Antisense oligomers for treating nonsense-mediated RNA decay-based conditions and diseases

Abstract

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

Description

[0001] Cross-references

[0002] 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 incorporated herein by reference in its entirety. Background Art

[0003] Alternative splicing events in genes can lead to 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 patients 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

[0004] In certain embodiments, described herein is a method of regulating expression of a target protein by a cell having an mRNA comprising a nonsense-mediated RNA decay-inducing exon (NMD exon) and encoding a target protein, the method comprising contacting a therapeutic agent with the cell, whereby the therapeutic agent regulates splicing of the NMD exon from the mRNA, thereby regulating the level of processed mRNA encoding the target protein, and regulating 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, NS D1, NSD1, OPA1, OPA1, PCCA, PKP2, PPARA, PRPF3, PRPF3, SCN2A, SCN8A, SCN8A, SCN9A, SEMA3C, SEMA3D, SIRT3, STK11, STK11, SYNGAP1, TOPORS and VCAN proteins.

[0005] In certain embodiments, described herein is a method of treating a disease or condition in a subject by modulating expression of a target protein in a cell of the subject in need thereof, the method comprising: contacting the cell of the subject with a therapeutic agent that modulates splicing of a nonsense-mediated mRNA decay-inducing exon (NMD exon) from mRNA in the cell, wherein the mRNA comprises an NMD exon and encodes a target protein, thereby modulating the level of processed mRNA encoding the target protein, and modulating expression of the target protein in the cell of the subject, wherein the target protein is selected from the group consisting of: AKT3, CACNA1A, CBS, CD46, CFH, CHD2, CLN3, COL11A2, COL4A3, COL4A4, COL4A4, CR 1. 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 some embodiments, the therapeutic agent: (a) binds to a targeting moiety of an mRNA encoding a target protein; (b) modulates the binding of a factor involved in splicing of the NMD exon; or (c) a combination of (a) and (b).

[0007] In some embodiments, the therapeutic agent interferes with the binding of factors involved in the splicing of the NMD exon to the region of the targeting moiety. In some embodiments, the targeting moiety is adjacent to the NMD exon. In some embodiments, the targeting moiety is 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 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, or about 1 nucleotide upstream of the 5' end of the NMD exon. In some embodiments, the targeting moiety is 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 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, or about 1 nucleotide downstream of the 3' end of the NMD exon.

[0008] In some embodiments, the targeting moiety is 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 upstream of a genomic site selected from the group consisting of 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:chr2227144833; 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:chrX109439175; 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.;

[0009] In some embodiments, the targeting moiety is 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 a genomic site selected from the group consisting of GRCh38 / hg38:chr1 243564388; GRCh38 / hg38:chr1913236618; 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:chr1947835403; GRCh38 / hg38:chr1 59904516; GRCh38 / hg38:chr1 26442335; GRCh38 / hg38:chr128230252; 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; 30115645;GRCh38 / hg38:chr2 148460219; GRCh38 / hg38:chr2 148490695; GRCh38 / hg38:chr2148505761; 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 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 downstream of a genomic site selected from the group consisting of 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:chr2227144653; 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:chrX109439038; 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.;

[0011] In some embodiments, the targeting moiety is 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 a genomic site selected from the group consisting of GRCh38 / hg38:chr1 243564285; GRCh38 / hg38:chr1913236449; 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:chr1947835579; GRCh38 / hg38:chr1 59904366; GRCh38 / hg38:chr1 26442372; GRCh38 / hg38:chr128230131; 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; 30115595;GRCh38 / hg38:chr2 148460304; GRCh38 / hg38:chr2 148490787; GRCh38 / hg38:chr2148505830; 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 portion 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 portion overlaps at least partially with the NMD exon. In some embodiments, the targeting portion overlaps at least partially with an intron upstream or downstream of the NMD exon. In some embodiments, the targeting portion comprises a 5'NMD exon-intron junction or a 3'NMD exon-intron junction. In some embodiments, the targeting portion is within the NMD exon. In some embodiments, the targeting portion 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 continuous nucleotides of the NMD exon.

[0013] 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 with a sequence selected from SEQ ID NO: 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 with a sequence selected from SEQ ID NO: 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 portion of the mRNA comprises a sequence having at least 80%, 85%, 90%, 95%, 97% or 100% sequence identity with a region containing at least 8 consecutive nucleic acids of a sequence selected from SEQ ID NO: 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.

[0014] 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 1323644913236618; GRCh38 / hg38:chr21 43059730 43060012; GRCh38 / hg38:chr1 207775610207775745; GRCh38 / hg38:chr1 196675450 196675529; GRCh38 / hg38:chr15 9299814992998261; GRCh38 / hg38:chr16 28479644 28479765; GRCh38 / hg38:chr6 3318363433183698; GRCh38 / hg38:chr2 227296487 227296526; GRCh38 / hg38:chr2 227144653227144833; GRCh38 / hg38:chr2 227015283 227015360; GRCh38 / hg38:chr1 207637688207637848; GRCh38 / hg38:chr19 47835403 47835579;GRCh38 / hg38:chr1 5990436659904516; GRCh38 / hg38:chr1 26442335 26442372; GRCh38 / hg38:chr1 2823013128230252; GRCh38 / hg38:chr2 88582755 88582824; GRCh38 / hg38:chr17 6410267364102804; GRCh38 / hg38:chr1 23798311 23798484; GRCh38 / hg38:chrX 109383365109383446; GRCh38 / hg38:chrX 109439038 109439175; GRCh38 / hg38:chr15 7236237672362466; GRCh38 / hg38:chr15 72345677 72345776; GRCh38 / hg38:chr16 3011559530115645;GRCh38 / hg38:chr2 148460219 148460304;GRCh38 / hg38:chr2 148490695148490787;GRCh38 / hg38:chr2 148505761 148505830;GRCh38 / hg38:chr6 4943652249436597;GRCh38 / hg38:chr19 50230825 50230999;GRCh38 / hg38:chr6 7586743175867523;GRCh38 / hg38:chr17 31249955 31250125;GRCh38 / hg38:chr22 2962865829628773;GRCh38 / hg38:chr5 37048127 37048354;GRCh38 / hg38:chr12 100499841100500024;GRCh38 / hg38:chr5 177169394 177169559;GRCh38 / hg38:chr5 177200761177200783;GRCh38 / hg38:chr5 177247924 177248079;GRCh38 / hg38:chr5 177275947177276101;GRCh38 / hg38:chr3 193628509 193628616;GRCh38 / hg38:chr3 193603500193603557;GRCh38 / hg38:chr13 100305751 100305834;GRCh38 / hg38:chr12 3289451632894778;GRCh38 / hg38:chr22 46203575 46203752;GRCh38 / hg38:chr1 150327557150327652;GRCh38 / hg38:chr1 150330401 150330498;GRCh38 / hg38:chr2 165327155165327202;GRCh38 / hg38:chr12 51688758 51688849;GRCh38 / hg38:chr12 5178020251780271;GRCh38 / hg38:chr2 166304238 166304329;GRCh38 / hg38:chr7 8079485480794957;GRCh38 / hg38:chr7 85059498 85059541;GRCh38 / hg38:chr11 225673 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. ;

[0015] 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:chr1913236449 13236618; GRCh38 / hg38:chr21 43059730 43060012; GRCh38 / hg38:chr1207775610 207775745; GRCh38 / hg38:chr1 196675450 196675529; GRCh38 / hg38:chr1592998149 92998261; GRCh38 / hg38:chr16 28479644 28479765; GRCh38 / hg38:chr633183634 33183698; GRCh38 / hg38:chr2 227296487 227296526; GRCh38 / hg38:chr2227144653 227144833; GRCh38 / hg38:chr2 227015283 227015360; GRCh38 / hg38:chr1207637688 207637848; GRCh38 / hg38:chr19 47835403 47835579;GRCh38 / hg38:chr159904366 59904516; GRCh38 / hg38:chr1 26442335 26442372; GRCh38 / hg38:chr128230131 28230252; GRCh38 / hg38:chr2 88582755 88582824; GRCh38 / hg38:chr1764102673 64102804; GRCh38 / hg38:chr1 23798311 23798484; GRCh38 / hg38:chrX109383365 109383446;GRCh38 / hg38:chrX 109439038 109439175; GRCh38 / hg38:chr1572362376 72362466; GRCh38 / hg38:chr15 72345677 72345776; GRCh38 / hg38:chr1630115595 30115645;GRCh38 / hg38:chr2 148460219 148460304;GRCh38 / hg38:chr2148490695 148490787;GRCh38 / hg38:chr2 148505761 148505830;GRCh38 / hg38:chr649436522 49436597;GRCh38 / hg38:chr19 50230825 50230999;GRCh38 / hg38:chr675867431 75867523;GRCh38 / hg38:chr17 31249955 31250125;GRCh38 / hg38:chr2229628658 29628773;GRCh38 / hg38:chr5 37048127 37048354;GRCh38 / hg38:chr12100499841 100500024;GRCh38 / hg38:chr5 177169394 177169559;GRCh38 / hg38:chr5177200761 177200783;GRCh38 / hg38:chr5 177247924 177248079;GRCh38 / hg38:chr5177275947 177276101;GRCh38 / hg38:chr3 193628509 193628616;GRCh38 / hg38:chr3193603500 193603557;GRCh38 / hg38:chr13 100305751 100305834;GRCh38 / hg38:chr1232894516 32894778;GRCh38 / hg38:chr22 46203575 46203752;GRCh38 / hg38:chr1150327557 150327652;GRCh38 / hg38:chr1 150330401 150330498;GRCh38 / hg38:chr2165327155 165327202;GRCh38 / hg38:chr12 51688758 51688849;GRCh38 / hg38:chr1251780202 51780271;GRCh38 / hg38:chr2 166304238 166304329;GRCh38 / hg38:chr780794854 80794957;GRCh38 / hg38:chr7 85059498 85059541;GRCh38 / hg38:chr11 225673226081;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 comprises an exon-intron junction of an exon selected from the group consisting of GRCh38 / hg38:chr1 243564285 243564388; GRCh38 / hg38:chr19 1323644913236618; GRCh38 / hg38:chr21 43059730 43060012; GRCh38 / hg38:chr1 207775610207775745; GRCh38 / hg38:chr1 196675450 196675529; GRCh38 / hg38:chr15 9299814992998261; GRCh38 / hg38:chr16 28479644 28479765; GRCh38 / hg38:chr6 3318363433183698; GRCh38 / hg38:chr2 227296487 227296526; GRCh38 / hg38:chr2 227144653227144833; GRCh38 / hg38:chr2 227015283 227015360; GRCh38 / hg38:chr1 207637688207637848; GRCh38 / hg38:chr19 47835403 47835579;GRCh38 / hg38:chr1 5990436659904516; GRCh38 / hg38:chr1 26442335 26442372; GRCh38 / hg38:chr1 2823013128230252; GRCh38 / hg38:chr2 88582755 88582824; GRCh38 / hg38:chr17 6410267364102804; GRCh38 / hg38:chr1 23798311 23798484; GRCh38 / hg38:chrX 109383365109383446; GRCh38 / hg38:chrX 109439038 109439175; GRCh38 / hg38:chr15 7236237672362466; GRCh38 / hg38:chr15 72345677 72345776; GRCh38 / hg38:chr16 3011559530115645;GRCh38 / hg38:chr2 148460219 148460304;GRCh38 / hg38:chr2 148490695148490787;GRCh38 / hg38:chr2 148505761 148505830;GRCh38 / hg38:chr6 4943652249436597;GRCh38 / hg38:chr19 50230825 50230999;GRCh38 / hg38:chr6 7586743175867523;GRCh38 / hg38:chr17 31249955 31250125;GRCh38 / hg38:chr22 2962865829628773;GRCh38 / hg38:chr5 37048127 37048354;GRCh38 / hg38:chr12 100499841100500024;GRCh38 / hg38:chr5 177169394 177169559;GRCh38 / hg38:chr5 177200761177200783;GRCh38 / hg38:chr5 177247924 177248079;GRCh38 / hg38:chr5 177275947177276101;GRCh38 / hg38:chr3 193628509 193628616;GRCh38 / hg38:chr3 193603500193603557;GRCh38 / hg38:chr13 100305751 100305834;GRCh38 / hg38:chr12 3289451632894778;GRCh38 / hg38:chr22 46203575 46203752;GRCh38 / hg38:chr1 150327557150327652;GRCh38 / hg38:chr1 150330401 150330498;GRCh38 / hg38:chr2 165327155165327202;GRCh38 / hg38:chr12 51688758 51688849;GRCh38 / hg38:chr12 5178020251780271;GRCh38 / hg38:chr2 166304238 166304329;GRCh38 / hg38:chr7 8079485480794957;GRCh38 / hg38:chr7 85059498 85059541;GRCh38 / hg38:chr11 225673 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. ;

[0017] In some embodiments, the target protein produced is a full-length protein or a wild-type protein.

[0018] In some embodiments, the therapeutic agent promotes the exclusion of the NMD exon from the processed mRNA encoding the target protein. In some embodiments, 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 times, about 1.5 to about 10 times, about 2 to about 10 times, about 3 to about 10 times, about 4 to about 10 times, about 1.1 to about 5 times, about 1.1 to about 6 times, about 1.1 to about 7 times, about 1.1 to about 8 times, about 1.1 to about 9 times, about 1.1 to about 10 times, about 1.1 to about 11 times, about 1.1 to about 12 times, about 1.1 to about 13 times, about 1.1 to about 14 times, about 1.1 to about 15 times, about 1.1 to about 16 times, about 1.1 to about 17 times, about 1.1 to about 18 times, about 1.1 to about 19 times, about 1.1 to about 20 times, about 1.1 to about 21 times, about 1.1 to about 22 times, about 1.1 to about 24 times, about 1.1 to about 25 times, about 1.1 to about 26 times, about 1.1 to about 27 times, about 1.1 to about 28 times, about 1.1 to about 29 times, about 1.1 to about 30 ... In some embodiments, the therapeutic agent increases the level of the processed mRNA encoding the target protein in the cell. In some embodiments, the level of the processed mRNA encoding the target protein produced in cells contacted with the therapeutic agent increases 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 processed mRNA encoding the target protein in the control cells. In some embodiments, the therapeutic agent increases expression of a target protein in the cell.In some embodiments, the level of 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 compared to the level of the target protein produced in a control cell.

[0019] In some embodiments, the disease or condition is induced by a loss-of-function mutation in the target protein.

[0020] In some embodiments, the disease or condition is associated with haploinsufficiency of a gene encoding a 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 target protein or a 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; arrhythmic right ventricular dysplasia 9; neurofibromatosis type 1; early infantile epileptic encephalopathy 11; benign familial infantile seizures 3; cognitive impairment with or without cerebellar ataxia; early infantile epileptic encephalopathy 13; benign familial infantile seizures 5; pathway (CNS); 16p11.2 deletion syndrome? ; autosomal dominant mental retardation 1; retinitis pigmentosa 18; retinitis pigmentosa 31; autosomal dominant deafness 13; cone-rod retinal atrophy -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 type 7+; and familial febrile seizures 3B.

[0021] 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 that (i) does not produce the target protein or produces the target protein at a reduced level compared to the wild-type allele; or (ii) produces a target protein that is non-functional or partially functional compared to the wild-type allele; and a second allele that: (iii) produces the target protein at a reduced level compared to the wild-type allele and produces a target protein that is at least partially functional compared to the wild-type allele; or (iv) produces a target protein that 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 reactive and non-responsive homocystinuria; methylmalonic aciduria; propionic acidemia; retinitis pigmentosa 59; Tay-Sachs disease; congenital analgesia; and autosomal recessive HSAN2D.

[0022] 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, the exclusion of the NMD exon from the processed mRNA encoding the target protein in the cell contacted with the therapeutic agent is reduced by about 1.1 to about 10 times, about 1.5 to about 10 times, about 2 to about 10 times, about 3 to about 10 times, about 4 to about 10 times, about 1.1 to about 5 times, about 1.1 to about 6 times, about 1.1 to about 7 times, about 1.1 to about 8 times, about 1.1 to about 9 times, about 1.1 to about 10 times, about 1.1 to about 11 times, about 1.1 to about 12 times, about 1.1 to about 13 times, about 1.1 to about 14 times, about 1.1 to about 15 times, about 1.1 to about 16 times, about 1.1 to about 17 times, about 1.1 to about 18 times, about 1.1 to about 19 times, about 1.1 to about 20 times, about 1.1 to about 21 times, about 1.1 to about 22 times, about 1.1 to about 24 times, about 1.1 to about 25 times, about 1.1 to about 26 times, about 1.1 to about 27 times, about 1.1 to about 28 times, about 1.1 to about 29 times, about 1.1 to about 30 ... In some embodiments, the therapeutic agent reduces the level of the processed mRNA encoding the target protein in the cell. In some embodiments, the level of the processed mRNA encoding the target protein 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 as compared to the level of the processed mRNA encoding the target protein in the control cells.

[0023] In some embodiments, the therapeutic agent reduces expression of a target protein in the cell. In some embodiments, the level of the target protein produced 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 compared to the level of the target protein produced in control cells.

[0024] 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 an elevated level, or an allele that encodes a mutant target protein that exhibits increased activity in a cell.

[0025] 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.

[0026] In some embodiments, the therapeutic agent is an antisense oligomer (ASO), and wherein the antisense oligomer comprises a backbone modification, and the backbone modification comprises a thiophosphate bond or a diaminophosphorothioate bond. In some embodiments, the therapeutic agent is an antisense oligomer (ASO), and wherein the antisense oligomer comprises a diaminophosphorothioate morpholino, a locked nucleic acid, a peptide nucleic acid, a 2'-O-methyl, a 2'-fluorine or a 2'-O-methoxyethyl moiety.

[0027] 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.

[0028] 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 3 or 12 to 15 nucleobases.

[0029] 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 targeting portion of the mRNA.

[0030] In some embodiments, the method further comprises assessing the mRNA level or expression level of the target protein.

[0031] 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 cell is ex vivo. In some embodiments, the therapeutic agent is administered by intrathecal injection, intraventricular injection, intraperitoneal injection, intramuscular injection, subcutaneous injection, intravitreal injection or intravenous injection of the subject. In some embodiments, the method further comprises administering a second therapeutic agent to the subject.

[0032] 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.

[0033] In some embodiments, the disease or condition is selected from: 16p11.2 deletion syndrome; Alport syndrome; arrhythmic right ventricular dysplasia 9; neuronal ceroid lipofuscinosis 3; cognitive impairment with or without cerebellar ataxia; early infantile epileptic encephalopathy 13; benign familial infantile seizures 5; cone-rod retinal 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 type 7+; familial febrile seizures 3B; congenital analgesia; autosomal recessive HSAN2D; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; benign familial infantile seizures 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 acidemia; retinitis pigmentosa 18; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Tay-Sachs disease; and Wagner syndrome 1.

[0034] Incorporation by reference

[0035] All publications, patents, and patent applications mentioned in this specification are herein 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

[0036] The novel features of the present disclosure are particularly set forth in the appended claims. The features and advantages of the present disclosure will be better understood by referring to the following detailed description of illustrative embodiments utilizing the principles of the present disclosure and the accompanying drawings, in which:

[0037] FIG1 depicts a schematic diagram of a target mRNA containing a nonsense-mediated mRNA decay-inducing exon (NMD-exon mRNA) and therapeutic agent-mediated depletion of the nonsense-mediated mRNA decay-inducing exon to increase expression of a full-length target protein or functional RNA. Figure 1A Shown are cells divided into nuclear and cytoplasmic compartments. In the nucleus, the pre-mRNA transcript of the target gene undergoes splicing to generate mRNA, and the mRNA is exported to the cytoplasm and translated into the target protein. For the target gene, some parts of the mRNA contain nonsense-mediated mRNA decay-inducing exons (NMD exon mRNAs) that are degraded in the cytoplasm, thus resulting in no target protein production.

[0038] Figure 1B An example of the same cell partitioned into nuclear and cytoplasmic compartments is shown. Treatment with therapeutic agents such as antisense oligomers (ASOs) promotes nonsense-mediated mRNA decay-inducing exon elimination and leads to an increase in mRNA that is in turn translated into higher levels of target protein.

[0039] Figure 2 Depict the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in CD46 gene.Show the use of RNA sequencing to identify NMD induction exons in CD46 gene, visualized in UCSC genome browser.The upper figure shows a diagram of CD46 gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr1207770363 207783291, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0040] Figure 3 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the COL11A2 gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the COL11A2 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the COL11A2 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr6 33181172 33184144, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0041] Figure 4 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in CR1 gene. Show the use of RNA sequencing to identify NMD induction exons in CR1 gene, visualized in UCSC genome browser. The upper figure shows a diagram of CR1 gene in proportion. The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr1 207630622207639396, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0042] 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 figure shows a diagram of the CRX gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr19 4783454547836242, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0043] Figure 6 Depict the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in DNAJC8 gene.Show the use of RNA sequencing to identify NMD induction exons in DNAJC8 gene, visualized in UCSC genome browser.The upper figure shows a diagram of DNAJC8 gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr128229025 28232920, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0044] Figure 7 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in MYH14 gene.Show the use of RNA sequencing to identify NMD induction exons in MYH14 gene, visualized in UCSC genome browser.The upper figure shows the diagram of MYH14 gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr1950230625 50231929, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0045] Figure 8Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-induced exons in the SEMA3C gene. Shows the identification of NMD-induced exons in the SEMA3C gene using RNA sequencing, visualized in the UCSC genome browser. The upper figure shows a diagram of the SEMA3C gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr780789529 80798091, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature stop codons, making the transcript a target for NMD.

[0046] Fig. 9 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in the VCAN gene. Show the use of RNA sequencing to identify the NMD induction exons in the VCAN gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the VCAN gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr583542270 83545536, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0047] Fig.10 Depict the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the OPAI gene.Show the use of RNA sequencing to identify the NMD inducing exons in the OPAI gene, visualized in the UCSC genome browser.The upper figure shows a diagram of the OPAI gene in proportion.The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr3193626204 193631611, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (below, the sequence highlighted in uppercase letters).The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0048] Fig.11Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the COL4A3 gene. Shows the identification of NMD inducing exons in the COL4A3 gene using RNA sequencing, visualized in the UCSC genome browser. The upper figure shows a diagram of the COL4A3 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr2 227295318 227297673, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0049] Fig.12 Depicted is the identification of an exemplary nonsense-mediated mRNA decay (NMD) inducing exon in the DHDDS gene. The identification of the NMD inducing exon in the DHDDS gene using RNA sequencing is shown, visualized in the UCSC genome browser. The upper figure shows a diagram of the DHDDS gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr126438286 26442730, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature stop codons, making the transcript a target for NMD.

[0050] Fig.13 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in CFH gene.Show the use of RNA sequencing to identify the NMD induction exons in CFH gene, visualized in the UCSC genome browser.The upper figure shows the diagram of CFH gene in proportion.The peak corresponding to RNA sequencing reading is identified in intron GRCh38 / hg38:chr1 196673964196675988, shown in the middle figure.Bioinformatics analysis identifies the exon-like sequence (below, the sequence highlighted in capital letters) flanked by 3' and 5' splice sites.Including this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0051] Fig.14Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in AKT3 gene.Show the use of RNA sequencing to identify the NMD induction exons in AKT3 gene, visualized in the UCSC genome browser.The upper figure shows the diagram of AKT3 gene in proportion.The peak corresponding to RNA sequencing reading is identified in intron GRCh38 / hg38:chr1243563849 243572925, shown in the middle figure.Bioinformatics analysis identifies the exon-like sequence (bottom figure, sequence highlighted in capital letters) flanking 3' and 5' splice sites.Including this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0052] Fig.15 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in the TOPORS gene.Show the use of RNA sequencing to identify the NMD induction exons in the TOPORS gene, visualized in the UCSC genome browser.The upper figure shows a diagram of the TOPORS gene in proportion.The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr9 32550970 32552433, shown in the middle figure.Bioinformatics analysis identifies the exon-like sequence (below, the sequence highlighted in uppercase letters) flanked by 3' and 5' splice sites.Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0053] Fig.16 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in PRPF3 gene.Show the use of RNA sequencing to identify NMD induction exons in PRPF3 gene, visualized in UCSC genome browser.The upper figure shows a diagram of PRPF3 gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr1150325883 150328319, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0054] Fig.17Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in PRPF3 gene.Show the use of RNA sequencing to identify NMD induction exons in PRPF3 gene, visualized in UCSC genome browser.The upper figure shows a diagram of PRPF3 gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr1150328468 150332683, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0055] Fig.18 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the NIPBL gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the NIPBL gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the NIPBL gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr537046201 37048501, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0056] Fig.19 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in CBS gene.Show the use of RNA sequencing to identify NMD induction exons in CBS gene, visualized in UCSC genome browser.The upper figure shows the diagram of CBS gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr21 4305930543060440, shown in the figure in the middle.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Including this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0057] Fig. 20Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in PKP2 gene.Show the use of RNA sequencing to identify the NMD induction exons in PKP2 gene, visualized in the UCSC genome browser.The upper figure shows the diagram of PKP2 gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr1232879034 32896508, shown in the middle figure.Bioinformatics analysis identifies the exon-like sequence (below, the sequence highlighted in capital letters) flanking 3' and 5' splice sites.Including this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0058] Fig.21 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-induced exons in the COL4A4 gene. Shows the identification of NMD-induced exons in the COL4A4 gene using RNA sequencing, visualized in the UCSC genome browser. The upper figure shows a diagram of the COL4A4 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr2 227144560 227147412, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature stop codons, making the transcript a target for NMD.

[0059] Fig. 22 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-induced exons in the COL4A4 gene. Shows the identification of NMD-induced exons in the COL4A4 gene using RNA sequencing, visualized in the UCSC genome browser. The upper figure shows a diagram of the COL4A4 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr2 227012299 227022047, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature stop codons, making the transcript a target for NMD.

[0060] Fig.23Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in CYP2J2 gene.Show the use of RNA sequencing to identify NMD induction exons in CYP2J2 gene, visualized in UCSC genome browser.The upper figure shows the diagram of CYP2J2 gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr1 59901104 59904870, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0061] Fig.24 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the PPARA gene. Shows the identification of NMD inducing exons in the PPARA gene using RNA sequencing, visualized in the UCSC genome browser. The upper figure shows a diagram of the PPARA gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr2246198592 46215172, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature stop codons, making the transcript a target for NMD.

[0062] Fig.25 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the SEMA3D gene.Shows the identification of NMD inducing exons in the SEMA3D gene using RNA sequencing, visualized in the UCSC genome browser.The upper figure shows a diagram of the SEMA3D gene in proportion.The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr7 85055860 85065423, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters).The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0063] Fig.26Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in the ERN1 gene. Shows the use of RNA sequencing to identify NMD induction exons in the ERN1 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the ERN1 gene in proportion. The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr1764098242 64129975, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0064] Fig. 27 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the GUCY2F gene. Show the use of RNA sequencing to identify the NMD inducing exons in the GUCY2F gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the GUCY2F gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chrX 109382213 109385183, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (below, the sequence highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0065] Fig.28 Depict the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the GUCY2F gene. Show the use of RNA sequencing to identify the NMD inducing exons in the GUCY2F gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the GUCY2F gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chrx 109430397 109441350, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0066] Fig.29Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in the SCN2A gene.Show the use of RNA sequencing to identify the NMD induction exons in the SCN2A gene, visualized in the UCSC genome browser.The upper figure shows a diagram of the SCN2A gene in proportion.The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr2165326986 165331329, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0067] Fig.30 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in SCN8A gene.Show the use of RNA sequencing to identify NMD induction exons in SCN8A gene, visualized in UCSC genome browser.The upper figure shows the diagram of SCN8A gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr1251687221 51689004, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0068] Fig.31 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in SCN8A gene.Show the use of RNA sequencing to identify NMD induction exons in SCN8A gene, visualized in UCSC genome browser.The upper figure shows the diagram of SCN8A gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr1251774364 51786541, shown in the figure in the middle.Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0069] Fig.32Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in SCN9A gene.Show the use of RNA sequencing to identify NMD induction exons in SCN9A gene, visualized in UCSC genome browser.The upper figure shows the diagram of SCN9A gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr2166304123 166305791, shown in the figure in the middle.Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0070] Fig.33 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in CLN3 gene.Show the use of RNA sequencing to identify the NMD induction exons in CLN3 gene, visualized in the UCSC genome browser.The upper figure shows the diagram of CLN3 gene in proportion.The peak corresponding to RNA sequencing reading is identified in intron GRCh38 / hg38:chr1628477879 28482104, shown in the middle figure.Bioinformatics analysis identifies the exon-like sequence (below, the sequence highlighted in capital letters) flanking 3' and 5' splice sites.Including this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0071] Fig.34 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the MAPK3 gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the MAPK3 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the MAPK3 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr1630114710 30116635, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0072] Fig.35Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the NF1 gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the NF1 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the NF1 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr17 3124912031252937, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0073] Fig.36 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the MBD5 gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the MBD5 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the MBD5 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr2148502511 148510059, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0074] Fig.37 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the MBD5 gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the MBD5 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the MBD5 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr2148458873 148462581, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0075] Fig.38Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the MBD5 gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the MBD5 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the MBD5 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr2148490596 148502435, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0076] Fig.39 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in NF2 gene.Show the use of RNA sequencing to identify NMD induction exons in NF2 gene, visualized in UCSC genome browser.The upper figure shows the diagram of NF2 gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr22 2960411429636750, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Including this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0077] Fig.40 Depicts 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 figure shows a diagram of the MYO6 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr675867107 75870646, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0078] Fig.41Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the SYNGAP1 gene. Show the use of RNA sequencing to identify the NMD inducing exons in the SYNGAP1 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the SYNGAP1 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr6 33447935 33451759, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0079] Fig.42 Depicted is the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the SIRT3 gene. The NMD inducing exons in the SIRT3 gene were identified using RNA sequencing, visualized in the UCSC genome browser. The figure above shows a diagram of the SIRT3 gene in scale. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr11224241 230451, shown in the figure in the middle. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (the figure below, the sequence highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0080] Fig.43 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the CACNA1A gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the CACNA1A gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the CACNA1A gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr19 13235732 13241520, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0081] Fig.44Depicted is the identification of an exemplary nonsense-mediated mRNA decay (NMD)-inducing exon 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 diagram of the CHD2 gene in proportion. The peak corresponding to the RNA sequencing read is identified in the intron GRCh38 / hg38:chr1592997404 92998498, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature stop codons, making the transcript a target for NMD.

[0082] Fig.45 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the NSD1 gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the NSD1 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the NSD1 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr5177136032 177191883, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0083] Fig.46 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the NSD1 gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the NSD1 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the NSD1 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr5177192021 177204119, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0084] Fig.47Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the NSD1 gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the NSD1 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the NSD1 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr5177246798 177248180, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0085] Fig.48 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the NSD1 gene. Shows the use of RNA sequencing to identify NMD-inducing exons in the NSD1 gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the NSD1 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr5177273786 177280564, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0086] Fig.49 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in the EIF2AK3 gene.Show the use of RNA sequencing to identify the NMD induction exons in the EIF2AK3 gene, visualized in the UCSC genome browser.The upper figure shows a diagram of the EIF2AK3 gene in proportion.The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr2 88579641 88583429, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0087] Fig.50Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) inducing exons in the GALE gene. Show the use of RNA sequencing to identify the NMD inducing exons in the GALE gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the GALE gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr123798232 23798614, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0088] Fig.51 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in the HEXA gene. Shows the use of RNA sequencing to identify NMD induction exons in the HEXA gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the HEXA gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr1572356652 72375719, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0089] Fig.52 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in the HEXA gene. Shows the use of RNA sequencing to identify NMD induction exons in the HEXA gene, visualized in the UCSC genome browser. The upper figure shows a diagram of the HEXA gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr1572345552 72346234, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0090] Fig.53Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in NR1H4 gene.Show the use of RNA sequencing to identify NMD induction exons in NR1H4 gene, visualized in UCSC genome browser.The upper figure shows the diagram of NR1H4 gene in proportion.The peak corresponding to RNA sequencing reading is identified in intron GRCh38 / hg38:chr12100493403 100505574, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).Inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0091] Fig.54 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-induced exons in the STK11 gene. Shows the identification of NMD-induced exons in the STK11 gene using RNA sequencing, visualized in the UCSC genome browser. The figure above shows a diagram of the STK11 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr191207204 1218416, shown in the middle figure. Bioinformatics analysis identifies exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0092] Fig.55 Depicts the identification of exemplary nonsense-mediated mRNA decay (NMD)-induced exons in the STK11 gene. Shows the identification of NMD-induced exons in the STK11 gene using RNA sequencing, visualized in the UCSC genome browser. The figure above shows a diagram of the STK11 gene in proportion. The peak corresponding to the RNA sequencing read is identified in intron GRCh38 / hg38:chr191221341 1221948, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature termination codons, making the transcript a target for NMD.

[0093] Fig.56Depict the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in PCCA gene.Show the use of RNA sequencing to identify NMD induction exons in PCCA gene, visualized in UCSC genome browser.The upper figure shows a diagram of PCCA gene in proportion.The peak corresponding to RNA sequencing reads is identified in intron GRCh38 / hg38:chr13100302999 100307191, shown in the middle figure.Bioinformatics analysis identifies exon-like sequences flanking 3' and 5' splice sites (lower figure, sequence highlighted in uppercase letters).The inclusion of this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0094] Fig.57 Describe the identification of exemplary nonsense-mediated mRNA decay (NMD) induction exons in the MUT gene.Show the use of RNA sequencing to identify the NMD induction exons in the MUT gene, visualized in the UCSC genome browser.The upper figure shows the diagram of the MUT gene in proportion.The peak corresponding to the RNA sequencing reading is identified in intron GRCh38 / hg38:chr6 4943562549440205, shown in the middle figure.Bioinformatics analysis identifies the exon-like sequence (bottom figure, sequence highlighted in capital letters) flanked by 3' and 5' splice sites.Including this exon leads to the introduction of premature termination codons, making transcripts the target of NMD.

[0095] Fig.58 Depicted is the identification of an exemplary nonsense-mediated mRNA decay (NMD)-inducing exon in the OPA1 gene. The identification of NMD-inducing exons in the OPA1 gene using RNA sequencing is shown, visualized in the UCSC genome browser. The upper figure shows a diagram of the OPA1 gene to scale. The peak corresponding to the RNA sequencing read is identified in the intron GRCh38 / hg38:chr3193593374 193614710, shown in the middle figure. Bioinformatics analysis identified exon-like sequences flanked by 3' and 5' splice sites (below, sequences highlighted in uppercase letters). The inclusion of this exon leads to the introduction of premature stop codons, making the transcript a target for NMD.

[0096] Fig.59 Depicted is the confirmation of NMD-inducible 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 a band corresponding to NMD-inducible exon 8x (GRCh38 / hg38:chr1 243564285243564388) of the AKT3 gene.

[0097] Fig.60 Depicted is an exemplary ASO walk around the AKT3 exon 8x (GRCh38 / hg38: chr1 243564285 243564388) region. A graphical representation of ASO walks around the AKT3 exon 8x (GRCh38 / hg38: chr1 243564285 243564388) region targeting sequences upstream of the 3' splice site, in the 3' splice site, in exon 8x, in the 5' splice site, and downstream of the 5' splice site is shown. The ASOs are designed to cover these regions by shifting 5 nucleotides at a time.

[0098] Fig.61 Depicted is ASO walking in the AKT3 exon 8x (GRCh38 / hg38: chr1243564285 243564388) region evaluated by reverse transcription Taqman-qPCR. The fold change of AKT3 productive mRNA product relative to Sham is plotted.

[0099] Fig.62 Depicted is the confirmation of NMD-inducible exons by cycloheximide treatment in various cell lines. RT-PCR analysis using total RNA from DMSO-treated or cycloheximide-treated cells confirmed the presence of a band corresponding to NMD-inducible exon 14x of the PCCA gene (GRCh38 / hg38:chr13 100305751 100305834).

[0100] Fig.63 Depicted is an exemplary ASO walk around the PCCA exon 14x (GRCh38 / hg38: chr13 100305751 100305834) region. A graphical representation of ASO walks around the PCCA exon 14x (GRCh38 / hg38: chr13 100305751 100305834) region targeting sequences upstream of the 3' splice site, in the 3' splice site, in exon 14x, in 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.

[0101] Fig.64 Depicted is ASO walking in the PCCA exon 14x (GRCh38 / hg38:chr13 100305751 100305834) region evaluated by reverse transcription Taqman-qPCR and RT-PCR. Plotted are the fold change in PCCA productive mRNA product relative to Sham (grey) and the percent change in NMD exon inclusion (black).

[0102] Fig.65 Depicted are confirmation of NMD-inducible exons in various cell lines by puromycin or cycloheximide treatment, as well as confirmation of NMD-inducible exons in brain and retinal samples. RT-PCR analysis using total RNA from water-treated, DMSO-treated, puromycin-treated, or cycloheximide-treated cells confirmed the presence of a band corresponding to NMD-inducible exon 7x (GRCh38 / hg38: chr3 193628509 193628616) of the OPA1 gene.

[0103] Fig.66 Depicted are exemplary ASO walks around the OPA1 exon 7x (GRCh38 / hg38: chr3 193628509 193628616) region. A graphic representation of ASO walks around targeting sequences for the OPA1 exon 7x (GRCh38 / hg38: chr3 193628509 193628616) region upstream of the 3' splice site, in the 3' splice site, in exon 7x, in 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 or 3 nucleotides across the splice site region.

[0104] Fig.67 and 68 Depicted is ASO walking in the OPA1 exon 7x (GRCh38 / hg38: chr3193628509 193628616) region evaluated by Taqman RT-qPCR. The fold change of OPA1 productive mRNA product relative to Sham is plotted.

[0105] Fig.69 Depicted is the confirmation of the NMD-inducible exon in ReNCell VM by cycloheximide treatment and by the presence of NMD-inducible exon mRNA (NF1) in human and monkey cortex. RT-PCR analysis using total RNA from DMSO-treated or cycloheximide-treated cells confirmed the presence of a band corresponding to the NMD-inducible exon 31x of the NF1 gene (GRCh38 / hg38:chr17 31249955 31250125).

[0106] Fig.70Depicted is an exemplary ASO walk around the NF1 exon 31x (GRCh38 / hg38:chr17 31249955 31250125) region. A graphical representation of ASO walks around the NF1 exon 31x (GRCh38 / hg38:chr17 31249955 31250125) region targeting sequences upstream of the 3' splice site, in the 3' splice site, in exon 31x, in 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.

[0107] Fig.71 Depicted is ASO walking of the NF1 exon 31x (GRCh38 / hg38:chrl7 31249955 31250125) region evaluated by RT-PCR (upper panel) and RT-Taqman-qPCR (lower panel). A graph showing the fold change of NF1 productive mRNA product relative to Sham is shown.

[0108] Fig.72 Depicted is the confirmation of NMD-inducible 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 a band corresponding to NMD-inducible exon 18x (GRCh38 / hg38: chr6 3344878933448868) of the SYNGAP1 gene.

[0109] Fig.73 Depicted is an exemplary ASO walk around the SYNGAP1 exon 18x (GRCh38 / hg38: chr6 33448789 33448868) region. Shown is a diagram of an ASO walk around the SYNGAP1 exon 18x (GRCh38 / hg38: chr6 33448789 33448868) region targeting sequence upstream of the 3' splice site, in the 3' splice site, in exon 18x, in the 5' splice site, and downstream of the 5' splice site. The ASO is designed to cover these regions by shifting 5 nucleotides at a time.

[0110] Fig.74 ASO walking of the SYNGAP1 exon 18x (GRCh38 / hg38:chr6 33448789 33448868) region evaluated by RT-PCR (upper panel) and Taqman-qPCR (lower panel) is depicted. % Exon 18x inclusion and fold change of SYNGAP1 productive mRNA product relative to Sham are plotted (upper and lower panels, respectively).

[0111] Fig.75 Depicted is 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 NMD-induced exon 30x (GRCh38 / hg38:chr15 92998149 92998261) of the CHD2 gene. Also shown is RT-PCR analysis, which demonstrates the presence of mRNA containing NMD-induced exon 30x in cortical samples from mice, non-human primates, and humans.

[0112] Fig.76 Depicted is an exemplary ASO walk around the CHD2 exon 30x (GRCh38 / hg38: chr15 92998149 92998261) region. A graphical representation of ASO walks around targeting sequences for the CHD2 exon 30x (GRCh38 / hg38: chr15 92998149 92998261) region upstream of the 3' splice site, in the 3' splice site, in the exon 30x, in 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.

[0113] Fig.77 Depicted is ASO walking of the CHD2 exon 30x (GRCh38 / hg38:chrl5 9299814992998261) region evaluated by RT-PCR. RT-PCR results showing changes in the amount of mRNA containing the NMD-inducing exon 30x are shown.

[0114] Fig.78 Depicted are changes in CHD2 non-productive exon (exon 30x (GRCh38 / hg38: chr15 92998149 92998261)) and CHD2 productive mRNA levels induced by different ASOs. DETAILED DESCRIPTION

[0115] 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, RBFOX 2. Alternative splicing events in the 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 nonproductive mRNA transcripts, which in turn can lead to aberrant protein expression and can be targeted for AB CB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GR IN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, Therapeutic agents that target alternative splicing events in the 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 modulate the expression level of functional proteins in DS patients and / or inhibit abnormal protein expression.Such therapeutic agents can be used to treat diseases caused 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 Conditions caused by deficiency of , 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.

[0116] One of the alternative splicing events that can lead to non-productive mRNA transcripts is the inclusion of extra exons in the mRNA transcript, which can induce nonsense-mediated mRNA decay.The present disclosure provides methods for regulating 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, PRP Alternative splicing of F3, 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 of the encoded protein. RNA and thus the translation 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, Compositions and methods for increasing the amount of 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 pseudo exon skipping, and promote 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, Constitutive splicing of 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.In various 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, P CCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VC AN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2 or SYN GAP1 protein to treat 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 Conditions caused by deficiency of , 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.

[0117] Splicing and nonsense-mediated mRNA decay

[0118] Intervening sequences or introns are removed by a large and highly dynamic RNA-protein complex called the spliceosome, which coordinates a complex interaction between the primary transcript, small nuclear RNAs (snRNAs), and a large number of proteins. The spliceosome is assembled specifically on each intron in an orderly manner, beginning with the recognition of the 5' splice site (5'ss) by the U1 snRNA or the 3' splice site (3'ss) by the U2 pathway, which involves the binding of the U2 accessory 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 65kD subunit (U2AF65) encoded by U2AF2 that binds the polypyrimidine tract (PPT) and a 35kD 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 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 real splice sites to be recognized among a large number of cryptic sites or pseudo-sites in the genomes of higher eukaryotes. These cryptic sites or pseudo-sites have the same sequence, but their number is an order of magnitude greater than that of the real sites. Although they usually have regulatory functions, the exact mechanism of their activation or repression is poorly understood.

[0119] The decision to splice can generally be modeled as a stochastic process rather than a deterministic process, so that even the most clear splicing signals may sometimes be spliced ​​incorrectly. However, under normal conditions, pre-mRNA splicing is carried out with surprisingly high fidelity. This is partly due to the activity of adjacent cis-acting auxiliary exon and intron splicing regulatory elements (ESR or ISR). Generally, these functional elements are classified as exon or intron splicing enhancers (ESE or ISE) or silencers (ESS or ISS) according to their ability to stimulate or inhibit splicing, respectively. Although there is now evidence that some auxiliary cis-acting elements may play a role by affecting the dynamics of spliceosome assembly, such as the arrangement of the complex between U1 snRNP and 5'ss, it seems that many elements are likely to work in conjunction with trans-acting RNA binding proteins (RBPs). For example, the serine- and arginine-rich RBP (SR protein) family is a conserved protein family that plays a key role in defining exons. SR proteins promote exon recognition by recruiting components of the pre-spliceosome to adjacent splicing sites or by antagonizing the action of nearby ESSs. The repressive effects 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 their role in splicing regulation, silencer elements have been proposed to play a role in the repression of pseudoexons, which are arrays of decoy intronic splice sites with typical exon spacing but without functional open reading frames. ESEs and ESSs, in concert with their cognate trans-acting RBPs, represent an important component of a set of splicing controls that specify how, where, and when mRNAs are assembled from their precursors.

[0120] The sequence marking the exon-intron boundary is a degenerate signal of different strengths, which can occur at a high frequency in human genes. In multi-exon genes, different splice site pairs can be connected together in many different combinations, thereby creating a series of diverse transcripts from a single gene. This is generally referred to as variable pre-mRNA splicing. Although most mRNA isoforms produced by variable splicing can be exported from the nucleus and translated into functional polypeptides, different mRNA isoforms from a single gene may have great differences in their translation efficiency. Those mRNA isoforms with premature termination codons (PTC) at least 50bp upstream of the exon junction complex may be targeted by nonsense-mediated mRNA decay (NMD) pathways for degradation. Mutations in traditional (BPS / PPT / 3'ss / 5'ss) and auxiliary splicing motifs can lead to abnormal splicing, such as exon spanning or cryptic (or pseudo) exon inclusion or splice site activation, and significantly contribute to human morbidity and mortality. Both aberrant and alternative splicing patterns can be influenced by natural DNA variations in exons and introns.

[0121] Given that exon-intron boundaries can occur at any of the three positions of a codon, it is clear that only a subset of alternative splicing events can maintain a canonical open reading frame. For example, only exons divisible by 3 can be skipped or included in an mRNA without any reading frame change. Splicing events without compatible phases will induce frameshifts. Unless reversed by downstream events, frameshifts will certainly result in one or more PTCs, possibly 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 stop codons. In some cases, translation of these abnormal mRNAs can result in deleterious gain-of-function or dominant-negative activity of the resulting protein. NMD targets not only transcripts with PTCs, but also a large number of mRNA isoforms expressed from many endogenous genes, suggesting that NMD is a major regulator that drives both fine-tuning and coarse-tuning of steady-state RNA levels in cells.

[0122] An exon (NIE) that induces NMD is an exon or pseudo-exon that is a region within an intron and, if included in a mature RNA transcript, can activate the NMD pathway. In a constitutive splicing event, an intron containing NIE is usually spliced ​​out, but the intron or a portion thereof (e.g., NIE) can be retained during a variable or abnormal splicing event. Mature mRNA transcripts containing such NIEs may be non-productive due to frameshifts that induce the NMD pathway. Including NIE in a mature RNA transcript can downregulate gene expression. In the present disclosure, an mRNA transcript containing NIE may be referred to as "mRNA containing NIE" or "NMD exon mRNA".

[0123] Cryptic (or pseudo-splice sites) have the same splicing recognition sequence as the real splice sites, but are not used in the splicing reaction. Their number is one order of magnitude more than the real splice sites in the human genome, and they are usually suppressed by molecular mechanisms that are not yet fully understood. Cryptic 5' splice sites have a consensus NNN / GUNNNN or NNN / GCNNNN, where N is any nucleotide and / is an exon-intron boundary. Cryptic 3' splice sites have a consensus NAG / N. Their activation is positively affected by the surrounding nucleotides, which make them more similar to the optimal consensus sequences of the real 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.

[0124] The skilled person can readily identify splice sites and their regulatory sequences using suitable publicly available algorithms, 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).

[0125] Cryptic splice sites or splice regulatory sequences can compete with the splice sites of NIE for RNA binding proteins, such as U2AF. In some embodiments, an agent can bind to a cryptic splice site or splice regulatory sequence to prevent the binding of RNA binding proteins, thereby facilitating the binding of RNA binding proteins to the NIE splice sites.

[0126] In some embodiments, the cryptic splice site may not include the 5' or 3' splice site of NIE. In some embodiments, the cryptic splice site may 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, the cryptic splice site may be at least 10 nucleotides, at least 20 nucleotides, at least 50 nucleotides, at least 100 nucleotides, or at least 200 nucleotides downstream of the NIE 3' splice site.

[0127] Target transcript

[0128] In some embodiments, the methods of the present disclosure utilize proteins from 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 gene transcripts. Therapeutic agents that stimulate exon crossing of NIE, such as ASOs, can be used to induce 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, splicing of 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 produce 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, P LCB1, 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 skipping 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, PR PF31, 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 translated normally without activating the NMD pathway,Thereby 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, PLCB in patient cells. 1. The amount of 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 the reduction of Light and 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 deficiency,Alport syndrome; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmic 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 type 7 with febrile seizures +; 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's ataxia; Friedreich's ataxia with preserved reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6 reactive and non-reactive homocystinuria; autosomal recessive HSAN2D; congenital analgesia; 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 acidemia 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 retinal atrophy-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.

[0129] In some embodiments, the disease or the patient's condition that can be treated or improved by the method or composition disclosed herein is not directly related to the target protein (gene) targeted by the therapeutic agent. In some embodiments, the therapeutic agent provided herein can target the protein (gene) that is not directly related to the disease or the patient's condition, but the regulation of the target protein (gene) expression can treat or improve the disease or the patient's condition. For example, by the therapeutic agent targeting provided herein such as CD46, CFH, CR1, DNAJC8, EIF2AK3, ERN1, GUCY2F, GUCY2F, SEMA3C, SEMA3D, SIRT3 or AKT3 genes can treat or improve eye diseases or the patient's condition. In some embodiments, targeted gene CD46, CFH, CR1, DNAJC8, EIF2AK3, ERN1, GUCY2F, GUCY2F, SEMA3C, SEMA3D, SIRT3 or AKT3 are considered to indicate pathway (eye). In some embodiments, targeted genes such as SCN8A can treat or improve central nervous system diseases, e.g., epilepsy, e.g., Dravet syndrome. In some embodiments, such target genes such as SCN8A are considered to indicate pathways (central nervous system) or pathways (central nervous system, epilepsy).

[0130] In various embodiments, the present disclosure provides methods 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, P KP2, 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 regulate splicing or protein expression levels. The therapeutic agent can be a small molecule, a polynucleotide or a polypeptide. In some embodiments, the therapeutic agent is an ASO.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, Various regions or sequences on the 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 can be targeted by therapeutic agents such as ASOs. In some embodiments, the ASO targets 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 containing NIE , 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 transcripts.In some embodiments, the ASO targets 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, Sequences within the NIE of 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 transcripts. In some embodiments, the ASO targets 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, PRP The sequence is upstream (or 5') of the 5' end of the NIE (3'ss) of the F31, 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 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, PRP The sequence is downstream (or 3') of the 3' end of the NIE (5'ss) of the F31, 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 region located at 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, PRPF 3. Sequences within introns flanking the 5' end of NIE of 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 transcripts.In some embodiments, the ASO targets a region located at 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, PRPF 3. Sequences within introns flanking the 3' end of NIE of 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 transcripts. In some embodiments, the ASO targets a target comprising 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, PR Sequence of the NIE-intron boundaries of PF3, 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 transcripts.The NIE-intron boundary can refer to the junction of the intron sequence and the NIE region. The intron sequence can be located at the 5' end of the NIE or the 3' end of the NIE. In some embodiments, the ASO targets 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, Sequences within exons of the 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 transcripts.In some embodiments, the ASO targets 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, Sequences within introns of the 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 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, A portion of an intron of a 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 also includes a sequence of a portion of its exon.

[0131] In some embodiments, the ASO targets a sequence about 4 to about 300 nucleotides upstream (or 5') of the 5' end of NIE. In some embodiments, the ASO targets a sequence 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 may target a sequence more than 300 nucleotides upstream of the 5' end of NIE. In some embodiments, the ASO targets a sequence about 4 to about 300 nucleotides downstream (or 3') of the 3' end of NIE. In some embodiments, the ASO targets a sequence 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 NIE. In some embodiments, the ASO targets a sequence more than 300 nucleotides downstream of the 3' end of NIE.

[0132] In some embodiments, the protein contains 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, AKT 3. CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2 or SYNGAP1 The pre-mRNA transcript of NIE is encoded by a gene sequence having at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to any one of SEQ ID NOs. 1-59 or 192-211.In some embodiments, 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, P The LCB1, 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.

[0133] In some embodiments, the protein contains 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, The pre-mRNA transcript (or NMD exon mRNA) of 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 comprises 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 protein contains 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, The pre-mRNA transcript (or NMD exon mRNA) of 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 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 targeting 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.

[0134] In some embodiments, the ASO targets exon 8x of a pre-mRNA containing ABCB4 NIE comprising NIE exon 8, exon 9x of a pre-mRNA containing ASS1 NIE comprising NIE exon 9, exon 16x of a pre-mRNA containing ATP8B1NIE comprising NIE exon 16, exon 1x of a pre-mRNA containing BAG3 NIE comprising NIE exon 1, exon 31x of a pre-mRNA containing CACNA1A NIE comprising NIE exon 31, exon 36x of a pre-mRNA containing CACNA1A NIE comprising NIE exon 36, exon 37x of a pre-mRNA containing CACNA1A NIE comprising NIE exon 37, exon 3x of a pre-mRNA containing CBS NIE comprising NIE exon 3, exon 12x of a pre-mRNA containing CBS NIE comprising NIE exon 12, exon 13x of a pre-mRNA containing CD55 NIE comprising NIE exon 1. exon 1x of a pre-mRNA containing NIE, exon 16x of a pre-mRNA containing CDKL5 NIE comprising NIE exon 16, exon 3x of a pre-mRNA containing CFH NIE comprising NIE exon 3, exon 30x of a pre-mRNA containing CHD2 NIE comprising NIE exon 30, exon 4x of a pre-mRNA containing CHRNA7 NIE comprising NIE exon 4, exon 1x of a pre-mRNA containing CISD2 NIE comprising NIE exon 1, exon 15x of a pre-mRNA containing CLN3NIE comprising NIE exon 15, exon 11x of a pre-mRNA containing COL4A3 NIE comprising NIE exon 11, exon 41x of a pre-mRNA containing COL4A3 NIE comprising NIE exon 41, and exon 42x of a pre-mRNA containing COL4A4 NIE comprising NIE exon 22. exon 22x of a pre-mRNA containing NIE, exon 44x of a pre-mRNA containing COL4A4 NIE comprising NIE exon 44, exon 20x of a pre-mRNA containing DEPDC5 NIE comprising NIE exon 20, exon 2x of a pre-mRNA containing DHDDS NIE comprising NIE exon 2, exon 3x of a pre-mRNA containing ELOVL4 NIE comprising NIE exon 3, exon 5x of a pre-mRNA containing FAHNIE comprising NIE exon 5, exon 4x of a pre-mRNA containing FXN NIE comprising NIE exon 4, exon 4x of a pre-mRNA containing GALE NIE comprising NIE exon 4, exon 3x of a pre-mRNA containing GBE1 NIE comprising NIE exon 3, exon 11x of a pre-mRNA containing GRIN2A NIE comprising NIE exon 1, and exon 12x of a pre-mRNA containing GRN NIE comprising NIE exon 1.exon 1x of a pre-mRNA containing NIE, exon 2x of a pre-mRNA containing HEXA NIE comprising NIE exon 2, exon 2x of a pre-mRNA containing KANSL1 NIE comprising NIE exon 2, exon 1x of a pre-mRNA containing KCNQ2 NIE comprising NIE exon 1, exon 50x of a pre-mRNA containing KMT2D NIE comprising NIE exon 50, exon 8x of a pre-mRNA containing MAPK3NIE comprising NIE exon 8, exon 13x of a pre-mRNA containing MBD5 NIE comprising NIE exon 13, exon 2x of a pre-mRNA containing MECP2 NIE comprising NIE exon 2, exon 11x of a pre-mRNA containing MUT NIE comprising NIE exon 11, and exon 13x of a pre-mRNA containing NF1 NIE comprising NIE exon 31. exon 31x of a pre-mRNA containing NIE, exon 7x of a pre-mRNA containing NIPBLNIE comprising NIE exon 7, exon 38x of a pre-mRNA containing NIPBL NIE comprising NIE exon 38, exon 11x of a pre-mRNA containing NSD1 NIE comprising NIE exon 11, exon 6x of a pre-mRNA containing OPA1 NIE comprising NIE exon 6, exon 28x of a pre-mRNA containing OPA1 NIE comprising NIE exon 28, exon 1x of a pre-mRNA containing OPTN NIE comprising NIE exon 1, exon 1x of a pre-mRNA containing PCCA NIE comprising NIE exon 1, exon 5x of a pre-mRNA containing PCCB NIE comprising NIE exon 5, exon 6x of a pre-mRNA containing PCCB NIE comprising NIE exon 6, and exon 4 of a pre-mRNA containing PKP2 exon 4x of a pre-mRNA containing NIE, exon 23x of a pre-mRNA containing PLCB1 NIE comprising NIE exon 23, exon 3x of a pre-mRNA containing PRPF3 NIE comprising NIE exon 3, exon 9x of a pre-mRNA containing PRPF31 NIE comprising NIE exon 9, exon 1x of a pre-mRNA containing RAI1 NIE comprising NIE exon 1, exon 5x of a pre-mRNA containing RBFOX2 NIE comprising NIE exon 5, exon 13x of a pre-mRNA containing SCN2A NIE comprising NIE exon 13, exon 6x of a pre-mRNA containing SCN3A NIE comprising NIE exon 6, exon 7x of a pre-mRNA containing SCN3A NIE comprising NIE exon 7, exon 4x of a pre-mRNA containing SCN8A NIE comprising NIE exon 4, and exon 6 of a pre-mRNA containing SCN8A NIE comprising NIE exon 6. NIE pre-mRNA exon 6x, SCN8A containing NIE exon 20exon 20x of a pre-mRNA containing NIE, exon 6x of a pre-mRNA containing SCN9A NIE comprising NIE exon 6, exon 24x of a pre-mRNA containing SHANK3 NIE comprising NIE exon 24, exon 3x of a pre-mRNA containing SLC25A13 NIE comprising NIE exon 3, exon 6x of a pre-mRNA containing SLC25A13 NIE comprising NIE exon 6, exon 9x of a pre-mRNA containing SLC25A13 NIE comprising NIE exon 9, exon 11x of a pre-mRNA containing SLC25A13 NIE comprising NIE exon 11, exon 13x of a pre-mRNA containing SLC25A13 NIE comprising NIE exon 13, exon 1x of a pre-mRNA containing SLC6A1 NIE comprising NIE exon 1, and exon 12 of a pre-mRNA containing SPTAN1 NIE comprising NIE exon 13. exon 12x of a pre-mRNA containing NIE, exon 10x of a pre-mRNA containing TEK NIE comprising NIE exon 10, exon 15x of a pre-mRNA containing TEK NIE comprising NIE exon 15, exon 1x of a pre-mRNA containing TOPORS NIE comprising NIE exon 1, exon 11x of a pre-mRNA containing TSC2 NIE comprising NIE exon 11, exon 30x of a pre-mRNA containing TSC2 NIE comprising NIE exon 30, exon 1x of a pre-mRNA containing UBE3A NIE comprising NIE exon 1, or exon 7x of a pre-mRNA containing VCAN NIE comprising 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 4305973043060012); an exon of CD46 (GRCh38 / hg38: chr1 207775610 207775745); an exon of CFH (GRCh38 / hg38: chr1 196675450 196675529); an exon of CHD2 (GRCh38 / hg38: chr1592998149 92998261); exon of CLN3 (GRCh38 / hg38:chr16 28479644 28479765); exon of COL11A2 (GRCh38 / hg38:chr6 33183634 33183698); exon of COL4A3 (GRCh38 / hg38:chr2227296487227296526); exon of COL4A4 (GRCh38 / hg38:chr2 227144653 227144833); exon of COL4A4 (GRCh38 / hg38:chr2 227015283 227015360); exon of CR1 (GRCh38 / hg38:chr1 207637688 207637848); exon of CRX (GRCh38 / hg38:chr19 47835403 47835579); exon of CYP2J2 (GRCh38 / hg38:chr1 59904366 59904516); exon of DHDDS (GRCh38 / hg38:chr1 26442335 26442372); exon of DNAJC8 (GRCh38 / hg38:chr1 28230131 28230252); exon of EIF2AK3 (GRCh38 / hg38:chr2 88582755 88582824); exon of ERN1 (GRCh38 / hg38:chr17 64102673 64102804); exon of GALE (GRCh38 / hg38:chr1 23798311 23798484); exon of GUCY2F (GRCh38 / hg38:chrX 109383365 109383446); exon of GUCY2F (GRCh38 / hg38:chrX 109439038 109439175); exon of HEXA (GRCh38 / hg38:chr15 7236237672362466); exon of HEXA (GRCh38 / hg38:chr15 72345677 72345776); exon of MAPK3 (GRCh38 / hg38:chr16 30115595 30115645); exon of MBD5 (GRCh38 / hg38:chr2 148460219148460304); exon of MBD5 (GRCh38 / hg38:chr2 148490695 148490787); exon of MBD5 (GRCh38 / hg38:chr2 148505761 148505830); exon of MUT (GRCh38 / hg38:chr6 4943652249436597); exon of MYH14 (GRCh38 / hg38:chr19 50230825 50230999); exon of MYO6 (GRCh38 / hg38:chr6 7586743175867523); exon of NF1 (GRCh38 / hg38:chr17 3124995531250125); exon of NF2 (GRCh38 / hg38:chr22 29628658 29628773); exon of NIPBL (GRCh38 / hg38:chr5 37048127 37048354); exon of NR1H4 (GRCh38 / hg38:chr12100499841 100500024); exon of NSD1 (GRCh38 / hg38:chr5 177169394 177169559); exon of NSD1 (GRCh38 / hg38:chr5 177200761 177200783); exon of NSD1 (GRCh38 / hg38:chr5177247924 177248079); exon of NSD1 (GRCh38 / hg38:chr5 177275947 177276101); exon of OPA1 (GRCh38 / hg38:chr3 193628509 193628616); exon of OPA1 (GRCh38 / hg38:chr3193603500 193603557); exon of PCCA (GRCh38 / hg38:chr13 100305751 100305834); exon of PKP2 (GRCh38 / hg38:chr12 32894516 32894778); exon of PPARA (GRCh38 / hg38:chr2246203575 46203752); exon of PRPF3 (GRCh38 / hg38:chr1 150327557 150327652); exon of PRPF3 (GRCh38 / hg38:chr1 150330401 150330498); exon of SCN2A (GRCh38 / hg38:chr2165327155 165327202); exon of SCN8A (GRCh38 / hg38:chr12 51688758 51688849); exon of SCN8A (GRCh38 / hg38:chr12 51780202 51780271); exon of SCN9A (GRCh38 / hg38:chr2166304238 166304329); exon of SEMA3C (GRCh38 / hg38:chr7 80794854 80794957); exon of SEMA3D (GRCh38 / hg38:chr7 8505949885059541); exon of SIRT3 (GRCh38 / hg38:chr11 225673 226081); exon of STK11 (GRCh38 / hg38:chr19 1216268 1216398); exon of STK11 (GRCh38 / hg38:chr19 1221621 1221846); exon of SYNGAP1 (GRCh38 / hg38:chr633448789 33448868); exon of TOPORS (GRCh38 / hg38:chr9 32551365 32551469); exon of VCAN (GRCh38 / hg38:chr5 83544965 83545070).

[0135] 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 42x of COL4A4, exon 43x of COL4A5, exon 44x of COL4A6, exon 45x of COL4A7, exon 47x of COL4A8, exon 48x of COL4A9, exon 49x of COL4A10, exon 50x of COL4A11 exon 22x, 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, NIP Exon 38x of BL, 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, about 1500 nucleotides upstream (or 5') of the 5' end of 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.A sequence of 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. 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:chr1196675450 of CFH, GRCh38 / hg38:chr1592998149 of CHD2, GRCh38 / hg38:chr16 28479765 of CLN3, GRCh38 / hg38:chr6 28479765 of COL11A2. 33183698, GRCh38 / hg38:chr2 of COL4A3 227296487, GRCh38 / hg38:chr2 of COL4A4 227144833, GRCh38 / hg38:chr2 of COL4A4 227015360, GRCh38 / hg38:chr1 of CR1 207637688, GRCh38 / hg38:chr19 of CRX 47835403, GRCh38 / hg38:chr1 of CYP2J259904516, GRCh38 / hg38:chr1 of DHDDS 26442335, GRCh38 / hg38:chr1 of DNAJC8 28230252、GRCh38 / hg38 of EIF2AK3:chr2 88582824、GRCh38 / hg38 of ERN1:chr17 64102804、GRCh38 / hg38 of GALE:chr1 23798484、GRCh38 / hg38 of GUCY2F:chrX 109383446、GRCh38 / hg38 of GUCY2F:chrX 109439175、GRCh38 / hg38 of HEXA:chr15 72362466、GRCh38 / hg38 of HEXA:chr1572345776、GRCh38 / hg38 of MAPK3:chr16 30115645、GRCh38 / hg38:chr2 of MBD5 148460219、GRCh38 / hg38:chr2 of MBD5 148490695、GRCh38 / hg38:chr2 of MBD5 148505761、GRCh38 / hg38:chr6 49436597 of MUT, GRCh38 / hg38:chr19 50230825 of MYH14, GRCh38 / hg38:chr6 75867431 of MYO6, GRCh38 / hg38:chr17 31249955 of NF1, GRCh38 / hg38:chr2229628658 of NF2, GRCh38 / hg38:chr5 37048127 of NIPBL, GRCh38 / hg38:chr12 100499841 of NR1H4, GRCh38 / hg38:chr5 177169394 of NSD1. 177200761、GRCh38 / hg38:chr5 of NSD1 177247924、GRCh38 / hg38:chr5 of NSD1 177275947、GRCh38 / hg38:chr3 of OPA1 193628509、GRCh38 / hg38:chr3 of OPA1 193603500、GRCh38 / hg38:chr13100305751 of PCCA、GRCh38 / hg38:chr12 of PKP2 32894778、GRCh38 / hg38:chr22 of PPARA 46203575、GRCh38 / hg38:chr1 of PRPF3 150327557、GRCh38 / hg38:chr1 of PRPF3 150330401、GRCh38 / hg38:chr2 of SCN2A 165327155、GRCh38 / hg38:chr12 of SCN8A 51688758、GRCh38 / hg38:chr12 of SCN8A 51780202、GRCh38 / hg38:chr2 of SCN9A 166304329、GRCh38 / hg38:chr7 of SEMA3C 80794957、GRCh38 / hg38:chr7 of SEMA3D 85059541, about 1500 nucleotides upstream (or 5') of GRCh38 / hg38:chr11226081 of SIRT3, GRCh38 / hg38:chr19 1216268 of STK11, GRCh38 / hg38:chr19 1221621 of STK11, GRCh38 / hg38:chr6 33448789 of SYNGAP1, GRCh38 / hg38:chr9 32551469 of TOPORS, or GRCh38 / hg38:chr5 83544965 of VCAN,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.

[0136] 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 42x of COL4A4, exon 43x of COL4A5, exon 44x of COL4A6, exon 45x of COL4A7, exon 47x of COL4A8, exon 48x of COL4A9, exon 49x of COL4A10, exon 50x of COL4A11 exon 22x, 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, NIPB exon 38x of L, 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 SCN9A, exon 6x of SH Up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides upstream (or 5') of the 5' end of exon 24x of ANK3, 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,A sequence of 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. 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:chr1196675450 of CFH, GRCh38 / hg38:chr15 92998149 of CHD2, GRCh38 / hg38:chr16 28479765 of CLN3, GRCh38 / hg38:chr6 33183698, GRCh38 / hg38:chr2 of COL4A3 227296487, GRCh38 / hg38:chr2 of COL4A4 227144833, GRCh38 / hg38:chr2 of COL4A4 227015360, GRCh38 / hg38:chr1 of CR1 207637688, GRCh38 / hg38:chr19 of CRX 47835403, GRCh38 / hg38:chr1 of CYP2J259904516, GRCh38 / hg38:chr1 of DHDDS 26442335, GRCh38 / hg38:chr1 of DNAJC8 28230252、GRCh38 / hg38 of EIF2AK3:chr2 88582824、GRCh38 / hg38 of ERN1:chr17 64102804、GRCh38 / hg38 of GALE:chr1 23798484、GRCh38 / hg38 of GUCY2F:chrX 109383446、GRCh38 / hg38 of GUCY2F:chrX 109439175、GRCh38 / hg38 of HEXA:chr15 72362466、GRCh38 / hg38 of HEXA:chr1572345776、GRCh38 / hg38 of MAPK3:chr16 30115645、GRCh38 / hg38:chr2 of MBD5 148460219、GRCh38 / hg38:chr2 of MBD5 148490695、GRCh38 / hg38:chr2 of MBD5 148505761、GRCh38 / hg38:chr6 49436597 of MUT, GRCh38 / hg38:chr19 50230825 of MYH14, GRCh38 / hg38:chr6 75867431 of MYO6, GRCh38 / hg38:chr17 31249955 of NF1, GRCh38 / hg38:chr2229628658 of NF2, GRCh38 / hg38:chr5 37048127 of NIPBL, GRCh38 / hg38:chr12 100499841 of NR1H4, GRCh38 / hg38:chr5 177169394 of NSD1. 177200761、GRCh38 / hg38:chr5 of NSD1 177247924、GRCh38 / hg38:chr5 of NSD1 177275947、GRCh38 / hg38:chr3 of OPA1 193628509、GRCh38 / hg38:chr3 of OPA1 193603500、GRCh38 / hg38:chr1 of PCCA 3100305751、GRCh38 / hg38:chr12 of PKP2 32894778、GRCh38 / hg38:chr2246203575 of PPARA、GRCh38 / hg38:chr1 of PRPF3 150327557、GRCh38 / hg38:chr1 of PRPF3 150330401、GRCh38 / hg38:chr2 of SCN2A 165327155、GRCh38 / hg38:chr12 of SCN8A 51688758、GRCh38 / hg38:chr12 of SCN8A 51780202、GRCh38 / hg38:chr2 of SCN9A 166304329、GRCh38 / hg38:chr7 of SEMA3C 80794957、GRCh38 / hg38:chr7 of SEMA3D 85059541, GRCh38 / hg38:chr11226081 of SIRT3, GRCh38 / hg38:chr19 1216268 of STK11, GRCh38 / hg38:chr19 1221621 of STK11, GRCh38 / hg38:chr6 33448789 of SYNGAP1, GRCh38 / hg38:chr9 32551469 of TOPORS, or GRCh38 / hg38:chr5 83544965 of VCAN, up to about 1500 nucleotides upstream (or 5'), 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.

[0137] 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 42x of COL4A4, exon 43x of COL4A5, exon 44x of COL4A6, exon 45x of COL4A7, exon 47x of COL4A8, exon 48x of COL4A9, exon 49x of COL4A10, exon 50x of COL4A11 exon 22x, 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, NIP Exon 38x of BL, 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, about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, downstream of the 3' end (or 3') of 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.A sequence of 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. In some embodiments, the ASO targets GRCh38 / hg38:chr1 243564285 of AKT3, GRCh38 / hg38:chr19 13236449 of CACNA1A, GRCh38 / hg38:chr21 43059730 of CBS, GRCh38 / hg38:chr1 207775745 of CD46, GRCh38 / hg38:chr1196675529 of CFH, GRCh38 / hg38:chr15 92998261 of CHD2, GRCh38 / hg38:chr16 28479644 of CLN3, GRCh38 / hg38:chr6 33183634、GRCh38 / hg38:chr2 of COL4A3 227296526、GRCh38 / hg38:chr2 of COL4A4 227144653、GRCh38 / hg38:chr2 of COL4A4 227015283、GRCh38 / hg38:chr1 of CR1 207637848、GRCh38 / hg38:chr19 of CRX 47835579、GRCh38 / hg38:chr159904366 of CYP2J2、GRCh38 / hg38:chr1 of DHDDS 26442372、GRCh38 / hg38:chr1 of DNAJC8 28230131、GRCh38 / hg38 of EIF2AK3:chr2 88582755、GRCh38 / hg38 of ERN1:chr17 64102673、GRCh38 / hg38 of GALE:chr1 23798311、GRCh38 / hg38 of GUCY2F:chrX 109383365、GRCh38 / hg38 of GUCY2F:chrX 109439038、GRCh38 / hg38 of HEXA:chr15 72362376、GRCh38 / hg38 of HEXA:chr1572345677、GRCh38 / hg38 of MAPK3:chr16 30115595、GRCh38 / hg38:chr2 of MBD5 148460304、GRCh38 / hg38:chr2 of MBD5 148490787、GRCh38 / hg38:chr2 of MBD5 148505830、GRCh38 / hg38:chr6 49436522 of MUT, GRCh38 / hg38:chr19 50230999 of MYH14, GRCh38 / hg38:chr6 75867523 of MYO6, GRCh38 / hg38:chr17 31250125 of NF1, GRCh38 / hg38:chr2229628773 of NF2, GRCh38 / hg38:chr5 37048354 of NIPBL, GRCh38 / hg38:chr12 100500024 of NR1H4, GRCh38 / hg38:chr5 177169559 of NSD1. 177200783、GRCh38 / hg38:chr5 of NSD1 177248079、GRCh38 / hg38:chr5 of NSD1 177276101、GRCh38 / hg38:chr3 of OPA1 193628616、GRCh38 / hg38:chr3 of OPA1 193603557、GRCh38 / hg38:chr13100305834 of PCCA、GRCh38 / hg38:chr12 of PKP2 32894516、GRCh38 / hg38:chr22 of PPARA 46203752、GRCh38 / hg38:chr1 of PRPF3 150327652、GRCh38 / hg38:chr1 of PRPF3 150330498、GRCh38 / hg38:chr2 of SCN2A 165327202、GRCh38 / hg38:chr12 of SCN8A 51688849、GRCh38 / hg38:chr12 of SCN8A 51780271、GRCh38 / hg38:chr2 of SCN9A 166304238、GRCh38 / hg38:chr7 of SEMA3C 80794854、GRCh38 / hg38:chr7 of SEMA3D 85059498, about 1500 nucleotides downstream (or 3') of GRCh38 / hg38:chr11225673 of SIRT3, GRCh38 / hg38:chr19 1216398 of STK11, GRCh38 / hg38:chr19 1221846 of STK11, GRCh38 / hg38:chr6 33448868 of SYNGAP1, GRCh38 / hg38:chr9 32551365 of TOPORS, or GRCh38 / hg38:chr5 83545070 of VCAN,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.

[0138] 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 42x of COL4A4, exon 43x of COL4A5, exon 44x of COL4A6, exon 45x of COL4A7, exon 47x of COL4A8, exon 48x of COL4A9, exon 49x of COL4A10, exon 50x of COL4A11 exon 22x, 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, NIPB exon 38x of L, 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 SCN9A, exon 6x of SH Up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides downstream (or 3') of the 3' end of exon 24x of ANK3, 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.A sequence of 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. In some embodiments, the ASO targets GRCh38 / hg38:chr1 243564285 of AKT3, GRCh38 / hg38:chr19 13236449 of CACNA1A, GRCh38 / hg38:chr21 43059730 of CBS, GRCh38 / hg38:chr1 207775745 of CD46, GRCh38 / hg38:chr1 196675529 of CFH, GRCh38 / hg38:chr15 92998261 of CHD2, GRCh38 / hg38:chr1628479644 of CLN3, GRCh38 / hg38:chr6 33183634、GRCh38 / hg38 of COL4A3:chr2227296526、GRCh38 / hg38 of COL4A4:chr2 227144653、GRCh38 / hg38 of COL4A4:chr2227015283、GRCh38 / hg38 of CR1:chr1 207637848、GRCh38 / hg38 of CRX:chr19 47835579、GRCh38 / hg38 of CYP2J2:chr1 59904366、GRCh38 / hg38 of DHDDS:chr1 26442372、GRCh38 / hg38 of DNAJC8:chr1 28230131、GRCh38 / hg38 of EIF2AK3:chr2 88582755、GRCh38 / hg38 of ERN1:chr17 64102673、GRCh38 / hg38 of GALE:chr1 23798311、GRCh38 / hg38 of GUCY2F:chrX109383365、GRCh38 / hg38 of GUCY2F:chrX 109439038、GRCh38 / hg38 of HEXA:chr1572362376、GRCh38 / hg38 of HEXA:chr15 72345677、GRCh38 / hg38 of MAPK3:chr16 30115595、GRCh38 / hg38:chr2 of MBD5 148460304、GRCh38 / hg38:chr2 of MBD5 148490787、GRCh38 / hg38:chr2 of MBD5 148505830、GRCh38 / hg38:chr6 49436522 of MUT, GRCh38 / hg38:chr19 50230999 of MYH14, GRCh38 / hg38:chr6 75867523 of MYO6, GRCh38 / hg38:chr1731250125 of NF1, GRCh38 / hg38:chr22 29628773 of NIPBL, GRCh38 / hg38:chr5 37048354 of NR1H4, GRCh38 / hg38:chr12 100500024 of NSD1, GRCh38 / hg38:chr5 177200783、GRCh38 / hg38:chr5 of NSD1 177248079、GRCh38 / hg38:chr5 of NSD1 177276101、GRCh38 / hg38:chr3 of OPA1 193628616、GRCh38 / hg38:chr31 of OPA193603557、GRCh38 / hg38:chr13 of PCCA 100305834、GRCh38 / hg38:chr12 of PKP2 32894516、GRCh38 / hg38:chr22 of PPARA 46203752、GRCh38 / hg38:chr1 of PRPF3 150327652、GRCh38 / hg38:chr1 of PRPF3 150330498、GRCh38 / hg38:chr2 of SCN2A 165327202、GRCh38 / hg38:chr12 of SCN8A 51688849、GRCh38 / hg38:chr12 of SCN8A 51780271、GRCh38 / hg38:chr2 of SCN9A 166304238、GRCh38 / hg38:chr7 of SEMA3C 80794854、GRCh38 / hg38:chr7 of SEMA3D 85059498、GRCh38 / hg38:chr11 of SIRT3 225673, GRCh38 / hg38:chr19 1216398 of STK11, GRCh38 / hg38:chr19 1221846 of STK11, GRCh38 / hg38:chr6 33448868 of SYNGAP1, GRCh38 / hg38:chr9 32551365 of TOPORS, or GRCh38 / hg38:chr5 83545070 of VCAN, at most about 1500 nucleotides downstream (or 3'), 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.

[0139] In some embodiments, the ASO has a sequence that is complementary to a targeting portion of an NMD exon mRNA according to any one of SEQ ID NOs: 60-191.

[0140] In some embodiments, the ASO targets a sequence upstream of the 5' end of NIE. For example, the ASO targets a sequence upstream of the 5' end of NIE (e.g., 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 16x of COL4A4, exon 17x of COL4A5, exon 18x of COL4A6, exon 20x of COL4A7, exon 21x of COL4A8, exon 22x of COL4A9, exon 23x of COL4A10, exon 24x of COL4A11, exon 25x of COL4A12, exon 26x of COL4A13, exon 27x of COL4A14, exon 28x of COL4A15, exon 29x of COL4A16, exon 30x of CHD2, exon 4x of CHRNA7, exon 1x of CISD2, exon 15x of CLN3, exon 11x of COL4A1 exon 41x, 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 2x of NF1 exon 31x, 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 The ASO of exon 6x of SCN8A, exon 20x 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 the same sequence as SEQ ID NO:A sequence of at least 8 consecutive nucleic acids of any one of NOs: 60-134 that is at least about 80%, 85%, 90%, 95%, 97% or 100% complementary. For example, targeting the 5' end upstream sequence of NIE (e.g., exon of AKT3 (GRCh38 / hg38:chr1 243564285 243564388); exon of CACNA1A (GRCh38 / hg38:chr19 13236449 13236618); exon of CBS (GRCh38 / hg38:chr214305973043060012); exon of CD46 (GRCh38 / hg38:chr1 207775610 207775745); exon of CFH (GRCh38 / hg38:chr1 196675450 196675529); exon of CHD2 (GRCh38 / hg38:chr1592998149 92998261); exon of CLN3 (GRCh38 / hg38:chr16 28479644 28479765); exon of COL11A2 (GRCh38 / hg38:chr6 33183634 33183698); exon of COL4A3 (GRCh38 / hg38:chr2227296487 227296526); exon of COL4A4 (GRCh38 / hg38:chr2 227144653 227144833); exon of COL4A5 (GRCh38 / hg38:chr3 227015283 227015360); exon of CR1 (GRCh38 / hg38:chr1 207637688207637848); exon of CRX (GRCh38 / hg38:chr19 47835403 47835579); exon of CYP2J2 (GRCh38 / hg38:chr1 59904366 59904516); exon of DHDDS (GRCh38 / hg38:chr1 26442335 26442372); exon of DNAJC8 (GRCh38 / hg38:chr1 28230131 28230252); exon of EIF2AK3 (GRCh38 / hg38:chr2 88582755 88582824); exon of ERN1 (GRCh38 / hg38:chr17 64102673 64102804); exon of GALE (GRCh38 / hg38:chr1 23798311 23798484); exon of GUCY2F (GRCh38 / hg38:chrX 109383365109383446); exon of GUCY2F (GRCh38 / hg38:chrX 109439038109439175); exon of HEXA (GRCh38 / hg38:chr15 7236237672362466); exon of HEXA (GRCh38 / hg38:chr15 72345677 72345776); exon of MAPK3 (GRCh38 / hg38:chr16 30115595 30115645); exon of MBD5 (GRCh38 / hg38:chr2 148460219148460304); exon of MBD5 (GRCh38 / hg38:chr2 148490695 148490787); exon of MBD5 (GRCh38 / hg38:chr2 148505761 148505830); exon of MUT (GRCh38 / hg38:chr6 4943652249436597); exon of MYH14 (GRCh38 / hg38:chr19 50230825 50230999); exon of MYO6 (GRCh38 / hg38:chr6 75867431 75867523); exon of NF1 (GRCh38 / hg38:chr17 3124995531250125); exon of NF2 (GRCh38 / hg38:chr22 29628658 29628773); exon of NIPBL (GRCh38 / hg38:chr5 37048127 37048354); exon of NR1H4 (GRCh38 / hg38:chr12100499841 100500024); exon of NSD1 (GRCh38 / hg38:chr5 177169394 177169559); exon of NSD1 (GRCh38 / hg38:chr5 177200761 177200783); exon of NSD1 (GRCh38 / hg38:chr5177247924 177248079); exon of NSD1 (GRCh38 / hg38:chr5 177275947 177276101); exon of OPA1 (GRCh38 / hg38:chr3 193628509 193628616); exon of OPA1 (GRCh38 / hg38:chr3193603500 193603557); exon of PCCA (GRCh38 / hg38:chr13 100305751100305834); exon of PKP2 (GRCh38 / hg38:chr12 32894516 32894778); exon of PPARA (GRCh38 / hg38:chr2246203575 46203752); exon of PRPF3 (GRCh38 / hg38:chr1 150327557 150327652); exon of PRPF3 (GRCh38 / hg38:chr1 150330401 150330498); exon of SCN2A (GRCh38 / hg38:chr2165327155 165327202); exon of SCN8A (GRCh38 / hg38:chr12 51688758 51688849); exon of SCN8A (GRCh38 / hg38:chr12 51780202 51780271); exon of SCN9A (GRCh38 / hg38:chr2166304238 166304329); exon of SEMA3C (GRCh38 / hg38:chr7 80794854 80794957); exon of SEMA3D (GRCh38 / hg38:chr7 85059498 85059541); exon of SIRT3 (GRCh38 / hg38:chr11 225673 226081); exon of STK11 (GRCh38 / hg38:chr19 The ASO of the exon of SEQ ID NO: 135-191 may comprise a sequence having at least 80%, 85%, 90%, 95%, 97% or 100% sequence identity to any one of SEQ ID NO: 135-191.

[0141]

[0142] In some embodiments, the ASO targets exon 8x of a pre-mRNA containing ABCB4 NIE comprising NIE exon 8, exon 9x of a pre-mRNA containing ASS1 NIE comprising NIE exon 9, exon 16x of a pre-mRNA containing ATP8B1NIE comprising NIE exon 16, exon 1x of a pre-mRNA containing BAG3 NIE comprising NIE exon 1, exon 31x of a pre-mRNA containing CACNA1A NIE comprising NIE exon 31, exon 36x of a pre-mRNA containing CACNA1A NIE comprising NIE exon 36, exon 37x of a pre-mRNA containing CACNA1A NIE comprising NIE exon 37, exon 3x of a pre-mRNA containing CBS NIE comprising NIE exon 3, exon 12x of a pre-mRNA containing CBS NIE comprising NIE exon 12, exon 13x of a pre-mRNA containing CD55 NIE comprising NIE exon 1. exon 1x of a pre-mRNA containing NIE, exon 16x of a pre-mRNA containing CDKL5 NIE comprising NIE exon 16, exon 3x of a pre-mRNA containing CFH NIE comprising NIE exon 3, exon 30x of a pre-mRNA containing CHD2 NIE comprising NIE exon 30, exon 4x of a pre-mRNA containing CHRNA7 NIE comprising NIE exon 4, exon 1x of a pre-mRNA containing CISD2 NIE comprising NIE exon 1, exon 15x of a pre-mRNA containing CLN3NIE comprising NIE exon 15, exon 11x of a pre-mRNA containing COL4A3 NIE comprising NIE exon 11, exon 41x of a pre-mRNA containing COL4A3 NIE comprising NIE exon 41, and exon 42x of a pre-mRNA containing COL4A4 NIE comprising NIE exon 22. exon 22x of a pre-mRNA containing NIE, exon 44x of a pre-mRNA containing COL4A4 NIE comprising NIE exon 44, exon 20x of a pre-mRNA containing DEPDC5 NIE comprising NIE exon 20, exon 2x of a pre-mRNA containing DHDDS NIE comprising NIE exon 2, exon 3x of a pre-mRNA containing ELOVL4 NIE comprising NIE exon 3, exon 5x of a pre-mRNA containing FAHNIE comprising NIE exon 5, exon 4x of a pre-mRNA containing FXN NIE comprising NIE exon 4, exon 4x of a pre-mRNA containing GALE NIE comprising NIE exon 4, exon 3x of a pre-mRNA containing GBE1 NIE comprising NIE exon 3, exon 11x of a pre-mRNA containing GRIN2A NIE comprising NIE exon 1, and exon 12x of a pre-mRNA containing GRN NIE comprising NIE exon 1. Exon 1x of NIE pre-mRNA,exon 2x of a pre-mRNA containing HEXA NIE comprising NIE exon 2, exon 2x of a pre-mRNA containing KANSL1 NIE comprising NIE exon 2, exon 1x of a pre-mRNA containing KCNQ2 NIE comprising NIE exon 1, exon 50x of a pre-mRNA containing KMT2D NIE comprising NIE exon 50, exon 8x of a pre-mRNA containing MAPK3NIE comprising NIE exon 8, exon 13x of a pre-mRNA containing MBD5 NIE comprising NIE exon 13, exon 2x of a pre-mRNA containing MECP2 NIE comprising NIE exon 2, exon 11x of a pre-mRNA containing MUT NIE comprising NIE exon 11, and exon 11x of a pre-mRNA containing NF1 NIE comprising NIE exon 31. exon 31x of a pre-mRNA containing NIE, exon 7x of a pre-mRNA containing NIPBLNIE comprising NIE exon 7, exon 38x of a pre-mRNA containing NIPBL NIE comprising NIE exon 38, exon 11x of a pre-mRNA containing NSD1 NIE comprising NIE exon 11, exon 6x of a pre-mRNA containing OPA1 NIE comprising NIE exon 6, exon 28x of a pre-mRNA containing OPA1 NIE comprising NIE exon 28, exon 1x of a pre-mRNA containing OPTN NIE comprising NIE exon 1, exon 1x of a pre-mRNA containing PCCA NIE comprising NIE exon 1, exon 5x of a pre-mRNA containing PCCB NIE comprising NIE exon 5, exon 6x of a pre-mRNA containing PCCB NIE comprising NIE exon 6, and exon 4 of a pre-mRNA containing PKP2 exon 4x of a pre-mRNA containing NIE, exon 23x of a pre-mRNA containing PLCB1 NIE comprising NIE exon 23, exon 3x of a pre-mRNA containing PRPF3 NIE comprising NIE exon 3, exon 9x of a pre-mRNA containing PRPF31 NIE comprising NIE exon 9, exon 1x of a pre-mRNA containing RAI1 NIE comprising NIE exon 1, exon 5x of a pre-mRNA containing RBFOX2 NIE comprising NIE exon 5, exon 13x of a pre-mRNA containing SCN2A NIE comprising NIE exon 13, exon 6x of a pre-mRNA containing SCN3A NIE comprising NIE exon 6, exon 7x of a pre-mRNA containing SCN3A NIE comprising NIE exon 7, exon 4x of a pre-mRNA containing SCN8A NIE comprising NIE exon 4, and exon 6 of a pre-mRNA containing SCN8A NIE comprising NIE exon 6. exon 6x of the pre-mRNA of NIE, exon 20x of the pre-mRNA of SCN8A NIE including exon 20 of NIE,exon 6x of a pre-mRNA containing SCN9A NIE comprising NIE exon 6, exon 24x of a pre-mRNA containing SHANK3 NIE comprising NIE exon 24, exon 3x of a pre-mRNA containing SLC25A13 NIE comprising NIE exon 3, exon 6x of a pre-mRNA containing SLC25A13 NIE comprising NIE exon 6, exon 9x of a pre-mRNA containing SLC25A13 NIE comprising NIE exon 9, exon 11x of a pre-mRNA containing SLC25A13 NIE comprising NIE exon 11, exon 13x of a pre-mRNA containing SLC25A13 NIE comprising NIE exon 13, exon 1x of a pre-mRNA containing SLC6A1 NIE comprising NIE exon 1, and exon 12 of a pre-mRNA containing SPTAN1 comprising NIE exon 13. exon 12x of a pre-mRNA containing NIE, exon 10x of a pre-mRNA containing TEK NIE comprising NIE exon 10, exon 15x of a pre-mRNA containing TEK NIE comprising NIE exon 15, exon 1x of a pre-mRNA containing TOPORS NIE comprising NIE exon 1, exon 11x of a pre-mRNA containing TSC2 NIE comprising NIE exon 11, exon 30x of a pre-mRNA containing TSC2 NIE comprising NIE exon 30, exon 1x of a pre-mRNA containing UBE3A NIE comprising NIE exon 1, or exon 7x of a pre-mRNA containing VCAN NIE comprising 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, COL4A exon 11x of COL3, 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, SCN8 A sequence downstream (or 3') of the 5' end of pre-mRNA of exon 4x of SCNA, 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 16x of COL4A4, exon 17x of COL4A5, exon 18x of COL4A6, exon 19x of COL4A7, exon 20x of COL4A8, exon 21x of COL4A9, exon 22x of COL4A10, exon 23x of COL4A11, exon 24x of COL4A12, exon 25x of COL4A13, exon 26x of COL4A14, exon 27x of COL4A15 exon 41x, 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, S Exon 20x sequence upstream (or 5') of the 3' end of pre-mRNA of exon 20x of CN8A, 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.

[0143]

[0144]

[0145] Protein expression

[0146] In some embodiments, the methods described herein are 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 protein or RNA production. As used herein, the term "functional" refers 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, PC activity or functional amount of CB, 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,The condition or disease is, for example, Alport syndrome; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmic 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 type 7 with febrile seizures +; 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's ataxia; Friedreich's ataxia with preserved reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6 reactive and non-reactive homocystinuria; autosomal recessive HSAN2D; congenital analgesia; 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 acidemia; 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; Be ckwith-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 retinal atrophy-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 functional portion 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, PLCB 1. The amount of 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 produced. As used herein,The term "partially functional" refers 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, Any amount of activity or function of 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 is less than the amount of activity or function required to eliminate or prevent any one or more symptoms of the disease or condition. In some embodiments, a 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 a fully functional protein or RNA.

[0147] In some embodiments, the method is a method of increasing a gene encoding a gene 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, P KP2, 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 Subject cells containing pre-mRNA of NIE expressed 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,The subject has Alport syndrome; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmic 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 type 7 with febrile seizures +; 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's ataxia; Friedreich's ataxia with preserved reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6 reactive and non-reactive homocystinuria; autosomal recessive HSAN2D; congenital analgesia; 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 acidemia; 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; Be ckwith-Wiedemann syndrome; Stargardt disease3; Tay-Sachs disease; tuberous sclerosis; tyrosinemia type I; Wagner syndrome1; West syndrome; Wolfram syndrome2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant deafness13; cone-rod retinal atrophy-2; autosomal dominant deafness4A; peripheral neuropathy, myopathy, hoarseness, and hearing loss; autosomal dominant deafness22; neurofibromatosis type 2; NASH; or autosomal dominant mental retardation5,The above diseases are mediated 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, and PR Insufficient activity of PF3, 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 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, Insufficient amounts of 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 are caused by 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, PRPF 3. haploinsufficiency of 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 an embodiment,The subject has genes 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, PLC The first of B1, 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. 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, a second allele of a 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 genes 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, PLC The first allele of B1, 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 Genes and 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, a second allele of a 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 genes 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, PLCB 1. The first allele of 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 and encoding 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, a second allele of a 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 targeting portion of a pre-mRNA containing NIE transcribed from the second allele,Thereby inducing pseudo exon skipping from the exon of this pre-mRNA and causing the encoding 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 Increased levels of mature mRNA of proteins, as well 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, PKP in the subject cells. 2. Increased expression of 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. ,

[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, PL The method comprises the step of: in which the subject cell has an AB encoding a protein of the type B protein, wherein the cell has an AB encoding a protein of the type B protein, wherein the cell has an AB encoding a protein of the type B protein, and the cell has an AB encoding a protein of the type B protein. CB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, G RIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX 2. NIE-containing pre-mRNA of 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; arrhythmic 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 1; cognitive impairment with or without cerebral ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epileptic aphasia spectrum; generalized epilepsy type 7 with febrile seizures +; 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's ataxia; Friedreich's ataxia with preserved reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6 reactive and non-reactive homocystinuria; autosomal recessive HSAN2D; congenital analgesia; 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 acidemia; 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; Soto s 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 retinotrophic atrophy-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, which is caused 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, and 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 activity was not detected. 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 deficiency is caused by autosomal recessive inheritance. ;

[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, PL The method comprises the step of: in which the subject cell has an AB encoding a protein of the type B protein, wherein the cell has an AB encoding a protein of the type B protein, wherein the cell has an AB encoding a protein of the type B protein, and the cell has an AB encoding a protein of the type B protein. CB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, G RIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX 2. NIE-containing pre-mRNA of 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; arrhythmic 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 1; cognitive impairment with or without cerebral ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epileptic aphasia spectrum; generalized epilepsy type 7 with febrile seizures +; 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's ataxia; Friedreich's ataxia with preserved reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6 reactive and non-reactive homocystinuria; autosomal recessive HSAN2D; congenital analgesia; 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 acidemia; 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; Soto s 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 retinotrophic atrophy-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 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, PKP 2. The activity of 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 not 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 deficiency is caused by autosomal dominant 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, PL The method comprises the step of: in which the subject cell has an AB encoding a protein of the type B protein, wherein the cell has an AB encoding a protein of the type B protein, wherein the cell has an AB encoding a protein of the type B protein, and the cell has an AB encoding a protein of the type B protein. CB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, G RIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX 2. NIE-containing pre-mRNA of 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; arrhythmic 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 1; cognitive impairment with or without cerebral ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epileptic aphasia spectrum; generalized epilepsy type 7 with febrile seizures +; 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's ataxia; Friedreich's ataxia with preserved reflexes; galactose epimerase deficiency; primary congenital glaucoma 3, E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6 reactive and non-reactive homocystinuria; autosomal recessive HSAN2D; congenital analgesia; 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 acidemia; 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; Soto s 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 retinotrophic atrophy-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, which is caused 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, and 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 activity was not detected. 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 deficiency is caused by X-linked dominant inheritance. ;

[0151] 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 The subject cells have genes 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, NIE-containing pre-mRNA of 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,The subject had positive results 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, TOP Deficiency in the amount or function of an ORS, 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, e.g., Alport syndrome; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmic 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 type 7 with febrile seizures +; 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's ataxia; Friedreich's ataxia with preserved 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 analgesia; 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 acidemia; 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; Be ckwith-Wiedemann syndrome; Stargardt disease3; Tay-Sachs disease; tuberous sclerosis; tyrosinemia type I; Wagner syndrome1; West syndrome; Wolfram syndrome2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant deafness13; cone-rod retinal atrophy-2; autosomal dominant deafness4A; peripheral neuropathy, myopathy, hoarseness, and hearing loss; autosomal dominant deafness22; neurofibromatosis type 2; NASH; or autosomal dominant mental retardation5.

[0152] In some embodiments, a pre-mRNA transcript containing NIE that encodes a protein that causes a disease or condition is targeted by an ASO described herein. In some embodiments, a pre-mRNA transcript containing NIE that encodes a protein that does not cause a disease is targeted by the ASO. For example, a disease that is the result of a mutation or deficiency in a first protein in a particular pathway can be ameliorated by targeting a pre-mRNA containing NIE that encodes a second protein, thereby increasing the amount of production of the second protein. In some embodiments, the function of the second protein is able to compensate for the mutation or deficiency of the first protein (which causes the disease or condition).

[0153] In some embodiments, the subject has:

[0154] (a) a first mutant allele, wherein

[0155] (i) Generate 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, P The level of RPF31, 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.

[0156] (ii) producing 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, or

[0157] (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, P RPF3, 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

[0158] (b) a second mutant allele, wherein

[0159] (i) Generate 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, P The level of RPF31, 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.

[0160] (ii) producing 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, or

[0161] (iii) Does not produce ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, F AH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB 1. 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

[0162] wherein the NIE-containing pre-mRNA is transcribed from the first allele and / or the second allele. In these embodiments, the ASO binds to the targeting portion of the NIE-containing pre-mRNA transcribed from the first allele or the second allele, thereby inducing pseudo-exon crossing from the exon of the NIE-containing pre-mRNA and causing the coding 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, O Increased levels of mRNA for PTN, 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 increased expression of target protein or functional RNA in cells of the subject. In these embodiments, the target protein or functional RNA whose expression level is increased by exon spanning from the NIE-containing pre-mRNA by the pseudo-exon can be a form with reduced function compared to the equivalent wild-type protein (partial functionality), or a form with full function compared to the equivalent wild-type protein (full functionality).

[0163] In some embodiments, the present invention relates to a protein encoding a gene expressed in a control cell (e.g., a cell not treated with an antisense oligomer or a cell not treated with an antisense oligomer) comprising 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, OPT N, 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 SYNGA 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, P Compared with the amount of mRNA for KP2, 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,Coding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, G ALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PR The levels of mRNA for PF31, 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 increased by 1.1- to 10-fold.

[0164] In some embodiments, a subject treated using the methods of the present disclosure expresses 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, PC CA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCA N, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2 or SYNGAP1 eggs White, among which the functional part is 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, PR PF31, 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 frameshift mutations, nonsense mutations, missense mutations, or partial gene deletions.In some embodiments, a subject treated using the methods of the present disclosure expresses a nonfunctional 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, among which The nonfunctional 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, RA I1, 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 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, PC Whole-gene deletion of CB, 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.

[0165] Exon Contains

[0166] As used herein, "pre-mRNA containing NIE" is a pre-mRNA transcript containing at least one pseudo exon. Alternative or abnormal splicing can result in the inclusion of at least one pseudo exon in the mature mRNA transcript. The terms "mature mRNA" and "fully spliced ​​mRNA" are used interchangeably herein to describe fully processed mRNA. The inclusion of at least one pseudo exon can be a non-productive mRNA and result in NMD of the mature mRNA. Mature mRNA containing NIE can sometimes result in abnormal protein expression.

[0167] In some embodiments, the included pseudo exon is the most abundant pseudo exon in a population of pre-mRNAs containing NIE transcribed from a gene encoding a target protein in a cell. In some embodiments, the included pseudo exon is the most abundant pseudo exon in a population of pre-mRNAs containing NIE transcribed from a gene encoding a target protein in a cell, wherein the population of pre-mRNAs containing NIE comprises two or more included pseudo exons. In some embodiments, an antisense oligomer targeting the most abundant pseudo exon in a population of pre-mRNAs containing NIE encoding a target protein induces exon spanning of one or two or more pseudo exons in the population, including the pseudo exon targeted or bound by the antisense oligomer. In some embodiments, the targeted region is in a pseudo exon 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, PL The most abundant pseudo-exons in NIE-containing pre-mRNAs of CB1, 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.

[0168] The extent of exon inclusion can be expressed as a percentage of exon inclusion, e.g., the percentage of transcripts that include a given pseudo exon. 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.

[0169] In some embodiments, an included pseudo-exon is an exon identified as an included pseudo-exon based on a determination that it is 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% contained. In embodiments, the included pseudo exons are based on determining about 5% to about 100%, about 5% to about 95%, about 5% to about 90%, about 5% to about 85%, about 5% to about 80%, about 5% to about 75%, about 5% to about 70%, about 5% to about 65%, about 5% to about 60%, about 5% to about 55%, about 5% to about 50%, about 5% to about 45%, about 5% to about 40%, about 5% to about 35%, about 5% to about 30%, about 5% to about 25%, about 5% to about 20%, about 5% to about 15%, about 10% to about 100%, about 10% to about 95%, about 15% to about 100%, about 10% to about 95%, about 10% to about 100%. 0% to about 90%, about 10% to about 85%, about 10% to about 80%, about 10% to about 75%, about 10% to about 70%, about 10% to about 65%, about 10% to about 60%, about 10% to about 55%, about 10% to about 50%, about 10% to about 45%, about 10% to about 40%, about 10% to about 35%, about 10% to about 30%, about 10% to about 25%, about 10% to about 20%, about 15% to about 100%, about 15% to about 95%, about 15% to about 90%, about 15% to about 85%, about 15% to about 80%, about 15% to about 75 %, about 15% to about 70%, about 15% to about 65%, about 15% to about 60%, about 15% to about 55%, about 15% to about 50%, about 15% to about 45%, about 15% to about 40%, about 15% to about 35%, about 15% to about 30%, about 15% to about 25%, about 20% to about 100%, about 20% to about 95%, about 20% to about 90%, about 20% to about 85%, about 20% to about 80%, about 20% to about 75%, about 20% to about 70%, about 20% to about 65%, about 20% to about 60%, about 20% to about 55%, about 20% to about From about 25% 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% of the exons included are identified as included pseudo exons.ENCODE data (e.g., 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.

[0170] In some embodiments, the cell is contacted with 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, An ASO targeting a complementary portion of the 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, compared to the amount of protein produced by cells in the absence of the ASO / treatment.Leading to the production 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, SCN 8A, 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 at least 10%, 20%, 30%, 40%, 50%, 60%, 80%, 100%, 150%, 200%, 250%, 300%, 350%, 400%, 450%, 500%, or 1000%. In some embodiments, the amount of the target protein produced by the control compound is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 80%, 100%, 150%, 200%, 250%, 300%, 350%, 400%, 450%, 500%, or 1000%.The cells contacted by the antisense oligomer 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, and ME CP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN 8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DN The total amount of AJC8, MYH14, MYO6, 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%, From about 20% to about 250%, from about 50% to about 100%, from about 50% to about 150%, from about 50% to about 200%, from about 50% to about 250%, from about 100% to about 150%, from about 100% to about 200%, from about 100% to about 250%, from about 150% to about 200%, from about 150% to about 200%, from about 150% to about 250%, from 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, the amount of target protein produced by a control compound is compared to the amount produced by a control compound.The cells contacted by the antisense oligomers 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, MA PK3, 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, CD The total amount of 46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein increases by about 1.1 to about 10 times, about 1.5 to about 10 times, about 2 to about 10 times, about 3 to about 10 times, about 4 to about 10 times, about 1.1 to about 5 times, ... The control compound can be, for example, an oligonucleotide that is not complementary to the targeting portion of the pre-mRNA.

[0171] In some embodiments, the cell is contacted with 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 transcripts The complemented ASO resulted in increased expression of proteins 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, OP A1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, T SC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA,In some embodiments, the amount 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, N SD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, T OPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK 11. The amount of mRNA encoding PPARA, CYP2J2 or SYNGAP1 protein, or 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, TSC 2. 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, the amount of mature 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 produced in cells contacted with the antisense oligomer is compared to the amount of mature RNA produced in untreated cells, such as untreated cells or cells treated with a control compound. , MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SC N9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3 C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein mRNA or 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, and KC NQ2, 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 for 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 300%. 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, the amount of mature RNA 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, RB mRNA encoding FOX2, 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 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, RBFOX 2. SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE 3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK 3. The total amount of mature mRNA of ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2 or SYNGAP1 protein increases by about 1.1 to about 10 times, about 1.5 to about 10 times, about 2 to about 10 times, about 3 to about 10 times, about 4 to about 10 times, about 1.1 to about 5 times, about 1.1 to about 6 times, about 1.1 to about 7 times, about 1.1 to about 8 times, about 1.1 to about 10 times, about 1.1 to about 15 times, about 1.1 to about 16 times, about 1.1 to about 17 times, about 1.1 to about 18 times, about 1.1 to about 19 times, about 1.1 to about 20 times, about 1.1 to about 21 times, about 1.1 to about 22 times, about 1.1 to about 23 times, about 1.1 to about 24 times, about 1.1 to about 25 times, about 1.1 to about 26 times, about 1.1 to about 27 times, about 1.1 to about 28 times, about 1.1 to about 29 times, about 1.1 to about 30 ... about 9 times, about 2 to about 5 times, about 2 to about 6 times, about 2 to about 7 times, about 2 to about 8 times, about 2 to about 9 times, about 3 to about 6 times, about 3 to about 7 times, about 3 to about 8 times, about 3 to about 9 times, about 4 to about 7 times, about 4 to about 8 times, about 4 to about 9 times, at least about 1.1 times, at least about 1.5 times, at least about 2 times, at least about 2.5 times, at least about 3 times, at least about 3.5 times, at least about 4 times, at least about 5 times, or at least about 10 times. A control compound can be, for example, 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, M UT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, S HANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6,Oligonucleotides complementary to the targeted portion of NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 pre-mRNA.

[0172] 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 portion of an intron. In some embodiments, the NIE can be the 5' terminal portion of an intron comprising a 5'ss sequence. In some embodiments, the NIE can be the 3' terminal portion of an intron comprising a 3'ss sequence. In some embodiments, the NIE can be a portion within an intron that does not comprise a 5'ss sequence. In some embodiments, the NIE can be a portion within an intron that does not comprise a 3'ss sequence. In some embodiments, the NIE can be a portion within an intron that does not comprise a 5'ss or 3'ss sequence. In some embodiments, the length of the NIE can be 5 nucleotides to 10 nucleotides, 10 nucleotides to 15 nucleotides, 15 nucleotides to 20 nucleotides, 20 nucleotides to 25 nucleotides, 25 nucleotides to 30 nucleotides, 30 nucleotides to 35 nucleotides, 35 nucleotides to 40 nucleotides, 40 nucleotides to 45 nucleotides, 45 nucleotides to 50 nucleotides, 50 nucleotides to 55 nucleotides, 55 nucleotides to 60 nucleotides, 60 nucleotides to 65 nucleotides, 65 nucleotides to 70 nucleotides, 70 nucleotides to 75 nucleotides, 75 nucleotides to 80 nucleotides, 80 nucleotides to 85 nucleotides, 85 nucleotides to 90 nucleotides, 90 nucleotides to 95 nucleotides, or 95 nucleotides to 100 nucleotides. In some embodiments, the length of the NIE may 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 may 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 may be longer than 1,000 nucleotides.

[0173]

[0174] Therapeutic agents

[0175] In various embodiments of the present disclosure, compositions and methods comprising therapeutic agents are provided to modulate 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, Protein expression levels of 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 to modulate 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. In some embodiments,This article provides information on the expression of proteins 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, and 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 induce exon skipping in splicing, such as in ABCB4, ASS1, ATP8B, or SYNGAP1. 1. 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, SC Compositions and methods for inducing the crossing of pseudo exons during splicing of N8A, 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, in other embodiments, therapeutic agents can be used to induce the inclusion of exons so as to reduce protein expression levels. ,

[0176] The therapeutic agent disclosed herein may be a NIE inhibitor. The therapeutic agent may comprise a polynucleic acid polymer.

[0177]

[0178] When referring to reducing NIE inclusion in mature mRNA, the reduction can be complete, such as 100%, or can be partial. The reduction can be clinically significant. The reduction / correction can be relative to the level of NIE inclusion in an untreated subject, or relative to the amount of NIE inclusion in a population of similar subjects. The reduction / correction can be at least 10% lower NIE inclusion relative to an average subject or a subject before treatment. The reduction can be at least 20% lower NIE inclusion relative to an average subject or a subject before treatment. The reduction can be at least 40% lower NIE inclusion relative to an average subject or a subject before treatment. The reduction can be at least 50% lower NIE inclusion relative to an average subject or a subject before treatment. The reduction can be at least 60% lower NIE inclusion relative to an average subject or a subject before treatment. The reduction can be at least 80% lower NIE inclusion relative to an average subject or a subject before treatment. The reduction can be at least 90% lower NIE inclusion relative to an average subject or a subject before treatment.

[0179] When it comes to increased activity 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, The increase can be clinically significant when the level of 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 measured.The increase can be relative to the activity in untreated subjects 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, PK P2, 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 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, PKP 2. 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 amount.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, P CCB, 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. 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, P CCB, 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.The increase can be at least 40% 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, P CCB, 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. The increase can be at least 50% 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, P CCB, 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.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, P CCB, 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. 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, P CCB, 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.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, P CCB, 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. 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, P CCB, 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.

[0180] In embodiments where the NIE inhibitor comprises a polynucleic acid polymer, the polynucleic acid polymer may be about 50 nucleotides in length. The polynucleic acid polymer may be about 45 nucleotides in length. The polynucleic acid polymer may be about 40 nucleotides in length. The polynucleic acid polymer may be about 35 nucleotides in length. The polynucleic acid polymer may be about 30 nucleotides in length. The polynucleic acid polymer may be about 24 nucleotides in length. The polynucleic acid polymer may be about 25 nucleotides in length. The polynucleic acid polymer may be about 20 nucleotides in length. The polynucleic acid polymer may be about 19 nucleotides in length. The polynucleic acid polymer may be about 18 nucleotides in length. The polynucleic acid polymer may be about 17 nucleotides in length. The polynucleic acid polymer may be about 16 nucleotides in length. The polynucleic acid polymer may be about 15 nucleotides in length. The polynucleic acid polymer may be about 14 nucleotides in length. The polynucleic acid polymer may be about 13 nucleotides in length. The polynucleic acid polymer may be about 12 nucleotides in length. The polynucleic acid polymer may be about 11 nucleotides in length. The polynucleic acid polymer may be about 10 nucleotides in length. The polynucleic acid polymer may be about 10 to about 50 nucleotides in length. The length of the polynucleic acid polymer may be about 10 to about 45 nucleotides. The length of the polynucleic acid polymer may be about 10 to about 40 nucleotides. The length of the polynucleic acid polymer may be about 10 to about 35 nucleotides. The length of the polynucleic acid polymer may be about 10 to about 30 nucleotides. The length of the polynucleic acid polymer may be about 10 to about 25 nucleotides. The length of the polynucleic acid polymer may be about 10 to about 20 nucleotides. The length of the polynucleic acid polymer may be about 15 to about 25 nucleotides. The length of the polynucleic acid polymer may be about 15 to about 30 nucleotides. The length of the polynucleic acid polymer may be about 12 to about 30 nucleotides.

[0181] 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, e.g., 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.

[0182] The sequence of the polynucleic acid polymer may have 4 or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer may have 3 or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer may have 2 or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer may have 1 or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer may have no mismatches with the target sequence of the pre-mRNA transcript.

[0183] The polynucleic acid polymer can specifically hybridize to 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.

[0184] 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 to a sequence selected from SEQ ID NOs: 60-191. The polynucleic acid polymer may comprise a sequence having 100% sequence identity to a sequence selected from SEQ ID NOs: 60-191.

[0185] When referring to a polynucleic acid polymer sequence, the skilled person will understand that one or more substitutions, optionally two substitutions, can be tolerated in the sequence so that it retains the ability to hybridize to the target sequence; or the ability to be recognized as a target sequence when the substitution is in the target sequence. References 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 work. In other embodiments, according to the present disclosure, the sequence can have 98% identity and still work. In another embodiment, according to the present disclosure, the sequence can have 95% identity and still work. In another embodiment, according to the present disclosure, the sequence can have 90% identity and still work.

[0186] Antisense oligomers

[0187] Provided herein is a composition comprising an antisense oligomer that binds to 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 pre-mRNA to induce exon skipping.As used herein, the terms "ASO" and "antisense oligomer" are used interchangeably and refer to an oligomer, such as a polynucleotide, comprising a nucleobase that binds to a target nucleic acid (e.g., 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, The ASO may have an exact sequence complementary to the target sequence or close complementarity (e.g., sufficient complementarity to bind to the target sequence and enhance splicing at the splice site). ASOs are designed so that they bind (hybridize) to a target nucleic acid (e.g., a targeting 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 sequences of a limited number of non-target nucleic acids (some sites other than the target nucleic acid). The design of ASOs may take into account the presence of nucleic acid sequences of the targeting portion of the pre-mRNA transcript, or sufficiently similar nucleic acid sequences at other positions in the genome or cell pre-mRNA or transcriptome, so that the possibility that the ASO will bind to other sites and cause an "off-target" effect is limited. Any antisense oligomer known in the art, such as in PCT application PCT / US2014 / 054151 (which is incorporated herein by reference) entitled "Reducing Nonsense-Mediated mRNA Decay" disclosed as WO 2015 / 035091, may be used to implement the methods described herein.

[0188] In some embodiments, the ASO "specifically hybridizes" or is "specific" to a target nucleic acid or a targeting portion of a pre-mRNA containing NIE. Typically, such hybridization occurs with a T of substantially greater than 37°C, preferably at least 50°C, and typically from 60°C to about 90°C. m Such hybridization preferably corresponds to stringent hybridization conditions. At a given ionic strength and pH, T m The temperature at which 50% of the target sequence hybridizes to the complementary oligonucleotide.

[0189] When hybridization occurs in an antiparallel configuration between two single-stranded polynucleotides, oligomers such as oligonucleotides are "complementary" to each other. If hybridization can occur between one strand of a first polynucleotide and a second polynucleotide, a double-stranded polynucleotide can be "complementary" to another polynucleotide. Complementarity (the degree to which one polynucleotide is complementary to another) is quantifiable according to the ratio (e.g., percentage) of bases in the relative strands that are expected to form hydrogen bonds with each other according to generally accepted base pairing principles. The sequence of an antisense oligomer (ASO) does not have to be 100% complementary to the sequence of its target nucleic acid in order to hybridize. In certain embodiments, the ASO may 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, 18 of the 20 nucleobases of an oligomer compound are complementary to the target region and will therefore specifically hybridize to an ASO that will exhibit 90% complementarity. In this example, the remaining non-complementary nucleobases can be clustered together or interspersed with complementary nucleobases, and need not be adjacent to each other or to complementary nucleobases. The percentage of complementarity of an ASO to a region of a target nucleic acid can be determined routinely using BLAST programs (Basic Local Alignment Search Tool) and PowerBLAST programs known in the art (Altschul et al., J. Mol. Biol., 1990, 215, 403-410; Zhang and Madden, Genome Res., 1997, 7, 649-656).

[0190] ASOs do not need to hybridize to all nucleobases in the target sequence, and the nucleobases hybridized thereto may be continuous or discontinuous. ASOs may hybridize to one or more segments of the pre-mRNA transcript such that intervening or adjacent segments do not participate in the hybridization event (e.g., a loop structure or a hairpin structure may be formed). In certain embodiments, ASOs hybridize to discontinuous nucleobases in the target pre-mRNA transcript. For example, ASOs may hybridize to nucleobases in the pre-mRNA transcript that are separated by one or more nucleobases that do not hybridize to the ASO.

[0191] The ASOs described herein comprise a nucleobase complementary to a nucleobase present in a target portion of a pre-mRNA containing NIE. The term ASO is embodied as an oligonucleotide and any other oligomeric molecule comprising a nucleobase capable of hybridizing with a complementary nucleobase on a target mRNA but not comprising a sugar moiety such as a peptide nucleic acid (PNA). The ASO may 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 a modified backbone. In some embodiments, all nucleotides of the ASO are modified nucleotides. Chemical modifications of ASOs or components of ASOs that are compatible with the methods and compositions described herein will be apparent to those skilled in the art and can be found, for example, in U.S. Pat. No. 8,258,109 B2, U.S. Pat. No. 5,656,612, U.S. Pat. Publication No. 2012 / 0190728, and Dias and Stein, Mol. Cancer Ther. 2002, 347-355, which are incorporated herein by reference in their entireties.

[0192] The one or more nucleobases of the ASO can be any naturally occurring, unmodified nucleobase, such as adenine, guanine, cytosine, thymine and uracil, or any synthetic or modified nucleobase that is sufficiently similar to an unmodified nucleobase to enable it to hydrogen bond with a nucleobase present on the target pre-mRNA. Examples of modified nucleobases include, but are not limited to, hypoxanthine, xanthine, 7-methylguanine, 5,6-dihydrouracil, 5-methylcytosine and 5-hydroxymethylcytosine.

[0193] The ASOs described herein also include a backbone structure that connects the components of the oligomer. The terms "backbone structure" and "oligomer connection" are used interchangeably and refer to the connection between the monomers of the ASO. In naturally occurring oligonucleotides, the backbone includes a 3'-5' phosphodiester bond that connects the sugar portion of the oligomer. The backbone structure or oligomer connection of the ASOs described herein may include, but is not limited to, phosphorothioates, phosphorodithioates, selenophosphates, diselenphosphates, phosphoroanilothioate, phosphoraniladate, phosphoramidates, and the like. 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. Pat. No. 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 acids (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.

[0194] In some embodiments, the stereochemistry at the bond between each phosphorus nucleotide of the ASO skeleton is random. In some embodiments, the stereochemistry at the bond between each phosphorus nucleotide of the ASO skeleton is controlled and is not random. For example, the U.S. patent application publication number is 2014 / 0194610, "Methods for the Synthesis of Functionalized Nucleic Acids" (which is incorporated herein by reference) describes a method for independently selecting the partiality (handedness) of chirality (chirality) at each phosphorus atom in a nucleic acid oligomer. In some embodiments, the ASO used in the method disclosed herein (including but not limited to any ASO shown in Table 5 and Table 6 herein) includes an ASO with a non-random phosphorus nucleotide bond. In some embodiments, the composition used in the method disclosed herein includes pure diastereoisomerism ASO. In some embodiments, the compositions used in the methods of the present disclosure comprise an ASO 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%.

[0195] In some embodiments, the ASO has a non-random mixture of Rp and Sp configurations at its phosphorus internucleotide bond. 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 chiralphosphorothioate linkages," Nucleic Acids Research 42 (22): 13456-13468, which is incorporated herein by reference). In some embodiments, the ASO used in the methods of the present disclosure (including but not limited to any ASO shown in SEQ ID NOs: 60-191 herein) comprises 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 ASO used in the methods of the present disclosure, including but not limited to any ASO shown herein, comprises a polypeptide having the same structure as that comprising SEQ ID NOs: 60-191. NO:60-191 has a sequence with at least about 80%, 85%, 90%, 95%, 97% or 100% sequence identity over a region of at least 8 consecutive nucleic acids of any one of NO:60-191, comprising about 10% to about 100% Rp, about 15% to about 100% Rp, about 20% to about 100% Rp, about 25% to about 100% Rp, about 30% to about 100% Rp, about 35% to about 100% Rp, about 40% to about 100% Rp, about 45% to about 100% Rp, about 50% to about 100% Rp, about 55% to about 100% Rp, about 56% to about 100% Rp, about 57% to about 100% Rp, about 58% to about 100% Rp, about 59% to about 100% Rp, about 60% to about 100% Rp, about 61% to about 100% Rp, about 62% to about 100% Rp, about 64% to about 100% Rp, about 66% to about 100% Rp, about 67% to about 100% Rp, about 68% to about 100% Rp, about 69% to about 100% Rp, about 70% to about 100% Rp, about 71% to about 100% Rp, about 72% to about 100% Rp, about 73% to about 100% Rp, about 74% to about 100% Rp, about 75% to about 100% Rp, about 76% to about 100% Rp, about 77% to about About 55% to about 100% Rp, about 60% to about 100% Rp, about 65% to about 100% Rp, about 70% to about 100% Rp, about 75% to about 100% Rp, about 80% to about 100% Rp, about 85% to about 100% Rp, about 90% to about 100% Rp or about 95% to about 100% Rp, about 20% to about 80% Rp, about 25% to about 75% Rp, about 30% to about 70% Rp, about 40% to about 60% Rp or about 45% to about 55% Rp, and the rest is Sp.

[0196] In some embodiments, the ASO used in the methods of the present disclosure, including but not limited to any ASO set forth herein, comprises 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, comprises 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 (with 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 ASOs set forth 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 about 10% to about 100% Sp, about 15% to about 100% Sp, about 20% to about 100% Sp, about 25% to about 100% Sp, about 30% to about 100% Sp, about 35% to about 100% Sp, about 40% to about 100% Sp, about 45% to about 100% Sp, about 50% to about 100% Sp, about 55% to about 100% Sp, about 56% to about 100% Sp, about 57% to about 100% Sp, about 58% to about 100% Sp, about 59% to about 100% Sp, about 60% to about 100% Sp, about 61% to about 100% Sp, about 62% to about 100% Sp, about 64% to about 100% Sp, about 65% to about 100% Sp, about 66% to about 100% Sp, about 67% to about 100% Sp, about 68% to about 100% Sp, about 69% to about 100% Sp, about 70% to about 100% Sp, about 71% to about 100% Sp, about 72% to about 100% Sp, about 73% to about 100% Sp, about 74% to about 100% Sp, about 75% to about 100% Sp, about 76% to about 1 About 55% to about 100% Sp, about 60% to about 100% Sp, about 65% to about 100% Sp, about 70% to about 100% Sp, about 75% to about 100% Sp, about 80% to about 100% Sp, about 85% to about 100% Sp, about 90% to about 100% Sp or about 95% to about 100% Sp, about 20% to about 80% Sp, about 25% to about 75% Sp, about 30% to about 70% Sp, about 40% to about 60% Sp or about 45% to about 55% Sp, with the remainder being Rp.

[0197] Any ASO described herein may contain a sugar moiety comprising ribose or deoxyribose as present in naturally occurring nucleotides, or a modified sugar moiety or sugar analog 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-guanidineethyl, 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 a locked nucleic acid (LNA). In some embodiments, the sugar analog contains a morpholine ring, such as diaminophosphorothioate morpholino (PMO). In some embodiments, the sugar moiety comprises a furanose or 2' furanose modification. In some embodiments, the sugar moiety comprises a 2'4'-constrained 2'O-methyloxyethyl (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 are 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 purposes herein.

[0198] In some embodiments, each monomer of the ASO is modified in the same manner, for example, each connection of the backbone of the ASO comprises a phosphorothioate bond, or each ribose sugar moiety comprises 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 comprise a combination of a diaminophosphorothioate bond and a sugar moiety containing a morpholine ring (morpholino). The combination of different modifications of the ASO is referred to as "mixed modification" or "mixed chemistry".

[0199] 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 a 2'MOE modification and a phosphorothioate backbone. In some embodiments, the ASO comprises a diaminophosphorothioate morpholino (PMO). In some embodiments, the ASO comprises a peptide nucleic acid (PNA). Any ASO described herein or any component of an ASO (e.g., a nucleobase, a sugar moiety, a backbone) may be modified to obtain the desired properties or activity of the ASO, or to reduce the undesirable properties or activity of the ASO. For example, an ASO or one or more components of any ASO may be modified to enhance binding affinity to a target sequence on a pre-mRNA transcript; reduce binding to any non-target sequence; reduce degradation by a cellular nuclease (i.e., RNase H); improve the absorption of the ASO into a cell and / or into the nucleus of a cell; change the pharmacokinetics or pharmacodynamics of the ASO; and / or regulate the half-life of the ASO.

[0200] In some embodiments, the ASO is composed of 2'-O-(2-methoxyethyl) (MOE) phosphorothioate modified nucleotides. ASOs composed of such nucleotides are particularly suitable for the methods disclosed herein; oligomers with such modifications have been shown to have significantly enhanced resistance to nuclease degradation and increased bioavailability, making them suitable for oral delivery, for example, in some embodiments described herein. See, e.g., Geary et al., J Pharmacol Exp Ther. 2001; 296(3):890-7; Geary et al., J Pharmacol Exp Ther. 2001; 296(3):898-904.

[0201] Those skilled in the art will be aware of methods for synthesizing ASOs.Alternatively or additionally, ASOs may be obtained from commercial sources.

[0202] 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 referred to as 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. Typically, the region or sequence on the 5' side of a reference point in a nucleic acid is referred to as "upstream," while the region or sequence on the 3' side of a reference point in a nucleic acid is referred to as "downstream." Typically, the 5' direction or 5' end of an mRNA is the position where a start or initiation codon is located, while the 3' end or 3' direction is the position where a stop codon is located. In some aspects, the nucleotides upstream of a reference point in a nucleic acid can be represented by negative numbers, while the nucleotides downstream of the reference point can be represented by positive numbers. For example, a reference point (e.g., an exon-exon junction in an mRNA) can be represented as a "zero" position, and the nucleotide directly adjacent to and upstream of the reference point is represented as a "minus one," e.g., "-1," while the nucleotide directly adjacent to and downstream of the reference point is represented as a "plus one," e.g., "+1."

[0203] In some embodiments, the ASO is complementary to (and binds to) an NIE-containing protein, 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, PK targeting moieties of P2, 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 moiety is expressed in 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, and S Downstream (in the 3' direction) of the 5' splice site (or the 3' end of NIE) of an exon included in CN2A, 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., the direction represented by a positive number relative to the 5' splice site). In some embodiments,The ASO is complementary 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, RB A targeting portion of a pre-mRNA of FOX2, 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 a region of about +1 to about +500 relative to the 5' splice site (or 3' end) of the included exon. In some embodiments,This ASO can complement 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, RBFOX 2. A targeting portion of a pre-mRNA of 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, which is 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 5' splice site (or 3' end) 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 +1 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 +18 +1 to about +0, 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, of the targeting moiety. In some aspects, the ASO is complementary to a targeting moiety within a 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.

[0204] In some embodiments, the ASO is complementary to (and binds to) an NIE-containing protein, 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, A targeting portion of 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, wherein the targeting portion is in a There are NIE 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 upstream (in the 5' direction) of the 5' splice site (or the 3' end) of the exon included in the pre-mRNA (e.g.,In some embodiments, the ASO is complementary to an NIE-containing protein, 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, RAI 1, 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 targeting portion, the targeting portion relative to the 5' splice site (or 3' end) of the included exon about -4 to about -270 region. In some embodiments,This ASO can complement 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, RBFOX 2. A targeting portion of a pre-mRNA of 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, which is within a 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 locus 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 -1 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 -360 340, 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 -18 0, 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. ,

[0205] In some embodiments, the ASO is complementary to an 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, PLCB 1. A targeting portion of a 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, wherein the targeting portion is in a region containing N IE's ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, G BE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, upstream (in the 5' direction) of the 3' splice site (or 5' end) of an exon included in the pre-mRNA of 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 (e.g.,In some embodiments, the ASO is complementary to an NIE-containing protein, 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, RAI 1, 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 targeting portion, the targeting portion relative to the 3' splice site (or 5' end) of the included exon about -1 to about -500 region. In some embodiments,The ASO is complementary to 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 pre-mRNA, the targeting portion being within the -1 to -40,000 region relative to the 3' splice site of the included exon. In some aspects,The ASO is complementary to a 3' splice site 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 -500, about -1 to about -600, about -1 to about -700, about -1 to about -800, about -1 to about -900, about -1 to about -1000, about -1 to about -1500, about -10 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, a targeting moiety within a region. In some aspects, the ASO is complementary to a targeting moiety within a 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.

[0206] In some embodiments, the ASO is complementary to an 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, PLCB 1. 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 targeting sequence, the targeting portion of which is in the presence of N IE's ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, G BE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, downstream (in the 3' direction) of the 3' splice site (5' end) of an exon included in 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 some embodiments, the ASO is complementary to an 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, R AI1, 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 targeting portion that is within 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 3' splice site 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 +600, about +1 to about +700, about +1 to about +800, about +1 to about +900, about +1 to about +1000, about +1 to about +1100, about +1 to about +1200, about +1 to about +1300, about +1 to about +1400, about +1 to about +1500, about +1 to about +1600, about +1 to about +1700, about +1 to about +1800, about +1 to about +1900, about +1 to about +1900 +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 +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 + 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. ,

[0207] In some embodiments, 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, SCN, The targeting portion of the 2A, 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 is within the region of +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 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 pre-mRNA is within the NIE. In some embodiments, the 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, PR The targeted portion of PF3, 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 contains pseudo exon and intron boundaries.

[0208] The ASO can be 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 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 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 bases, 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 2 In some embodiments, the ASO is 18 nucleotides in length. In some embodiments, the ASO is 15 nucleotides in length. In some embodiments, the ASO is 25 nucleotides in length.

[0209] In some embodiments, two or more ASOs are used that have different chemistries but are complementary to the same targeting moiety of a pre-mRNA containing NIE. In some embodiments, two or more ASOs are used that are complementary to different targeting moieties of a pre-mRNA containing NIE.

[0210] In some embodiments, the antisense oligonucleotide of the present disclosure is chemically connected to one or more parts or conjugates, for example, a targeting part or other conjugates that enhances the activity of the oligonucleotide or cellular uptake. Such parts include but are not limited to lipid moieties, for example, cholesterol moieties, cholesterol-based moieties, fatty chains, for example, dodecanediol or undecyl residues, polyamines or polyethylene glycol chains or adamantane acetic acid. Oligonucleotides and preparation methods comprising lipophilic moieties have been described in disclosed documents. In embodiments, the antisense oligonucleotide is conjugated to a certain part, which includes but is not limited to abasic nucleotides, polyethers, polyamines, polyamides, peptides, carbohydrates, for example, N-acetylgalactosamine (GalNAc), N-Ac-glucosamine (GluNAc) or mannose (for example, mannose-6-phosphate), lipids or polyhydrocarbon compounds. As understood in the art and described in the literature, for example, a conjugate can be connected to any one or more of any nucleotides constituting the antisense oligonucleotide at any position in a sugar, base or phosphate group. A connector can include a divalent or trivalent branched connector. In an embodiment, the conjugate is attached to the 3' end of the antisense oligonucleotide.Methods of preparing oligonucleotide conjugates are described, for example, in US Patent No. 8,450,467, "Carbohydrate conjugates as delivery agents for oligonucleotides," which is incorporated herein by reference.

[0211] In some embodiments, the nucleic acid targeted by the ASO is 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, containing NIE, expressed in cells such as eukaryotic cells. , 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. 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 separated from a subject. In some embodiments, the cell is in vitro. In some embodiments, the cell is a cell or cell line associated with a condition or disease. In some embodiments, the cell is in vitro (e.g., in cell culture).

[0212] Pharmaceutical composition

[0213] The medicament comprising the composition, such as antisense oligonucleotide and the pharmaceutical composition or preparation for any of the methods can be prepared according to conventional techniques known in the pharmaceutical industry and described in the open literature. In embodiments, the pharmaceutical composition or preparation for treating a subject comprises an effective amount of any antisense oligomer as described herein, or a pharmaceutically acceptable salt, solvate, hydrate or ester thereof. The pharmaceutical preparation comprising the antisense oligomer may further comprise a pharmaceutically acceptable excipient, diluent or carrier.

[0214] Pharmaceutically acceptable salts are suitable for contact with human and lower animal tissues without undue toxicity, irritation, allergic reactions, etc., and correspond to a reasonable benefit / risk ratio. See, for example, SM Berge et al., J. Pharmaceutical Sciences, 66: 1-19 (1977), which is incorporated herein by reference for this purpose. The salt can be prepared in situ during the final separation and purification of the compound, or prepared separately by reacting the free alkali form with a suitable organic acid. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts formed by amino groups with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid, or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid, or by using other recorded methods such as ion exchange salts. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate, and the like. Representative alkali metal or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium salts, etc. Where appropriate, additional pharmaceutically acceptable salts include non-toxic salts formed with ammonium, quaternary ammonium and amine cations using counter ions such as halides, hydroxides, carboxylates, sulfates, phosphates, nitrates, lower alkyl sulfonates and aryl sulfonates.

[0215] In some embodiments, the composition is formulated into any of many possible dosage forms, such as but not limited to tablets, capsules, gel capsules, liquid syrups, soft gels, suppositories and enemas. In embodiments, the composition is formulated as a suspension in an aqueous, non-aqueous or mixed medium. The aqueous suspension may further contain a substance that increases the viscosity of the suspension, including, for example, sodium carboxymethylcellulose, sorbitol and / or dextran. The suspension may also contain a stabilizer. In embodiments, the pharmaceutical preparations or compositions of the present disclosure include, but are not limited to, solutions, emulsions, microemulsions, foams or liposome-containing preparations (e.g., cationic or non-cationic liposomes).

[0216] The pharmaceutical compositions or preparations described herein may include one or more penetration enhancers, carriers, excipients or other active or inactive ingredients that are suitable and well known to those skilled in the art or described in the open literature. In embodiments, liposomes also include sterically stabilized liposomes, for example, liposomes comprising one or more specialized lipids. These specialized lipids result in liposomes with extended circulation life. In embodiments, sterically stabilized liposomes include one or more sugar esters, or are derivatized with one or more hydrophilic polymers such as polyethylene glycol (PEG) moieties. In some embodiments, surfactants are included in the pharmaceutical preparations or compositions. The use of surfactants in pharmaceutical products, preparations and emulsions is well known in the art. In embodiments, the present disclosure uses penetration enhancers to achieve effective delivery of antisense oligonucleotides, for example, to help diffusion across cell membranes and / or to enhance the permeability of lipophilic drugs. In some embodiments, the penetration enhancer is a surfactant, a fatty acid, a bile salt, a chelating agent or a non-chelating non-surfactant.

[0217] In some embodiments, the pharmaceutical formulation comprises a plurality of antisense oligonucleotides. In embodiments, the antisense oligonucleotide is administered in combination with another drug or therapeutic agent.

[0218] Combination therapy

[0219] In some embodiments, the ASO 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 may include small molecules. For example, the one or more additional therapeutic agents may include small molecules described in WO2016128343A1, WO2017053982A1, WO2016196386A1, WO201428459A1, WO201524876A2, WO2013119916A2 and WO2014209841A2, and these applications are incorporated herein by reference in their entirety. In some embodiments, the one or more additional therapeutic agents include ASOs that can be used to correct intron retention.

[0220] Treatment of subjects

[0221] Any composition provided herein can be administered to an individual. "Individual" can be used interchangeably with "subject" or "patient". An individual can be a mammal, such as a human or an animal, such as a non-human primate, a rodent, a rabbit, a rat, a mouse, a horse, a donkey, a goat, a cat, a dog, a cow, a pig, or a sheep. In embodiments, the individual is a human. In embodiments, the individual is a fetus, an embryo, or a child. In other embodiments, the individual can be another eukaryotic organism, such as a plant. In some embodiments, a composition provided herein is administered to an ex vivo cell.

[0222] In some embodiments, the compositions provided herein are applied to an individual as a method for treating a disease or condition. In some embodiments, the individual suffers from a genetic disease, such as any disease described herein. In some embodiments, the individual is at risk of suffering from a disease such as any disease described herein. In some embodiments, the individual suffers from an increased risk of a disease or condition caused by an insufficient amount of protein or insufficient activity of the protein. If an individual suffers from an "increased risk" of a disease or condition caused by an insufficient amount of protein or insufficient activity of the protein, the method includes preventive or preventive treatment. For example, an individual may suffer from an increased risk of such a disease or condition due to a family history of the disease. Typically, individuals with an increased risk of suffering from such a disease or condition benefit from preventive treatment (e.g., by preventing or delaying the onset or progression of the disease or condition). In embodiments, the fetus is treated in utero, for example, by directly or indirectly (e.g., by the mother) applying the ASO composition to the fetus.

[0223] Suitable routes for administering the ASOs of the present disclosure may vary depending on the cell type to which the ASO is to be delivered. A variety of tissues and organs are affected by Dravet syndrome, with the brain being the most severely affected tissue. The ASOs of the present disclosure may be administered to a patient parenterally, for example, by intrathecal, intracerebroventricular, intraperitoneal, intramuscular, subcutaneous, or intravenous injection.

[0224] In an embodiment, the antisense oligonucleotide is administered with one or more agents that can promote the penetration of the antisense oligonucleotide across the blood-brain barrier by any method known in the art. For example, U.S. Pat. No. 6,632,427, "Adenoviral-vector-mediated gene transfer into medullary motor neurons", describes the delivery of agents by administering adenoviral vectors to motor neurons in muscle tissue, which is incorporated herein by reference. For example, U.S. Pat. No. 6,756,523, "Adenovirus vectors for the transfer of foreign genes into cells of the central nervous system particularly in brain", describes the delivery of vectors directly to the brain, e.g., striatum, thalamus, hippocampus or substantia nigra, which is incorporated herein by reference.

[0225] In some embodiments, the antisense oligonucleotide is connected or conjugated to an agent that provides the desired drug or pharmacodynamic properties. In an embodiment, the antisense oligonucleotide is coupled to an antibody to a substance known in the art, such as a transferrin receptor, to promote penetration or transport across the blood-brain barrier. In an embodiment, the antisense oligonucleotide is connected to a viral vector, for example, to make the antisense compound more effective or increase transport across the blood-brain barrier. In an embodiment, 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, styraxol, D(+) arabinose, Primary sugar alcohols, L(-)arabinitol, 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, to assist in permeable blood-brain barrier disruption. Methods and materials for enhancing blood-brain barrier penetration are described, for example, in U.S. Pat. No. 9,193,969, “Compositions and methods for selective delivery of oligonucleotide molecules to specific neuron types,” U.S. Pat. No. 4,866,042, “Method for the delivery of genetic material across the blood brain barrier,” U.S. Pat. No. 6,294,520, “Material for passagethrough the blood-brain barrier,” and U.S. Pat. No. 6,936,589, “Parenteral delivery systems,” each of which is incorporated herein by reference.

[0226] In some embodiments, the ASOs of the present disclosure are coupled to dopamine reuptake inhibitors (DRIs), selective serotonin reuptake inhibitors (SSRIs), norepinephrine reuptake inhibitors (NRIs), norepinephrine-dopamine reuptake inhibitors (NDRIs), and serotonin-norepinephrine-dopamine reuptake inhibitors (SNDRIs) using the methods described, for example, in U.S. Pat. No. 9,193,969, which is incorporated herein by reference.

[0227] In some embodiments, a subject treated using the methods and compositions is assessed for improvement in condition using any method known and described in the art.

[0228] Methods for Identifying Additional ASOs that Induce Exon Skipping

[0229] Also included within the scope of the disclosure are methods for identifying or determining the induction 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, PLC Methods for exon-spanning ASOs of pre-mRNA of B1, 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, a method can include identifying or determining whether an NIE-containing protein induces 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, PL Pseudo-exon spanning ASOs of CB1, 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.ASOs that specifically hybridize to different nucleotides in the target region of the pre-mRNA can be screened to identify or determine the ASOs that improve the splicing rate and / or degree of the target intron. In some embodiments, the ASO can block or interfere with the binding site of the splicing repressor / silencer. Any method known in the art can be used to identify (determine) the ASOs that cause the desired effect (e.g., pseudo exon spanning, protein or functional RNA production) when hybridizing with the target region of the exon. These methods can also be used to identify the ASOs that induce the exon spanning of the included exons by binding to the targeting region in the introns flanking the included exons or in the non-included exons. The following provides examples of methods that can be used.

[0230] A round of screening, known as ASO "walking", can be performed using ASOs designed to hybridize to a target region of a pre-mRNA. For example, the ASOs used in the ASO walk can be tiled every 5 nucleotides from about 100 nucleotides upstream of the 3' splice site of the included exon (e.g., a portion of an exon sequence located upstream of the target / included exon) to about 100 nucleotides downstream of the 3' splice site of the target / included exon, and / or from about 100 nucleotides upstream of the 5' splice site of the included exon to about 100 nucleotides downstream of the 5' splice site of the target / included exon (e.g., a portion of an exon sequence located downstream of the target / included exon). For example, a first ASO of 15 nucleotides in length can be designed to specifically hybridize to +6 to +20 nucleotides relative to the 3' splice site of the target / included exon. A second ASO can be designed to specifically hybridize to +11 to +25 nucleotides relative to the 3' splice site of the target / included exon. The ASO is designed to span the target region of the pre-mRNA. In embodiments, the ASO can be tiled more tightly, for example, every 1, 2, 3 or 4 nucleotides. In addition, the ASO can be tiled from 100 nucleotides downstream of the 5' splice site to 100 nucleotides upstream of the 3' splice site. In some embodiments, the ASO can be tiled from about 1,160 nucleotides upstream of the 5' splice site to about 500 nucleotides downstream of the 3' splice site. In some embodiments, the ASO can be ...

Claims

1. A pharmaceutical composition comprising a therapeutic agent or a vector encoding the therapeutic agent and a pharmaceutically acceptable excipient, wherein the therapeutic agent is used to bind to a targeting portion of a pre-mRNA in a cell, the pre-mRNA comprising a nonsense-mediated mRNA decay-inducing exon (NMD exon) and encoding a target protein, wherein the NMD exon is defined by genomic loci GRCh38 / hg38: chr3 193628509 and GRCh38 / hg38: chr3 193628616, wherein the therapeutic agent is used to promote the exclusion of the NMD exon from the pre-mRNA and increase the level of processed mRNA encoding the target protein, thereby increasing the expression of the target protein in the cell, wherein the target protein is OPA1 protein, wherein the targeting portion of the pre-mRNA (a) is within the NMD exon and spans a region of +1 to +60 nucleotides downstream relative to the 5' end of the NMD exon; or (b) comprises the 3' end of the NMD exon. NMD exon-intron junction; and wherein the therapeutic agent comprises an antisense oligomer consisting of 16 to 50 nucleotides and at least 90% complementary to SEQ ID NO:

173.

2. The pharmaceutical composition of claim 1, wherein the exclusion of the NMD exon from the processed mRNA encoding the target protein is increased by at least about 1.1-fold in cells contacted with the therapeutic agent compared to the exclusion of the NMD exon from the processed mRNA encoding the target protein in control cells.

3. The pharmaceutical composition of claim 1, wherein the level of the processed mRNA encoding the target protein produced in cells contacted with the therapeutic agent is increased by at least about 1.1 times compared to the level of the processed mRNA encoding the target protein in control cells.

4. The pharmaceutical composition of claim 1, wherein the level of the target protein produced in cells contacted with the therapeutic agent is increased by at least about 1.1 fold compared to the level of the target protein produced in control cells.

5. The pharmaceutical composition of claim 1, wherein the therapeutic agent interferes with the binding of a factor involved in splicing of the NMD exon to a region of the targeting moiety. The pharmaceutical composition according to claim 1 , wherein the target protein is a full-length protein or a wild-type protein.

7. The pharmaceutical composition according to claim 1, wherein the pre-mRNA encoding the target protein comprises the sequence of SEQ ID NO:

173.

8. The pharmaceutical composition according to claim 1, wherein the pre-mRNA encoding the target protein is encoded by a gene sequence having 100% sequence identity with the sequence of SEQ ID NO:

12.

9. pharmaceutical composition according to claim 1, wherein the targeting moiety comprises a sequence of at least 8 consecutive nucleic acids containing the sequence of SEQ ID NO:

173.

10. The pharmaceutical composition of claim 1, wherein the targeting moiety comprises the 3' exon-intron junction of the NMD exon.

11. The pharmaceutical composition of claim 1, wherein the targeting moiety is within the NMD exon and spans a region of +1 to +50 nucleotides downstream relative to the 5' end of the NMD exon.

12. The pharmaceutical composition of claim 1, wherein the targeting moiety comprises about 5 or more consecutive nucleotides of the NMD exon.

13. The pharmaceutical composition of claim 1, wherein the antisense oligomer comprises a backbone modification comprising a phosphorothioate bond or a phosphorodiamidate bond.

14. The pharmaceutical composition of claim 1, wherein the antisense oligomer comprises a phosphorothioate bond.

15. The pharmaceutical composition of claim 1, wherein the antisense oligomer comprises a phosphorodiamidate morpholino, a locked nucleic acid, a peptide nucleic acid, a 2'-O-methyl, a 2'-fluoro, or a 2'-O-methoxyethyl moiety.

16. The pharmaceutical composition of claim 1, wherein the antisense oligomer comprises a 2'-O-methoxyethyl moiety.

17. The pharmaceutical composition of claim 1, wherein the antisense oligomer comprises at least one modified sugar moiety.

18. The pharmaceutical composition of claim 17, wherein each sugar moiety is a modified sugar moiety.

19. The pharmaceutical composition of claim 1, wherein the antisense oligomer is 16 to 30 nucleotides in length.

20. Use of the pharmaceutical composition according to any one of claims 1-19 in the preparation of a medicament for treating a disease or condition in a subject in need thereof, wherein the disease or condition comprises type 1 optic atrophy.

21. The use according to claim 20, wherein the subject is a human.

22. The use according to claim 20, wherein the subject is a non-human animal.

23. The use according to claim 20, wherein the subject is a fetus, an embryo or a child.

24. The use according to claim 20, wherein the cells are isolated.

25. The use according to claim 20, wherein the therapeutic agent is administered to the subject by intrathecal injection, intracerebroventricular injection, intraperitoneal injection, intramuscular injection, subcutaneous injection, intravitreal injection or intravenous injection.

Images