing loss; Autosomal dominant deafness 22; Neurofibromatosis type 2; NASH; or Autosomal dominant mental retardation 5.,

[0153] In some embodiments, a pre-mRNA transcript containing an NIE that encodes a protein that causes a disease or condition is targeted by an ASO as described herein. In some embodiments, a pre-mRNA transcript containing an NIE that encodes a protein that does not cause a disease is targeted by the ASO. For example, a disease that results from a mutation or deficiency of a first protein in a particular pathway can be ameliorated by targeting a pre-mRNA containing an NIE that encodes a second protein, thereby increasing the amount of the second protein produced. In some embodiments, the function of the second protein is capable of compensating for the mutation or deficiency of the first protein (which causes the disease or condition).

[0154] In some embodiments, a subject has:

[0155] (a) A first mutant allele, from which

[0156] (i) the level of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein is reduced compared to that produced by the wild-type allele,

[0157] (ii) produces a form of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein with reduced function compared to the equivalent wild-type protein, or

[0158] (iii) does not produce ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein or functional RNA; and

[0159] (b) a second mutant allele, from which

[0160] (i) The level of the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein is reduced compared to that produced by the wild-type allele,

[0161] (ii) produces a form of the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein that has reduced function compared to the equivalent wild-type protein, or

[0162] (iii) does not produce ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein, and

[0163] Wherein the pre-mRNA containing NIE is transcribed from the first allele and / or the second allele. In these embodiments, the ASO binds to the targeted portion of the pre-mRNA containing NIE transcribed from the first allele or the second allele, thereby inducing a pseudoexon to span across the exon of the pre-mRNA containing NIE, and causing an increase in the level of mRNA encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein, and an increase in the expression of the target protein or functional RNA in the cells of the subject. In these embodiments, the target protein or functional RNA whose expression level is increased due to the pseudoexon spanning across the exon of the pre-mRNA containing NIE can be in a form with reduced function (partially functional) compared to the equivalent wild-type protein, or in a form with full function (fully functional) compared to the equivalent wild-type protein.

[0164] In some embodiments, compared to the amount of mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 produced in control cells (e.g., cells not treated with an antisense oligomer or cells treated with an antisense oligomer that does not bind to the targeted portion of the pre-mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1),The level of mRNA encoding the proteins ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 is increased by 1.1 to 10-fold.,

[0165] In some embodiments, a subject being treated using the methods of the present disclosure expresses a partially functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein from one allele, wherein the partially functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein is caused by a frameshift mutation, a nonsense mutation, a missense mutation or a partial gene deletion.In some embodiments, a subject treated using the methods of the present disclosure expresses a non-functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein from one allele, wherein the non-functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein is caused by a frameshift mutation, nonsense mutation, missense mutation, or partial gene deletion in one allele.In some embodiments, a subject treated using the methods of the present disclosure has a complete gene deletion of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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, or SYNGAP1 in one allele.

[0166] Exon inclusion

[0167] As used herein, a "pre-mRNA containing an NIE" is a pre-mRNA transcript containing at least one pseudoexon. Alternative or aberrant splicing can result in the inclusion of at least one pseudoexon in the mature mRNA transcript. The terms "mature mRNA" and "fully spliced mRNA" are used interchangeably herein to describe a fully processed mRNA. The inclusion of at least one pseudoexon can result in a non-productive mRNA and lead to NMD of the mature mRNA. A mature mRNA containing an NIE can sometimes result in aberrant protein expression.

[0168] In some embodiments, the included pseudoexon is the most abundant pseudoexon in the population of pre-mRNAs containing NIEs transcribed from the gene encoding the target protein in the cell. In some embodiments, the included pseudoexon is the most abundant pseudoexon in the population of pre-mRNAs containing NIEs transcribed from the gene encoding the target protein in the cell, wherein the population of pre-mRNAs containing NIEs contains two or more of the included pseudoexons. In some embodiments, an antisense oligomer targeting the most abundant pseudoexon in the population of pre-mRNAs containing NIEs encoding the target protein induces exon skipping of one or two or more pseudoexons in the population, including the pseudoexon targeted or bound by the antisense oligomer. In some embodiments, the targeted region is in a pseudoexon that is the most abundant pseudoexon in a pre-mRNA containing NIEs encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein.

[0169] The degree of exon inclusion can be expressed as a percentage of exon inclusion, e.g., the percentage of transcripts that include a given pseudoexon. Briefly, the percentage of exon inclusion can be calculated as the percentage of the amount of RNA transcripts with exon inclusion relative to the sum of the average amount of RNA transcripts with exon inclusion plus the average amount of RNA transcripts with exon exclusion.

[0170] In some embodiments, the included pseudoexons are exons identified as included pseudoexons based on determining that they are included at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, or at least about 50%. In an embodiment, the included pseudoexons are exons identified as included pseudoexons based on determining that they are included from about 5% to about 100%, from about 5% to about 95%, from about 5% to about 90%, from about 5% to about 85%, from about 5% to about 80%, from about 5% to about 75%, from about 5% to about 70%, from about 5% to about 65%, from about 5% to about 60%, from about 5% to about 55%, from about 5% to about 50%, from about 5% to about 45%, from about 5% to about 40%, from about 5% to about 35%, from about 5% to about 30%, from about 5% to about 25%, from about 5% to about 20%, from about 10% to about 100%, from about 10% to about 95%, from about 10% to about 90%, from about 10% to about 85%, from about 10% to about 80%, from about 10% to about 75%, from about 10% to about 70%, from about 10% to about 65%, from about 10% to about 60%, from about 10% to about 55%, from about 10% to about 50%, from about 10% to about 45%, from about 10% to about 40%, from about 10% to about 35%, from about 10% to about 30%, from about 10% to about 25%, from about 10% to about 20%, from about 15% to about 100%, from about 15% to about 95%, from about 15% to about 90%, from about 15% to about 85%, from about 15% to about 80%, from about 15% to about 75%, from about 15% to about 70%, from about 15% to about 65%, from about 15% to about 60%, from about 15% to about 55%, from about 15% to about 50%, from about 15% to about 45%, from about 15% to about 40%, from about 15% to about 35%, from about 15% to about 30%, from about 15% to about 25%, from about 20% to about 100%, from about 20% to about 95%, from about 20% to about 90%, from about 20% to about 85%, from about 20% to about 80%, from about 20% to about 75%, from about 20% to about 70%, from about 20% to about 65%, from about 20% to about 60%, from about 20% to about 55%, from about 20% to about 50%, from about 20% to about 45%, from about 20% to about 40%, from about 20% to about 35%, from about 20% to about 30%, from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, or from about 25% to about 35%.ENCODE data (e.g., as described by Tilgner et al., 2012, “Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs,” Genome Research 22(9):1616-25) can be used to help identify exon inclusion.

[0171] In some embodiments, cells are contacted with an ASO that is partially complementary to a target portion of the pre-mRNA transcript of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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, or SYNGAP1, as compared to the amount of protein produced by the cells in the absence of the ASO / absence of treatmentresulting in an increase in the amount of the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein by at least 10%, 20%, 30%, 40%, 50%, 60%, 80%, 100%, 150%, 200%, 250%, 300%, 350%, 400%, 450%, 500% or 1000%. In some embodiments, compared to the amount of the target protein produced by a control compound,The total amount of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein produced by the cells contacted by the antisense oligomer increases by about 20% to about 300%, about 50% to about 300%, about 100% to about 300%, about 150% to about 300%, about 20% to about 50%, about 20% to about 100%, about 20% to about 150%, about 20% to about 200%, about 20% to about 250%, about 50% to about 100%, about 50% to about 150%, about 50% to about 200%, about 50% to about 250%, about 100% to about 150%, about 100% to about 200%, about 100% to about 250%, about 150% to about 200%, about 150% to about 250%, about 200% to about 250%, at least about 10%, at least about 20%, at least about 50%, at least about 100%, at least about 150%, at least about 200%, at least about 250% or at least about 300%. In some embodiments, compared to the amount of the target protein produced by a control compound,The total amount of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins produced by the cells contacted by the antisense oligomer is increased by about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8-fold, about 1.1 to about 9-fold, about 2 to about 5-fold, about 2 to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold or at least about 10-fold. The control compound can be, for example, an oligonucleotide that is not complementary to the targeted portion of the pre-mRNA.,

[0172] In some embodiments, contacting the cell with an ASO that is partially complementary to a target of the pre-mRNA transcript of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 results in a change in the amount of protein produced by the cell as compared to the amount of protein produced by the cell in the absence of the ASO / absence of treatment.The amount of mRNA of CYP2J2 or SYNGAP1 (including the mature mRNA encoding the target protein) is increased. In some embodiments, compared to the amount of protein produced by the cells in the absence of the ASO / absence of treatment, the amount of mRNA of the protein encoded by ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1, or the amount of mRNA of the protein encoded by ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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,The amount of mature mRNA of CYP2J2 or SYNGAP1 protein is increased by at least 10, 20, 30, 40, 50, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450, 500 or 1000%. In some embodiments, compared to the amount of mature RNA produced in untreated cells such as untreated cells or cells treated with a control compound, the mRNA encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein or the mRNA encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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,The total amount of mature mRNA of NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2 or SYNGAP1 protein is increased by about 20% to about 300%, about 50% to about 300%, about 100% to about 300%, about 150% to about 300%, about 20% to about 50%, about 20% to about 100%, about 20% to about 150%, about 20% to about 200%, about 20% to about 250%, about 50% to about 100%, about 50% to about 150%, about 50% to about 200%, about 50% to about 250%, about 100% to about 150%, about 100% to about 200%, about 100% to about 250%, about 150% to about 200%, about 150% to about 250%, about 200% to about 250%, at least about 10%, at least about 20%, at least about 50%, at least about 100%, at least about 150%, at least about 200%, at least about 250% or at least about 300%. In some embodiments, compared to the amount of mature RNA produced in untreated cells such as untreated cells or cells treated with a control compound, the mRNA encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein or the mRNA encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS,The total amount of mature mRNA of the ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, 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 or SYNGAP1 protein is increased by about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8-fold, about 1.1 to about 9-fold, about 2 to about 5-fold, about 2 to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold or at least about 10-fold. The control compound can be, for example, not binding to ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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,Oligonucleotides that are partially complementary to the target of the pre-mRNA of NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2 or SYNGAP1.

[0173] The NIE can be of any length. In some embodiments, the NIE comprises the complete sequence of an intron, in which case this can be referred to as intron retention. In some embodiments, the NIE can be a part of an intron. In some embodiments, the NIE can be the 5'-terminal portion of an intron that includes the 5'ss sequence. In some embodiments, the NIE can be the 3'-terminal portion of an intron that includes the 3'ss sequence. In some embodiments, the NIE can be a part within an intron that does not contain the 5'ss sequence. In some embodiments, the NIE can be a part within an intron that does not contain the 3'ss sequence. In some embodiments, the NIE can be a part within an intron that does not contain either the 5'ss or 3'ss sequence. In some embodiments, the length of the NIE can be 5 to 10 nucleotides, 10 to 15 nucleotides, 15 to 20 nucleotides, 20 to 25 nucleotides, 25 to 30 nucleotides, 30 to 35 nucleotides, 35 to 40 nucleotides, 40 to 45 nucleotides, 45 to 50 nucleotides, 50 to 55 nucleotides, 55 to 60 nucleotides, 60 to 65 nucleotides, 65 to 70 nucleotides, 70 to 75 nucleotides, 75 to 80 nucleotides, 80 to 85 nucleotides, 85 to 90 nucleotides, 90 to 95 nucleotides or 95 to 100 nucleotides. In some embodiments, the length of the NIE can be at least 10 nucleotides, at least 20 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least 90 nucleotides or at least 100 nucleotides. In some embodiments, the length of the NIE can be 100 to 200 nucleotides, 200 to 300 nucleotides, 300 to 400 nucleotides, 400 to 500 nucleotides, 500 to 600 nucleotides, 600 to 700 nucleotides, 700 to 800 nucleotides, 800 to 900 nucleotides, 900 to 1,000 nucleotides. In some embodiments, the length of the NIE can be longer than 1,000 nucleotides.

[0174]

[0175] Therapeutic agent

[0176] In various embodiments of the present disclosure, provided are compositions and methods that modulate the protein expression levels of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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, or SYNGAP1. In some embodiments, provided herein are compositions and methods that modulate the alternative splicing of pre-mRNAs of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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, or SYNGAP1. In some embodiments,Compositions and methods are provided that induce exon skipping in the splicing of pre-mRNAs of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1, such as inducing the skipping of pseudo-exons during the splicing of the pre-mRNAs of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1. In other embodiments, therapeutic agents can be used to induce exon inclusion in order to reduce protein expression levels.,

[0177] The therapeutic agent disclosed herein can be an NIE inhibitor. The therapeutic agent can comprise a polynucleic acid polymer.

[0178]

[0179] When referring to reducing the inclusion of NIE in mature mRNA, the reduction can be complete, e.g., 100%, or can be partial. The reduction can be clinically significant. The reduction / correction can be relative to the level of NIE inclusion in untreated subjects, or relative to the amount of NIE inclusion in a population of similar subjects. The reduction / correction can be an NIE inclusion that is at least 10% lower relative to normal subjects or subjects prior to treatment. The reduction can be an NIE inclusion that is at least 20% lower relative to normal subjects or subjects prior to treatment. The reduction can be an NIE inclusion that is at least 40% lower relative to normal subjects or subjects prior to treatment. The reduction can be an NIE inclusion that is at least 50% lower relative to normal subjects or subjects prior to treatment. The reduction can be an NIE inclusion that is at least 60% lower relative to normal subjects or subjects prior to treatment. The reduction can be an NIE inclusion that is at least 80% lower relative to normal subjects or subjects prior to treatment. The reduction can be an NIE inclusion that is at least 90% lower relative to normal subjects or subjects prior to treatment.

[0180] When referring to an increase in the protein levels of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1, such an increase can be clinically meaningful.This increase can be relative to the levels of active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins in untreated subjects, or relative to the amounts of active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 proteins in a population of similar subjects.The increase can be at least 10% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein relative to normal subjects or subjects before treatment. The increase can be at least 20% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein relative to normal subjects or subjects before treatment.The increase can be at least 40% more of the active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein relative to normal subjects or subjects before treatment. The increase can be at least 50% more of the active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein relative to normal subjects or subjects before treatment.The increase can be at least 80% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein relative to normal subjects or subjects before treatment. The increase can be at least 100% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein relative to normal subjects or subjects before treatment.The increase can be at least 200% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein compared to a normal subject or a subject before treatment. The increase can be at least 500% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 protein compared to a normal subject or a subject before treatment.

[0181] In embodiments where the NIE inhibitor comprises a polynucleic acid polymer, the length of the polynucleic acid polymer can be about 50 nucleotides. The length of the polynucleic acid polymer can be about 45 nucleotides. The length of the polynucleic acid polymer can be about 40 nucleotides. The length of the polynucleic acid polymer can be about 35 nucleotides. The length of the polynucleic acid polymer can be about 30 nucleotides. The length of the polynucleic acid polymer can be about 24 nucleotides. The length of the polynucleic acid polymer can be about 25 nucleotides. The length of the polynucleic acid polymer can be about 20 nucleotides. The length of the polynucleic acid polymer can be about 19 nucleotides. The length of the polynucleic acid polymer can be about 18 nucleotides. The length of the polynucleic acid polymer can be about 17 nucleotides. The length of the polynucleic acid polymer can be about 16 nucleotides. The length of the polynucleic acid polymer can be about 15 nucleotides. The length of the polynucleic acid polymer can be about 14 nucleotides. The length of the polynucleic acid polymer can be about 13 nucleotides. The length of the polynucleic acid polymer can be about 12 nucleotides. The length of the polynucleic acid polymer can be about 11 nucleotides. The length of the polynucleic acid polymer can be about 10 nucleotides. The length of the polynucleic acid polymer can be from about 10 to about 50 nucleotides. The length of the polynucleic acid polymer can be from about 10 to about 45 nucleotides. The length of the polynucleic acid polymer can be from about 10 to about 40 nucleotides. The length of the polynucleic acid polymer can be from about 10 to about 35 nucleotides. The length of the polynucleic acid polymer can be from about 10 to about 30 nucleotides. The length of the polynucleic acid polymer can be from about 10 to about 25 nucleotides. The length of the polynucleic acid polymer can be from about 10 to about 20 nucleotides. The length of the polynucleic acid polymer can be from about 15 to about 25 nucleotides. The length of the polynucleic acid polymer can be from about 15 to about 30 nucleotides. The length of the polynucleic acid polymer can be from about 12 to about 30 nucleotides.

[0182] The sequence of the polynucleic acid polymer can be at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5% complementary to a target sequence of an mRNA transcript, such as a partially processed mRNA transcript. The sequence of the polynucleic acid polymer can be 100% complementary to a target sequence of a pre-mRNA transcript.

[0183] The sequence of the polynucleic acid polymer can have 4 or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer can have 3 or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer can have 2 or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer can have 1 or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer can have no mismatches with the target sequence of the pre-mRNA transcript.

[0184] The polynucleic acid polymer can specifically hybridize with the target sequence of the pre-mRNA transcript. For example, the polynucleic acid polymer can have 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or 100% sequence complementarity with the target sequence of the pre-mRNA transcript. The hybridization can be under high stringency hybridization conditions.

[0185] The polynucleic acid polymer comprises a sequence having at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5% sequence identity with a sequence selected from SEQ ID NOs: 60-191. The polynucleic acid polymer can comprise a sequence having 100% sequence identity with a sequence selected from SEQ ID NOs: 60-191.

[0186] When referring to the polynucleic acid polymer sequence, one of ordinary skill in the art will understand that one or more substitutions, optionally two substitutions, can be tolerated in the sequence such that it retains the ability to hybridize with the target sequence; or in the case where the substitution is in the target sequence, the ability to be recognized as the target sequence. The reference to sequence identity can be determined by BLAST sequence alignment using standard / default parameters. For example, according to the present disclosure, the sequence can have 99% identity and still function. In other embodiments, according to the present disclosure, the sequence can have 98% identity and still function. In another embodiment, according to the present disclosure, the sequence can have 95% identity and still function. In another embodiment, according to the present disclosure, the sequence can have 90% identity and still function.

[0187] Antisense oligomer

[0188] The present disclosure provides a composition comprising an antisense oligomer that induces exon skipping by binding to a targeting portion of the pre-mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 that contains NIE.As used herein, the terms “ASO” and “antisense oligomer” are used interchangeably and refer to an oligomer containing nucleobases, such as a polynucleotide, that hybridizes to a target nucleic acid (e.g., an ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA containing NIE) sequence by Watson-Crick base pairing or wobble base pairing (G-U). The ASO can have an exact sequence complementary to the target sequence or approximate complementarity (e.g., complementarity sufficient to bind to the target sequence and enhance splicing at the splice site). The ASOs are designed such that they bind (hybridize) to the target nucleic acid (e.g., the targeted portion of a pre-mRNA transcript) and remain hybridized under physiological conditions. Typically, if they hybridize to sites outside the expected (targeted) nucleic acid sequence, they hybridize to the sequences of a limited number of non-target nucleic acids (some sites other than the target nucleic acid). The design of the ASOs can take into account the nucleic acid sequence of the targeted portion of the pre-mRNA transcript, or nucleic acid sequences at other positions in the genome or cellular pre-mRNAs or transcriptomes that are sufficiently similar such that the likelihood that the ASO will bind to other sites and cause “off-target” effects is limited. As is known in the art, any antisense oligomer, for example, in PCT application PCT / US2014 / 054151, entitled “Reducing Nonsense-Mediated mRNA Decay” and published as WO 2015 / 035091 (which is incorporated herein by reference), can be used to practice the methods described herein.

[0189] In some embodiments, the ASO “specifically hybridizes” to, or is “specific for,” a target nucleic acid or a targeting portion of a pre-mRNA containing an NIE. Typically, such hybridization occurs with a T substantially greater than 37° C., preferably at least 50° C., and typically 60° C. to about 90° C. m . Such hybridization preferably corresponds to stringent hybridization conditions. The T is the temperature at which 50% of the target sequence hybridizes to a complementary oligonucleotide at a given ionic strength and pH. m

[0190] When hybridization occurs between two single-stranded polynucleotides in an antiparallel configuration, oligomers such as oligonucleotides are “complementary” to each other. If hybridization can occur between one strand of a first polynucleotide and a second polynucleotide, the double-stranded polynucleotide can be “complementary” to another polynucleotide. Complementarity (the degree to which one polynucleotide is complementary to another) is quantifiable as the proportion (e.g., percentage) of bases in the opposing strands that are expected to form hydrogen bonds with each other according to the generally accepted base-pairing rules. The sequence of an antisense oligomer (ASO) need not be 100% complementary to the sequence of its target nucleic acid to hybridize. In certain embodiments, the ASO can comprise at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence complementarity to a target region within the target nucleic acid sequence to which it is targeted. For example, an ASO in which 18 of 20 nucleobases of an oligomeric compound are complementary to a target region and will thus specifically hybridize will exhibit 90% complementarity. In this example, the remaining non-complementary nucleobases can be clustered together or dispersed among the complementary nucleobases and need not be contiguous to each other or to the complementary nucleobases. The BLAST program (Basic Local Alignment Search Tool) and the PowerBLAST program known in the art (Altschul et al., J. Mol. Biol., 1990, 215, 403-410; Zhang and Madden, Genome Res., 1997, 7, 649-656) can be routinely used to determine the percentage of complementarity of an ASO to a region of a target nucleic acid.

[0191] The ASO need not hybridize to all of the nucleobases in the target sequence, and the nucleobases to which it hybridizes can be contiguous or non-contiguous. The ASO can hybridize to one or more segments of a pre-mRNA transcript such that intervening or adjacent segments do not participate in the hybridization event (e.g., loop structures or hairpin structures can form). In certain embodiments, the ASO hybridizes to non-contiguous nucleobases in a target pre-mRNA transcript. For example, the ASO can hybridize to nucleobases in a pre-mRNA transcript that are separated by one or more nucleobases that do not hybridize to the ASO.

[0192] The ASO described herein comprises nucleobases complementary to the nucleobases present in the target portion of the pre-mRNA containing NIE. The term ASO encompasses oligonucleotides as well as any other oligomeric molecules that contain nucleobases capable of hybridizing to complementary nucleobases on the target mRNA but do not contain a sugar moiety such as peptide nucleic acid (PNA). The ASO can comprise naturally occurring nucleotides, nucleotide analogs, modified nucleotides, or any combination of two or three of the foregoing. The term "naturally occurring nucleotides" includes deoxyribonucleotides and ribonucleotides. The term "modified nucleotides" includes nucleotides having modified or substituted sugar groups and / or having modified backbones. In some embodiments, all of the nucleotides of the ASO are modified nucleotides. Chemical modifications of the ASO or components of the ASO that are compatible with the methods and compositions described herein will be apparent to those skilled in the art and are found, for example, in U.S. Patent 8,258,109 B2, U.S. Patent 5,656,612, U.S. Patent Publication 2012 / 0190728, and Dias and Stein, Mol. Cancer Ther. 2002, 347-355, which are incorporated herein by reference in their entirety.

[0193] One or more nucleobases of the ASO can be any naturally occurring, unmodified nucleobases such as adenine, guanine, cytosine, thymine, and uracil, or any synthetic or modified nucleobases that are sufficiently similar to the unmodified nucleobases such that they are capable of hydrogen bonding to the nucleobases present on the target pre-mRNA. Examples of modified nucleobases include, but are not limited to, hypoxanthine, xanthine, 7-methylguanine, 5,6-dihydro-uracil, 5-methylcytosine, and 5-hydroxymethylcytosine.

[0194] The ASO described herein also includes a backbone structure that connects the components of the oligomer. The terms "backbone structure" and "oligomer linkage" are used interchangeably and refer to the linkages between the monomers of the ASO. In naturally occurring oligonucleotides, the backbone comprises 3'-5' phosphodiester bonds that link the sugar moieties of the oligomer. The backbone structure or oligomer linkage of the ASO described herein can include (but is not limited to) phosphorothioate, dithiophosphate, selenophosphate, diselenophosphate, phosphoroanilothioate, phosphoraniladate, phosphoramidate, etc. See, e.g., LaPlanche et al., Nucleic Acids Res. 14:9081 (1986); Stec et al., J. Am. Chem. Soc. 106:6077 (1984), Stein et al., Nucleic Acids Res. 16:3209 (1988), Zon et al., Anti-Cancer Drug Design 6:539 (1991); Zon et al., Oligonucleotides and Analogues: A Practical Approach, pp. 87-108 (F. Eckstein, Ed., Oxford University Press, Oxford England (1991)); Stec et al., U.S. Patent 5,151,510; Uhlmann and Peyman, Chemical Reviews 90:543 (1990). In some embodiments, the backbone structure of the ASO does not contain phosphorus but contains peptide bonds, such as in peptide nucleic acid (PNA), or contains linking groups, including carbamates, amides, and straight-chain and cyclic hydrocarbon groups. In some embodiments, the backbone modification is a phosphorothioate bond. In some embodiments, the backbone modification is a phosphoramidate bond.

[0195] In some embodiments, the stereochemistry at each internucleotidic phosphate bond of the ASO backbone is random. In some embodiments, the stereochemistry at each internucleotidic phosphate bond of the ASO backbone is controlled and not random. For example, U.S. Patent Application Publication No. 2014 / 0194610, “Methods for the Synthesis of Functionalized Nucleic Acids” (which is incorporated herein by reference), describes methods for independently selecting the handedness of chirality at each phosphorus atom in a nucleic acid oligomer. In some embodiments, the ASOs used in the methods of the present disclosure (including but not limited to any of the ASOs shown in Tables 5 and 6 herein) include ASOs having non-random internucleotidic phosphate bonds. In some embodiments, the compositions used in the methods of the present disclosure comprise pure diastereomeric ASOs. In some embodiments, the compositions used in the methods of the present disclosure comprise ASOs having a diastereomeric purity of at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, about 100%, about 90% to about 100%, about 91% to about 100%, about 92% to about 100%, about 93% to about 100%, about 94% to about 100%, about 95% to about 100%, about 96% to about 100%, about 97% to about 100%, about 98% to about 100%, or about 99% to about 100%.

[0196] In some embodiments, the ASO has a non-random mixture of Rp and Sp configurations at its phosphoronucleotide internucleotide linkages. For example, it has been proposed that a mixture of Rp and Sp is required in antisense oligonucleotides to achieve a balance between good activity and nuclease stability (Wan et al., 2014, “Synthesis, biophysical properties and biological activity of second generation antisense oligonucleotides containing chiral phosphorothioate linkages,” Nucleic Acids Research 42(22):13456-13468, which is incorporated herein by reference). In some embodiments, the ASO (including but not limited to any ASO shown in SEQ ID NO: 60-191 herein) used in the methods of the present disclosure comprises from about 5% - 100% Rp, at least about 5% Rp, at least about 10% Rp, at least about 15% Rp, at least about 20% Rp, at least about 25% Rp, at least about 30% Rp, at least about 35% Rp, at least about 40% Rp, at least about 45% Rp, at least about 50% Rp, at least about 55% Rp, at least about 60% Rp, at least about 65% Rp, at least about 70% Rp, at least about 75% Rp, at least about 80% Rp, at least about 85% Rp, at least about 90% Rp, or at least about 95% Rp (the remainder being Sp), or about 100% Rp.In some embodiments, the ASOs used in the methods of the present disclosure, including but not limited to any ASO shown herein, comprise a sequence having at least about 80%, 85%, 90%, 95%, 97% or 100% sequence identity to a region comprising at least 8 contiguous nucleic acids of any one of SEQ ID NOs: 60 - 191, comprising from about 10% to about 100% Rp, from about 15% to about 100% Rp, from about 20% to about 100% Rp, from about 25% to about 100% Rp, from about 30% to about 100% Rp, from about 35% to about 100% Rp, from about 40% to about 100% Rp, from about 45% to about 100% Rp, from about 50% to about 100% Rp, from about 55% to about 100% Rp, from about 60% to about 100% Rp, from about 65% to about 100% Rp, from about 70% to about 100% Rp, from about 75% to about 100% Rp, from about 80% to about 100% Rp, from about 85% to about 100% Rp, from about 90% to about 100% Rp or from about 95% to about 100% Rp, from about 20% to about 80% Rp, from about 25% to about 75% Rp, from about 30% to about 70% Rp, from about 40% to about 60% Rp or from about 45% to about 55% Rp, the remainder being Sp.

[0197] In some embodiments, the ASOs used in the methods of the present disclosure, including but not limited to any ASO shown herein, comprise a sequence having at least about 80%, 85%, 90%, 95%, 97% or 100% sequence identity to a region comprising at least 8 contiguous nucleic acids of any one of SEQ ID NOs: 60 - 191, comprising from about 5% - 100% Sp, at least about 5% Sp, at least about 10% Sp, at least about 15% Sp, at least about 20% Sp, at least about 25% Sp, at least about 30% Sp, at least about 35% Sp, at least about 40% Sp, at least about 45% Sp, at least about 50% Sp, at least about 55% Sp, at least about 60% Sp, at least about 65% Sp, at least about 70% Sp, at least about 75% Sp, at least about 80% Sp, at least about 85% Sp, at least about 90% Sp or at least about 95% Sp (the remainder being Rp), or about 100% Sp. In embodiments, the ASOs used in the methods of the present disclosure, including but not limited to any ASO shown herein, comprise a sequence having at least about 80%, 85%, 90%, 95%, 97% or 100% sequence identity to a region comprising at least 8 contiguous nucleic acids of any one of SEQ ID NOs: 60 - 191, comprising from about 10% to about 100% Sp, from about 15% to about 100% Sp, from about 20% to about 100% Sp, from about 25% to about 100% Sp, from about 30% to about 100% Sp, from about 35% to about 100% Sp, from about 40% to about 100% Sp, from about 45% to about 100% Sp, from about 50% to about 100% Sp, from about 55% to about 100% Sp, from about 60% to about 100% Sp, from about 65% to about 100% Sp, from about 70% to about 100% Sp, from about 75% to about 100% Sp, from about 80% to about 100% Sp, from about 85% to about 100% Sp, from about 90% to about 100% Sp or from about 95% to about 100% Sp, from about 20% to about 80% Sp, from about 25% to about 75% Sp, from about 30% to about 70% Sp, from about 40% to about 60% Sp or from about 45% to about 55% Sp, the remainder being Rp.

[0198] Any ASO described herein may contain a sugar moiety comprising ribose or deoxyribose as found in natural nucleotides, or a modified sugar moiety or sugar analogue including a morpholine ring. Non-limiting examples of modified sugar moieties include 2'-substitutions such as 2'-O-methyl (2'-O-Me), 2'-O-methoxyethyl (2'-MOE), 2'-O-aminoethyl, 2'-F; N3'->P5' phosphoramidate, 2'-dimethylaminooxyethoxy, 2'-dimethylaminoethoxyethoxy, 2'-guanidine, 2'-O-guanidinoethyl, carbamate-modified sugars and bicyclic-modified sugars. In some embodiments, the sugar moiety modification is selected from 2'-O-Me, 2'-F and 2'-MOE. In some embodiments, the sugar moiety modification is an additional bridge bond, such as in locked nucleic acid (LNA). In some embodiments, the sugar analogue contains a morpholine ring, such as phosphorodiamidate morpholino (PMO). In some embodiments, the sugar moiety comprises a furanosyl or 2'-furanodeoxyribosyl modification. In some embodiments, the sugar moiety comprises a 2',4'-constrained 2'-O-methoxyethyl (cMOE) modification. In some embodiments, the sugar moiety comprises a cEt 2',4'-constrained 2'-O-ethyl BNA modification. In some embodiments, the sugar moiety comprises a tricyclic DNA (tcDNA) modification. In some embodiments, the sugar moiety comprises an ethylene nucleic acid (ENA) modification. In some embodiments, the sugar moiety comprises an MCE modification. Modifications are known in the art and described in the literature, for example, Jarver et al., 2014, "A Chemical View of Oligonucleotides for Exon Skipping and Related Drug Applications," Nucleic Acid Therapeutics 24(1):37-47, which is incorporated herein by reference for the purposes herein.

[0199] In some embodiments, each monomer of the ASO is modified in the same manner, for example each linkage of the backbone of the ASO contains a phosphorothioate bond, or each ribose sugar moiety contains a 2'-O-methyl modification. Such modifications present on each monomer component of the ASO are referred to as "uniform modifications". In some instances, a combination of different modifications may be desired, for example, the ASO may contain a combination of phosphorodiamidate bonds and a sugar moiety containing a morpholine ring (morpholino). A combination of different modifications of the ASO is referred to as "mixed modifications" or "mixed chemistry".

[0200] In some embodiments, the ASO comprises one or more backbone modifications. In some embodiments, the ASO comprises one or more sugar moiety modifications. In some embodiments, the ASO comprises one or more backbone modifications and one or more sugar moiety modifications. In some embodiments, the ASO comprises 2’-MOE modifications and a phosphorothioate backbone. In some embodiments, the ASO comprises a phosphorodiamidate morpholino (PMO). In some embodiments, the ASO comprises a peptide nucleic acid (PNA). Any ASO or any component of an ASO described herein (e.g., nucleobase, sugar moiety, backbone) can be modified in order to obtain desired properties or activities of the ASO or to reduce undesired properties or activities of the ASO. For example, one or more components of an ASO or any ASO can be modified to enhance the binding affinity to a target sequence on a pre-mRNA transcript; reduce binding to any non-target sequence; reduce degradation by cellular nucleases (i.e., RNase H); improve uptake of the ASO into cells and / or into the cell nucleus; alter the pharmacokinetics or pharmacodynamics of the ASO; and / or modulate the half-life of the ASO.

[0201] In some embodiments, the ASO consists of nucleotides modified with 2'-O-(2-methoxyethyl) (MOE) phosphorothioate. An ASO consisting of such nucleotides is particularly suitable for the methods disclosed herein; oligomers having such modifications have been shown to have significantly enhanced resistance to nuclease degradation and increased bioavailability, making them suitable for, e.g., oral delivery in some of the embodiments described herein. See, e.g., Geary et al., J Pharmacol ExpTher. 2001;296(3):890-7; Geary et al., J Pharmacol Exp Ther. 2001;296(3):898-904.

[0202] Those skilled in the art will be aware of methods for synthesizing ASOs. Alternatively or additionally, ASOs can be obtained from commercial sources.

[0203] Unless otherwise indicated, the left-hand end of a single-stranded nucleic acid (e.g., pre-mRNA transcript, oligonucleotide, ASO, etc.) sequence is the 5' end, and the left-hand direction of a single-stranded or double-stranded nucleic acid sequence is called the 5' direction. Similarly, the right-hand end or right-hand direction of a nucleic acid sequence (single-stranded or double-stranded) is the 3' end or 3' direction. Generally, a region or sequence on the 5' side of a reference point in a nucleic acid is referred to as "upstream", while a region or sequence on the 3' side of a reference point in a nucleic acid is referred to as "downstream". Generally, the 5' direction or 5' end of an mRNA is the location where the start or initiation codon is located, and the 3' end or 3' direction is the location where the stop codon is located. In some aspects, nucleotides upstream of a reference point in a nucleic acid can be represented by negative numbers, while nucleotides downstream of the reference point can be represented by positive numbers. For example, a reference point (e.g., exon-exon junction in an mRNA) can be represented as the "zero" site, and the nucleotide immediately adjacent to and upstream of this reference point is represented as "negative one", e.g., "-1", while the nucleotide immediately adjacent to and downstream of this reference point is represented as "positive one", e.g., "+1".

[0204] In some embodiments, the ASO is complementary to (and binds to) a targeted portion of the pre-mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 that contains an NIE,The targeting moiety is downstream (in the 3' direction) (e.g., in the positively numbered direction relative to the 5' splice site) of the 5' splice site of an exon included in the pre-mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 that contains an NIE (or the 3' end of the NIE). In some embodiments,The ASO is complementary to a targeting portion of the pre-mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1, the targeting portion being within the region of about +1 to about +500 relative to the 5' splice site (or 3' end) of the included exon. In some embodiments,The ASO is complementary to a targeting portion of an ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA, the targeting portion being within a region between +6 and +40,000 nucleotides relative to the 5' splice site (or 3' end) of the included exon. In some aspects,The ASO is complementary to a target portion within the region of about +1 to about +40,000, about +1 to about +30,000, about +1 to about +20,000, about +1 to about +15,000, about +1 to about +10,000, about +1 to about +5,000, about +1 to about +4,000, about +1 to about +3,000, about +1 to about +2,000, about +1 to about +1,000, about +1 to about +500, about +1 to about +490, about +1 to about +480, about +1 to about +470, about +1 to about +460, about +1 to about +450, about +1 to about +440, about +1 to about +430, about +1 to about +420, about +1 to about +410, about +1 to about +400, about +1 to about +390, about +1 to about +380, about +1 to about +370, about +1 to about +360, about +1 to about +350, about +1 to about +340, about +1 to about +330, about +1 to about +320, about +1 to about +310, about +1 to about +300, about +1 to about +290, about +1 to about +280, about +1 to about +270, about +1 to about +260, about +1 to about +250, about +1 to about +240, about +1 to about +230, about +1 to about +220, about +1 to about +210, about +1 to about +200, about +1 to about +190, about +1 to about +180, about +1 to about +170, about +1 to about +160, about +1 to about +150, about +1 to about +140, about +1 to about +130, about +1 to about +120, about +1 to about +110, about +1 to about +100, about +1 to about +90, about +1 to about +80, about +1 to about +70, about +1 to about +60, about +1 to about +50, about +1 to about +40, about +1 to about +30 or about +1 to about +20 relative to the 5' splice site (or 3' end) of the included exon. In some aspects, the ASO is complementary to a target portion within the region of about +1 to about +100, about +100 to about +200, about +200 to about +300, about +300 to about +400 or about +400 to about +500 relative to the 5' splice site (or 3' end) of the included exon.,

[0205] In some embodiments, the ASO is complementary to (and binds to) a targeting portion of an ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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, or SYNGAP1 pre-mRNA that contains an NIE, the targeting portion being upstream (in the 5' direction) of the 5' splice site (or 3' end) of an exon included in the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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, or SYNGAP1 pre-mRNA (e.g.,in the direction represented by a negative number relative to the 5' splice site). In some embodiments, the ASO is complementary to a targeting portion of the pre-mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 that contains an NIE, and the targeting portion is within the region of about -4 to about -270 relative to the 5' splice site (or 3' end) of the included exon. In some embodiments,The ASO is complementary to a targeting portion of the pre-mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 that is within the region between -1 and -40,000 nucleotides relative to the 5' splice site (or 3' end) of the included exon. In some aspects,The ASO is complementary to a targeting moiety within the region of approximately -1 to approximately -40,000, approximately -1 to approximately -30,000, approximately -1 to approximately -20,000, approximately -1 to approximately -15,000, approximately -1 to approximately -10,000, approximately -1 to approximately -5,000, approximately -1 to approximately -4,000, approximately -1 to approximately -3,000, approximately -1 to approximately -2,000, approximately -1 to approximately -1,000, approximately -1 to approximately -500, approximately -1 to approximately -490, approximately -1 to approximately -480, approximately -1 to approximately -470, approximately -1 to approximately -460, approximately -1 to approximately -450, approximately -1 to approximately -440, approximately -1 to approximately -430, approximately -1 to approximately -420, approximately -1 to approximately -410, approximately -1 to approximately -400, approximately -1 to approximately -390, approximately -1 to approximately -380, approximately -1 to approximately -370, approximately -1 to approximately -360, approximately -1 to approximately -350, approximately -1 to approximately -340, approximately -1 to approximately -330, approximately -1 to approximately -320, approximately -1 to approximately -310, approximately -1 to approximately -300, approximately -1 to approximately -290, approximately -1 to approximately -280, approximately -1 to approximately -270, approximately -1 to approximately -260, approximately -1 to approximately -250, approximately -1 to approximately -240, approximately -1 to approximately -230, approximately -1 to approximately -220, approximately -1 to approximately -210, approximately -1 to approximately -200, approximately -1 to approximately -190, approximately -1 to approximately -180, approximately -1 to approximately -170, approximately -1 to approximately -160, approximately -1 to approximately -150, approximately -1 to approximately -140, approximately -1 to approximately -130, approximately -1 to approximately -120, approximately -1 to approximately -110, approximately -1 to approximately -100, approximately -1 to approximately -90, approximately -1 to approximately -80, approximately -1 to approximately -70, approximately -1 to approximately -60, approximately -1 to approximately -50, approximately -1 to approximately -40, approximately -1 to approximately -30 or approximately -1 to approximately -20 relative to the 5' splice site (or 3' end) of the included exon.,

[0206] In some embodiments, the ASO is complementary to a targeting portion of an ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA containing an NIE, the targeting portion being upstream (in the 5' direction) of the 3' splice site (or 5' end) of an exon included in the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA containing an NIE (e.g.,The direction represented by a negative number). In some embodiments, the ASO is complementary to a targeting portion of the pre-mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 that contains NIE, and the targeting portion is within the region of about -1 to about -500 relative to the 3' splice site (or 5' end) of the included exon. In some embodiments,The ASO is complementary to a targeting portion of the pre-mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 that is within the region from -1 to -40,000 relative to the 3' splice site of the included exon. In some aspects,The ASO is complementary to a targeting moiety within the region of about -1 to about -40,000, about -1 to about -30,000, -1 to about -20,000, about -1 to about -15,000, about -1 to about -10,000, about -1 to about -5,000, about -1 to about -4,000, about -1 to about -3,000, about -1 to about -2,000, about -1 to about -1,000, about -1 to about -500, about -1 to about -490, about -1 to about -480, about -1 to about -470, about -1 to about -460, about -1 to about -450, about -1 to about -440, about -1 to about -430, about -1 to about -420, about -1 to about -410, about -1 to about -400, about -1 to about -390, about -1 to about -380, about -1 to about -370, about -1 to about -360, about -1 to about -350, about -1 to about -340, about -1 to about -330, about -1 to about -320, about -1 to about -310, about -1 to about -300, about -1 to about -290, about -1 to about -280, about -1 to about -270, about -1 to about -260, about -1 to about -250, about -1 to about -240, about -1 to about -230, about -1 to about -220, about -1 to about -210, about -1 to about -200, about -1 to about -190, about -1 to about -180, about -1 to about -170, about -1 to about -160, about -1 to about -150, about -1 to about -140, about -1 to about -130, about -1 to about -120, about -1 to about -110, about -1 to about -100, about -1 to about -90, about -1 to about -80, about -1 to about -70, about -1 to about -60, about -1 to about -50, about -1 to about -40, about -1 to about -30 or about -1 to about -20 relative to the 3' splice site of the included exon. In some aspects, the ASO is complementary to a targeting moiety within the region of about -1 to about -100, about -100 to about -200, about -200 to about -300, about -300 to about -400 or about -400 to about -500 relative to the 3' splice site of the included exon.,

[0207] In some embodiments, the ASO is complementary to a targeting sequence of an ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA containing an NIE, the targeting moiety being downstream (in the 3' direction) of the 3' splice site (5' end) of an exon included in the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA containing an NIE (e.g.,The direction represented by a positive number). In some embodiments, the ASO is complementary to a targeting portion of the pre-mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 that contains an NIE, and the targeting portion is within the region of about +1 to about +40,000 relative to the 3' splice site of the included exon. In some aspects,The ASO is complementary to a targeting moiety within the region of about +1 to about +40,000, about +1 to about +30,000, about +1 to about +20,000, about +1 to about +15,000, about +1 to about +10,000, about +1 to about +5,000, about +1 to about +4,000, about +1 to about +3,000, about +1 to about +2,000, about +1 to about +1,000, about +1 to about +500, about +1 to about +490, about +1 to about +480, about +1 to about +470, about +1 to about +460, about +1 to about +450, about +1 to about +440, about +1 to about +430, about +1 to about +420, about +1 to about +410, about +1 to about +400, about +1 to about +390, about +1 to about +380, about +1 to about +370, about +1 to about +360, about +1 to about +350, about +1 to about +340, about +1 to about +330, about +1 to about +320, about +1 to about +310, about +1 to about +300, about +1 to about +290, about +1 to about +280, about +1 to about +270, about +1 to about +260, about +1 to about +250, about +1 to about +240, about +1 to about +230, about +1 to about +220, about +1 to about +210, about +1 to about +200, about +1 to about +190, about +1 to about +180, about +1 to about +170, about +1 to about +160, about +1 to about +150, about +1 to about +140, about +1 to about +130, about +1 to about +120, about +1 to about +110, about +1 to about +100, about +1 to about +90, about +1 to about +80, about +1 to about +70, about +1 to about +60, about +1 to about +50, about +1 to about +40, about +1 to about +30 or about +1 to about +20 or about +1 to about +10 relative to the 3' splice site of the included exon.,

[0208] In some embodiments, the targeting portion of the pre-mRNA of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 containing NIE is within the region from +100 relative to the 5' splice site (3' end) of the included exon to -100 relative to the 3' splice site (5' end) of the included exon.In some embodiments, the targeting portion of the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA containing the NIE is within the NIE. In some embodiments, the targeting portion of the ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA containing the NIE contains pseudo-exons and intron boundaries.

[0209] The ASO can be of any length suitable for specific binding and effective enhancement of splicing. In some embodiments, the ASO consists of 8 to 50 nucleobases. For example, the length of the ASO can be 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 45, or 50 nucleobases. In some embodiments, the ASO consists of more than 50 nucleobases. In some embodiments, the length of the ASO is 8 to 50 nucleobases, 8 to 40 nucleobases, 8 to 35 nucleobases, 8 to 30 nucleobases, 8 to 25 nucleobases, 8 to 20 nucleobases, 8 to 15 nucleobases, 9 to 50 nucleobases, 9 to 40 nucleobases, 9 to 35 nucleobases, 9 to 30 nucleobases, 9 to 25 nucleobases, 9 to 20 nucleobases, 9 to 15 nucleobases, 10 to 50 nucleobases, 10 to 40 nucleobases, 10 to 35 nucleobases, 10 to 30 nucleobases, 10 to 25 nucleobases, 10 to 20 nucleobases, 10 to 15 nucleobases, 11 to 50 nucleobases, 11 to 40 nucleobases, 11 to 35 nucleobases, 11 to 30 nucleobases, 11 to 25 nucleobases, 11 to 20 nucleobases, 11 to 15 nucleobases, 12 to 50 nucleobases, 12 to 40 nucleobases, 12 to 35 nucleobases, 12 to 30 nucleobases, 12 to 25 nucleobases, 12 to 20 nucleobases, 12 to 15 nucleobases, 13 to 50 nucleobases, 13 to 40 nucleobases, 13 to 35 nucleobases, 13 to 30 nucleobases, 13 to 25 nucleobases, 13 to 20 nucleobases, 14 to 50 nucleobases, 14 to 40 nucleobases, 14 to 35 nucleobases, 14 to 30 nucleobases, 14 to 25 nucleobases, 14 to 20 nucleobases, 15 to 50 nucleobases, 15 to 40 nucleobases, 15 to 35 nucleobases, 15 to 30 nucleobases, 15 to 25 nucleobases, 15 to 20 nucleobases, 20 to 50 nucleobases, 20 to 40 nucleobases, 20 to 35 nucleobases, 20 to 30 nucleobases, 20 to 25 nucleobases, 25 to 50 nucleobases, 25 to 40 nucleobases, 25 to 35 nucleobases, or 25 to 30 nucleobases. In some embodiments, the length of the ASO is 18 nucleotides. In some embodiments, the length of the ASO is 15 nucleotides. In some embodiments, the length of the ASO is 25 nucleotides.

[0210] In some embodiments, two or more ASOs are used that have different chemistries but are complementary to the same targeting portion of the pre-mRNA containing the NIE. In some embodiments, two or more ASOs are used that are complementary to different targeting portions of the pre-mRNA containing the NIE.

[0211] In some embodiments, the antisense oligonucleotides of the disclosure are chemically linked to one or more moieties or conjugates, e.g., targeting moieties or other conjugates that enhance the activity or cellular uptake of the oligonucleotide. Such moieties include, but are not limited to, lipid moieties, e.g., cholesterol moieties, cholesteryl moieties, fatty chains, e.g., dodecanediol or undecyl residues, polyamines or polyethylene glycol chains or adamantane acetic acid. Oligonucleotides containing lipophilic moieties and methods of preparation have been described in the published literature. In an embodiment, the antisense oligonucleotide is conjugated to a moiety that includes, but is not limited to, abasic nucleotides, polyethers, polyamines, polyamides, peptides, carbohydrates, e.g., N-acetylgalactosamine (GalNAc), N-Ac-glucosamine (GluNAc) or mannose (e.g., mannose-6-phosphate), lipids or polyhydrocarbon compounds. As understood in the art and described in the literature, the conjugate can be linked to one or more of any of the nucleotides making up the antisense oligonucleotide at any of several positions on the sugar, base or phosphate groups, for example, using a linker. The linker can include divalent or trivalent branched linkers. In an embodiment, the conjugate is attached to the 3' end of the antisense oligonucleotide. Methods for preparing oligonucleotide conjugates are described, for example, in U.S. Patent 8,450,467, "Carbohydrate conjugates as delivery agents for oligonucleotides", which is incorporated herein by reference.

[0212] In some embodiments, the nucleic acid targeted by the ASO is an ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, 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, OPA1, 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 or SYNGAP1 pre-mRNA expressed in a cell such as a eukaryotic cell. In some embodiments, the term "cell" may refer to a cell population. In some embodiments, the cell is in a subject. In some embodiments, the cell is isolated from a subject. In some embodiments, the cell is ex vivo. In some embodiments, the cell is a disease- or disorder-related cell or cell line. In some embodiments, the cell is in vitro (e.g., in cell culture).

[0213] Pharmaceutical composition

[0214] Agents comprising the compositions, such as antisense oligonucleotides, and pharmaceutical compositions or formulations for use in any of the methods described herein can be prepared according to conventional techniques known in the pharmaceutical industry and described in the published literature. In an embodiment, a pharmaceutical composition or formulation for treating a subject comprises an effective amount of any of the antisense oligomers described herein, or a pharmaceutically acceptable salt, solvate, hydrate or ester thereof. A pharmaceutical formulation comprising an antisense oligomer may further comprise a pharmaceutically acceptable excipient, diluent or carrier.

[0215] Pharmaceutically acceptable salts are suitable for contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response, etc., and corresponding to a reasonable benefit / risk ratio. See, for example, S.M. Berge et al., J. Pharmaceutical Sciences, 66:1-19 (1977), which is incorporated herein by reference for this purpose. The salts can be prepared in situ during the final isolation and purification of the compound, or separately by reacting the free base form with a suitable organic acid. Examples of pharmaceutically acceptable, non-toxic acid addition salts are salts formed by the reaction of an amino group with an inorganic acid such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid, or with an organic acid such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid, or salts formed by using other documented methods such as ion exchange. Other pharmaceutically acceptable salts include adipates, alginates, ascorbates, aspartates, benzenesulfonates, benzoates, bisulfates, borates, butyrates, camphorates, camphorsulfonates, citrates, cyclopentanepropionates, digluconates, dodecyl sulfates, ethanesulfonates, formates, fumarates, glucoheptanoates, glycerophosphates, gluconates, hemisulfates, heptanoates, hexanoates, hydroiodides, 2-hydroxyethanesulfonates, lactobionates, lactates, laurates, lauryl sulfates, malates, maleates, malonates, methanesulfonates, 2-naphthalenesulfonates, nicotinates, nitrates, oleates, oxalates, palmitates, pamoates, pectinates, persulfates, 3-phenylpropionates, phosphates, picrates, pivalates, propionates, stearates, succinates, sulfates, tartrates, thiocyanates, p-toluenesulfonates, undecanoates, valerates, etc. Representative alkali metal or alkaline earth metal salts include sodium, lithium, potassium, calcium salts, etc. Where appropriate, additional pharmaceutically acceptable salts include non-toxic salts formed with counterions such as halide ions, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate ions with ammonium, quaternary ammonium, and amine cations.

[0216] In some embodiments, the composition is formulated into any one of a number of possible dosage forms, such as but not limited to tablets, capsules, gel capsules, liquid syrups, soft gels, suppositories, and enemas. In an embodiment, the composition is formulated as a suspension in an aqueous, non-aqueous, or mixed medium. The aqueous suspension may further contain substances that increase the viscosity of the suspension, including, for example, sodium carboxymethylcellulose, sorbitol, and / or dextran. The suspension may also contain stabilizers. In an embodiment, the pharmaceutical formulations or compositions of the present disclosure include but are not limited to solutions, emulsions, microemulsions, foams, or liposome-containing formulations (e.g., cationic or non-cationic liposomes).

[0217] The pharmaceutical compositions or formulations described herein may comprise one or more penetration enhancers, carriers, excipients, or other active or inactive ingredients that are suitable and known to those skilled in the art or described in the published literature. In embodiments, liposomes also include sterically stabilized liposomes, e.g., liposomes comprising one or more specialized lipids. These specialized lipids result in liposomes having an extended circulation lifetime. In embodiments, the sterically stabilized liposomes comprise one or more glycolipids, or are derivatized with one or more hydrophilic polymers such as polyethylene glycol (PEG) moieties. In some embodiments, surfactants are included in the pharmaceutical formulations or compositions. The use of surfactants in pharmaceutical products, formulations, and emulsions is well known in the art. In embodiments, the present disclosure employs penetration enhancers to effectuate efficient delivery of antisense oligonucleotides, e.g., to aid diffusion across cell membranes and / or enhance the permeability of lipophilic drugs. In some embodiments, the penetration enhancer is a surfactant, fatty acid, bile salt, chelating agent, or non-chelating non-surfactant.

[0218] In some embodiments, the pharmaceutical formulation comprises multiple antisense oligonucleotides. In embodiments, the antisense oligonucleotide is co-administered with another drug or therapeutic agent.

[0219] Combination therapy

[0220] In some embodiments, the ASOs disclosed in the present disclosure can be used in combination with one or more additional therapeutic agents. In some embodiments, the one or more additional therapeutic agents can comprise small molecules. For example, the one or more additional therapeutic agents can comprise the small molecules described in WO2016128343A1, WO2017053982A1, WO2016196386A1, WO201428459A1, WO201524876A2, WO2013119916A2, and WO2014209841A2, which applications are incorporated herein by reference in their entirety. In some embodiments, the one or more additional therapeutic agents comprise ASOs that can be used to correct intron retention.

[0221] Treatment of a subject

[0222] Any of the compositions provided herein can be administered to an individual. "Individual" can be used interchangeably with "subject" or "patient". An individual can be a mammal, e.g., a human or an animal such as a non-human primate, rodent, rabbit, rat, mouse, horse, donkey, goat, cat, dog, cow, pig, or sheep. In embodiments, the individual is a human. In embodiments, the individual is a fetus, embryo, or child. In other embodiments, the individual can be another eukaryotic organism, such as a plant. In some embodiments, the compositions provided herein are administered to isolated cells.

[0223] In some embodiments, the compositions provided herein are administered to an individual as a method of treating a disease or disorder. In some embodiments, the individual has a genetic disease, such as any of the diseases described herein. In some embodiments, the individual is at risk of developing a disease such as any of the diseases described herein. In some embodiments, the individual has an increased risk of developing a disease or disorder caused by insufficient amount or activity of a protein. If an individual has an "increased risk" of developing a disease or disorder caused by insufficient amount or activity of a protein, then the method includes prophylactic or preventive treatment. For example, an individual may have an increased risk of developing such a disease or disorder due to a family history of the disease. Generally, individuals with an increased risk of developing such a disease or disorder benefit from prophylactic treatment (e.g., by preventing or delaying the onset or progression of the disease or disorder). In an embodiment, a fetus is treated in utero, for example, by administering an ASO composition directly or indirectly (e.g., through the mother) to the fetus.

[0224] Suitable routes for administering the ASOs of the present disclosure can vary depending on the cell type to which the ASO needs to be delivered. Multiple tissues and organs are affected by Dravet syndrome, and the brain is the most severely affected tissue. The ASOs of the present disclosure can be administered parenterally, for example, by intrathecal injection, intraventricular injection, intraperitoneal injection, intramuscular injection, subcutaneous injection, or intravenous injection to a patient.

[0225] In an embodiment, the antisense oligonucleotide is administered together with one or more agents known in the art that can facilitate penetration of the antisense oligonucleotide across the blood-brain barrier. For example, U.S. Patent 6,632,427, "Adenoviral-vector-mediated gene transfer into medullary motor neurons," describes the delivery of an agent by administering an adenoviral vector to motor neurons in muscle tissue, which is incorporated herein by reference. For example, U.S. Patent 6,756,523, "Adenovirus vectors for the transfer of foreign genes into cells of the central nervous system particularly in brain," describes the direct delivery of a vector to the brain, e.g., the striatum, thalamus, hippocampus, or substantia nigra, which is incorporated herein by reference.

[0226] In some embodiments, the antisense oligonucleotide is linked or conjugated to an agent that provides the desired pharmaceutical or pharmacodynamic properties. In an embodiment, the antisense oligonucleotide is conjugated to a substance known in the art, such as an antibody to the transferrin receptor, to facilitate penetration or transport across the blood-brain barrier. In an embodiment, the antisense oligonucleotide is linked to a viral vector, for example, to make the antisense compound more effective or to increase transport across the blood-brain barrier. In an embodiment, the permeability of the blood-brain barrier is assisted by infusion of sugars, such as meso-erythritol, xylitol, D(+)-galactose, D(+)-lactose, D(+)-xylose, dulcitol, inositol, L(−)-fructose, D(−)-mannitol, D(+)-glucose, D(+)-arabinose, D(−)-arabinose, cellobiose, D(+)-maltose, D(+)-raffinose, L(+)-rhamnose, D(+)-melibiose, D(−)-ribose,adonitol, D(+)-arabitol, L(−)-arabitol, D(+)-fucose, L(−)-fucose, D(−)-lyxose, L(+)-lyxose, and L(−)-lyxose, or amino acids, such as glutamine, lysine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glycine, histidine, leucine, methionine, phenylalanine, proline, serine, threonine, tyrosine, valine, and taurine. Methods and materials for enhancing blood-brain barrier penetration are described, for example, in U.S. Patent No. 9,193,969, “Compositions and methods for selective delivery of oligonucleotide molecules to specific neuron types”, U.S. Patent No. 4,866,042, “Method for the delivery of genetic material across the blood brain barrier”, U.S. Patent No. 6,294,520, “Material for passage through the blood-brain barrier”, and U.S. Patent No. 6,936,589, “Parenteral delivery systems”, each of which is incorporated herein by reference.

[0227] In some embodiments, the ASO of the present disclosure is conjugated to a dopamine reuptake inhibitor (DRI), a selective serotonin reuptake inhibitor (SSRI), a norepinephrine reuptake inhibitor (NRI), a norepinephrine-dopamine reuptake inhibitor (NDRI), and a serotonin-norepinephrine-dopamine reuptake inhibitor (SNDRI) using the methods described, for example, in U.S. Patent No. 9,193,969, which is incorporated herein by reference.

[0228] In some embodiments, the improvement of the condition of a subject being treated with the methods and compositions is evaluated using any method known and described in the art.

[0229] Method for identifying additional ASOs that induce exon skipping

[0230] Also included withi...

Claims

1. A method of modulating the expression of a target protein in a cell having an mRNA that includes a nonsense-mediated RNA decay-inducing exon (NMD exon) and encodes the target protein, the method comprising contacting the cell with a therapeutic agent, whereby the therapeutic agent modulates splicing of the NMD exon from the mRNA, thereby modulating the level of the 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: AKT3, CACNA1A, CBS, CD46, CFH, CHD2, CLN3, COL11A2, COL4A3, COL4A4, COL4A4, CR1, CRX, CYP2J2, DHDDS, DNAJC8, EIF2AK3, ERN1, GALE, GUCY2F, GUCY2F, HEXA, HEXA, MAPK3, MBD5, MBD5, MBD5, MUT, MYH14, MYO6, NF1, NF2, NIPBL, NR1H4, NSD1, NSD1, NSD1, NSD1, OPA1, OPA1, PCCA, PKP2, PPARA, PRPF3, PRPF3, SCN2A, SCN8A, SCN8A, SCN9A, SEMA3C, SEMA3D, SIRT3, STK11, STK11, SYNGAP1, TOPORS, and VCAN proteins.

2. A method of treating a disease or condition in a subject in need thereof by modulating the expression of a target protein in the cells of the subject, the method comprising: Contacting the cells of a subject with a therapeutic agent that modulates splicing of a nonsense-mediated mRNA decay-inducing exon (NMD exon) from an mRNA in the cells, wherein the mRNA includes the NMD exon and encodes a target protein, thereby modulating the level of the processed mRNA encoding the target protein and modulating the expression of the target protein in the cells of the subject, wherein the target protein is selected from the group consisting of: AKT3, CACNA1A, CBS, CD46, CFH, CHD2, CLN3, COL11A2, COL4A3, COL4A4, COL4A4, CR1, CRX, CYP2J2, DHDDS, DNAJC8, EIF2AK3, ERN1, GALE, GUCY2F, GUCY2F, HEXA, HEXA, MAPK3, MBD5, MBD5, MBD5, MUT, MYH14, MYO6, NF1, NF2, NIPBL, NR1H4, NSD1, NSD1, NSD1, NSD1, OPA1, OPA1, PCCA, PKP2, PPARA, PRPF3, PRPF3, SCN2A, SCN8A, SCN8A, SCN9A, SEMA3C, SEMA3D, SIRT3, STK11, STK11, SYNGAP1, TOPORS, and VCAN proteins.

3. The method according to claim 1 or 2, wherein the therapeutic agent (a) binds to a targeting portion of the mRNA encoding the target protein; (b) Modulate the binding of factors involved in the splicing of the NMD exon; or (c) A combination of (a) and (b).

4. The method according to claim 3, wherein the therapeutic agent interferes with the binding of factors involved in the splicing of the NMD exon to the region of the targeting moiety.

5. The method according to claim 3, wherein the targeting moiety is adjacent to the NMD exon.

6. The method according to claim 5, wherein the targeting moiety is upstream of a genomic locus selected from the group consisting of up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides: GRCh38 / hg38:chr1 243564388; GRCh38 / hg38:chr19 13236618; GRCh38 / hg38:chr21 43060012; GRCh38 / hg38:chr1 207775610; GRCh38 / hg38:chr11 96675450; GRCh38 / hg38:chr15 92998149; GRCh38 / hg38:chr16 28479765; GRCh38 / hg38:chr6 33183698; GRCh38 / hg38:chr2 227296487; GRCh38 / hg38:chr2 227144833; GRCh38 / hg38:chr2 227015360; GRCh38 / hg38:chr1 207637688; GRCh38 / hg38:chr19 47835403; GRCh38 / hg38:chr1 59904516; GRCh38 / hg38:chr1 26442335; GRCh38 / hg38:chr1 28230252; GRCh38 / hg38:chr2 88582824; GRCh38 / hg38:chr17 64102804; GRCh38 / hg38:chr1 23798484; GRCh38 / hg38:chrX 109383446; GRCh38 / hg38:chrX 109439175; GRCh38 / hg38:chr15 72362466; GRCh38 / hg38:chr15 72345776; GRCh38 / hg38:chr16 30115645; GRCh38 / hg38:chr2 148460219; GRCh38 / hg38:chr2 148490695; GRCh38 / hg38:chr2 148505761; GRCh38 / hg38:chr6 49436597; GRCh38 / hg38:chr19 50230825; GRCh38 / hg38:chr6 75867431; GRCh38 / hg38:chr17 31249955;GRCh38 / hg38: chr22 29628658; GRCh38 / hg38: chr5 37048127; GRCh38 / hg38: chr12 100499841; GRCh38 / hg38: chr5 177169394; GRCh38 / hg38: chr5 177200761; GRCh38 / hg38: chr5 177247924; GRCh38 / hg38: chr5 177275947; GRCh38 / hg38: chr3 193628509; GRCh38 / hg38: chr3 193603500; GRCh38 / hg38: chr13 100305751; GRCh38 / hg38: chr12 32894778; GRCh38 / hg38: chr22 46203575; GRCh38 / hg38: chr1 150327557; GRCh38 / hg38: chr1 150330401; GRCh38 / hg38: chr2 165327155; GRCh38 / hg38: chr12 51688758; GRCh38 / hg38: chr12 51780202; GRCh38 / hg38: chr2 166304329; GRCh38 / hg38: chr7 80794957; GRCh38 / hg38: chr7 85059541; GRCh38 / hg38: chr11 226081; GRCh38 / hg38: chr19 1216268; GRCh38 / hg38: chr19 1221621; GRCh38 / hg38: chr6 33448789; GRCh38 / hg38: chr9 32551469; and GRCh38 / hg38: chr5 83544965.; 7. The method according to claim 5, wherein the targeting moiety is located upstream of a genomic locus selected from the group consisting of about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides: GRCh38 / hg38:chr1 243564388; GRCh38 / hg38:chr19 13236618; GRCh38 / hg38:chr21 43060012; GRCh38 / hg38:chr1 207775610; GRCh38 / hg38:chr1196675450; GRCh38 / hg38:chr15 92998149; GRCh38 / hg38:chr1628479765; GRCh38 / hg38:chr6 33183698; GRCh38 / hg38:chr2 227296487; GRCh38 / hg38:chr2 227144833; GRCh38 / hg38:chr2 227015360; GRCh38 / hg38:chr1 207637688; GRCh38 / hg38:chr19 47835403; GRCh38 / hg38:chr1 59904516; GRCh38 / hg38:chr126442335; GRCh38 / hg38:chr1 28230252; GRCh38 / hg38:chr2 88582824; GRCh38 / hg38:chr17 64102804; GRCh38 / hg38:chr1 23798484; GRCh38 / hg38:chrX109383446; GRCh38 / hg38:chrX 109439175; GRCh38 / hg38:chr1572362466; GRCh38 / hg38:chr15 72345776; GRCh38 / hg38:chr1630115645; GRCh38 / hg38:chr2 148460219; GRCh38 / hg38:chr2148490695; GRCh38 / hg38:chr2 148505761; GRCh38 / hg38:chr649436597; GRCh38 / hg38:chr19 50230825; GRCh38 / hg38:chr6 75867431; GRCh38 / hg38:chr17 31249955;GRCh38 / hg38: chr22 29628658; GRCh38 / hg38: chr5 37048127; GRCh38 / hg38: chr12 100499841; GRCh38 / hg38: chr5 177169394; GRCh38 / hg38: chr5 177200761; GRCh38 / hg38: chr5 177247924; GRCh38 / hg38: chr5 177275947; GRCh38 / hg38: chr3 193628509; GRCh38 / hg38: chr3 193603500; GRCh38 / hg38: chr13 100305751; GRCh38 / hg38: chr12 32894778; GRCh38 / hg38: chr22 46203575; GRCh38 / hg38: chr1 150327557; GRCh38 / hg38: chr1 150330401; GRCh38 / hg38: chr2 165327155; GRCh38 / hg38: chr12 51688758; GRCh38 / hg38: chr12 51780202; GRCh38 / hg38: chr2 166304329; GRCh38 / hg38: chr7 80794957; GRCh38 / hg38: chr7 85059541; GRCh38 / hg38: chr11 226081; GRCh38 / hg38: chr19 1216268; GRCh38 / hg38: chr19 1221621; GRCh38 / hg38: chr6 33448789; GRCh38 / hg38: chr9 32551469; and GRCh38 / hg38: chr5 83544965.; 8. The method according to claim 5, wherein the targeting moiety is downstream of a genomic locus selected from the group consisting of at most about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides: GRCh38 / hg38:chr1 243564285; GRCh38 / hg38:chr19 13236449; GRCh38 / hg38:chr21 43059730; GRCh38 / hg38:chr1 207775745; GRCh38 / hg38:chr11 96675529; GRCh38 / hg38:chr15 92998261; GRCh38 / hg38:chr16 28479644; GRCh38 / hg38:chr6 33183634; GRCh38 / hg38:chr2 227296526; GRCh38 / hg38:chr2 227144653; GRCh38 / hg38:chr2 227015283; GRCh38 / hg38:chr1 207637848; GRCh38 / hg38:chr19 47835579; GRCh38 / hg38:chr1 59904366; GRCh38 / hg38:chr1 26442372; GRCh38 / hg38:chr1 28230131; GRCh38 / hg38:chr2 88582755; GRCh38 / hg38:chr17 64102673; GRCh38 / hg38:chr1 23798311; GRCh38 / hg38:chrX 109383365; GRCh38 / hg38:chrX 109439038; GRCh38 / hg38:chr15 72362376; GRCh38 / hg38:chr15 72345677; GRCh38 / hg38:chr16 30115595; GRCh38 / hg38:chr2 148460304; GRCh38 / hg38:chr2 148490787; GRCh38 / hg38:chr2 148505830; GRCh38 / hg38:chr6 49436522; GRCh38 / hg38:chr19 50230999; GRCh38 / hg38:chr6 75867523; GRCh38 / hg38:chr17 31250125;GRCh38 / hg38: chr22 29628773; GRCh38 / hg38: chr5 37048354; GRCh38 / hg38: chr12 100500024; GRCh38 / hg38: chr5 177169559; GRCh38 / hg38: chr5 177200783; GRCh38 / hg38: chr5 177248079; GRCh38 / hg38: chr5 177276101; GRCh38 / hg38: chr3 193628616; GRCh38 / hg38: chr3 193603557; GRCh38 / hg38: chr13 100305834; GRCh38 / hg38: chr12 32894516; GRCh38 / hg38: chr22 46203752; GRCh38 / hg38: chr1 150327652; GRCh38 / hg38: chr1 150330498; GRCh38 / hg38: chr2 165327202; GRCh38 / hg38: chr12 51688849; GRCh38 / hg38: chr12 51780271; GRCh38 / hg38: chr2 166304238; GRCh38 / hg38: chr7 80794854; GRCh38 / hg38: chr7 85059498; GRCh38 / hg38: chr11 225673; GRCh38 / hg38: chr19 1216398; GRCh38 / hg38: chr19 1221846; GRCh38 / hg38: chr6 33448868; GRCh38 / hg38: chr9 32551365; and GRCh38 / hg38: chr5 83545070.; 9. The method according to claim 3, wherein the targeting portion of the mRNA is upstream or downstream of a nonsense-mediated RNA decay-inducing exon selected from the group consisting of: GRCh38 / hg38:chr1 243564285 243564388; GRCh38 / hg38:chr19 132364491 3236618; GRCh38 / hg38:chr21 43059730 43060012; GRCh38 / hg38:chr1 207775610 207775745; GRCh38 / hg38:chr1 196675450 196675529; GRCh38 / hg38:chr15 92998149 92998261; GRCh38 / hg38:chr16 28479644 28479765; GRCh38 / hg38:chr6 33183634 33183698; GRCh38 / hg38:chr2 227296487 227296526; GRCh38 / hg38:chr22 27144653 227144833; GRCh38 / hg38:chr2 227015283 227015360; GRCh38 / hg38:chr1 207637688 207637848; GRCh38 / hg38:chr19 47835403 47835579; GRCh38 / hg38:chr15 9904366 59904516; GRCh38 / hg38:chr1 26442335 26442372; GRCh38 / hg38:chr1 28230131 28230252; GRCh38 / hg38:chr2 88582755 88582824; GRCh38 / hg38:chr17 64102673 64102804; GRCh38 / hg38:chr1 23798311 23798484; GRCh38 / hg38:chrX 109383365 109383446; GRCh38 / hg38:chrX 109439038 109439175; GRCh38 / hg38:chr15 72362376 72362466; GRCh38 / hg38:chr15 72345677 72345776; GRCh38 / hg38:chr16 30115595 30115645; GRCh38 / hg38:chr21 48460219 148460304; GRCh38 / hg38:chr21 48490695 148490787;GRCh38 / hg38: chr2 148505761 148505830; GRCh38 / hg38: chr6 49436522 49436597; GRCh38 / hg38: chr19 50230825 50230999; GRCh38 / hg38: chr6 75867431 75867523; GRCh38 / hg38: chr17 31249955 31250125; GRCh38 / hg38: chr22 29628658 29628773; GRCh38 / hg38: chr5 37048127 37048354; GRCh38 / hg38: chr12 10049984 100500024; GRCh38 / hg38: chr5 17716939 177169559; GRCh38 / hg38: chr5 17720076 177200783; GRCh38 / hg38: chr5 17724792 177248079; GRCh38 / hg38: chr5 17727594 177276101; GRCh38 / hg38: chr3 19362850 193628616; GRCh38 / hg38: chr3 19360350 193603557; GRCh38 / hg38: chr13 10030575 100305834; GRCh38 / hg38: chr12 32894516 32894778; GRCh38 / hg38: chr22 46203575 46203752; GRCh38 / hg38: chr11 50327557 150327652; GRCh38 / hg38: chr1 15033040 150330498; GRCh38 / hg38: chr2 16532715 165327202; GRCh38 / hg38: chr12 51688758 51688849; GRCh38 / hg38: chr12 51780202 51780271; GRCh38 / hg38: chr2 16630423 166304329; GRCh38 / hg38: chr7 8079485 80794957; GRCh38 / hg38: chr7 8505949 85059541; GRCh38 / hg38: chr11 2256732 226081; GRCh38 / hg38: chr19 1216268 1216398; GRCh38 / hg38: chr19 1221621 1221846;GRCh38 / hg38: chr6 33448789 33448868; GRCh38 / hg38: chr9 32551365 32551469; and GRCh38 / hg38: chr5 83544965 83545070.; 10. The method according to claim 3, wherein the targeting portion of the mRNA comprises exon-intron junctions of exons selected from the group consisting of: GRCh38 / hg38:chr12 43564285 243564388; GRCh38 / hg38:chr19 13236449 13236618; GRCh38 / hg38:chr21 43059730 43060012; GRCh38 / hg38:chr12 07775610 207775745; GRCh38 / hg38:chr1 196675450 196675529; GRCh38 / hg38:chr15 92998149 92998261; GRCh38 / hg38:chr16 28479644 28479765; GRCh38 / hg38:chr6 33183634 33183698; GRCh38 / hg38:chr2 227296487 227296526; GRCh38 / hg38:chr22 271446532 27144833; GRCh38 / hg38:chr2 227015283 227015360; GRCh38 / hg38:chr12 07637688 207637848; GRCh38 / hg38:chr19 47835403 47835579; GRCh38 / hg38:chr15 9904366 59904516; GRCh38 / hg38:chr1 26442335 26442372; GRCh38 / hg38:chr1 28230131 28230252; GRCh38 / hg38:chr2 88582755 88582824; GRCh38 / hg38:chr17 64102673 64102804; GRCh38 / hg38:chr1 23798311 23798484; GRCh38 / hg38:chrX 109383365 109383446; GRCh38 / hg38:chrX 109439038 109439175; GRCh38 / hg38:chr15 72362376 72362466; GRCh38 / hg38:chr15 72345677 72345776; GRCh38 / hg38:chr16 30115595 30115645; GRCh38 / hg38:chr21 48460219 148460304; GRCh38 / hg38:chr21 48490695 148490787;GRCh38 / hg38: chr2 148505761 148505830; GRCh38 / hg38: chr6 49436522 49436597; GRCh38 / hg38: chr19 50230825 50230999; GRCh38 / hg38: chr6 75867431 75867523; GRCh38 / hg38: chr17 31249955 31250125; GRCh38 / hg38: chr22 29628658 29628773; GRCh38 / hg38: chr5 37048127 37048354; GRCh38 / hg38: chr12 100499841 100500024; GRCh38 / hg38: chr5 177169394 177169559; GRCh38 / hg38: chr5 177200761 177200783; GRCh38 / hg38: chr5 177247924 177248079; GRCh38 / hg38: chr5 177275947 177276101; GRCh38 / hg38: chr3 193628509 193628616; GRCh38 / hg38: chr3 193603500 193603557; GRCh38 / hg38: chr13 100305751 100305834; GRCh38 / hg38: chr12 32894516 32894778; GRCh38 / hg38: chr22 46203575 46203752; GRCh38 / hg38: chr11 50327557 150327652; GRCh38 / hg38: chr1 150330401 150330498; GRCh38 / hg38: chr2 165327155 165327202; GRCh38 / hg38: chr12 51688758 51688849; GRCh38 / hg38: chr12 51780202 51780271; GRCh38 / hg38: chr2 166304238 166304329; GRCh38 / hg38: chr7 80794854 80794957; GRCh38 / hg38: chr7 85059498 85059541; GRCh38 / hg38: chr11 22567322 6081; GRCh38 / hg38: chr19 1216268 1216398; GRCh38 / hg38:; chr19 1221621 1221846; GRCh38 / hg38:chr6 33448789 33448868; GRCh38 / hg38:chr9 32551365 32551469; and GRCh38 / hg38:chr5 83544965 83545070.

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