Targeted augmentation of nuclear gene output

A method of treating a disease or condition in a subject in need thereof, wherein the subject has a deficient amount or activity of a first protein or a first functional RNA;

• wherein the deficient amount or activity of the first protein or the first functional RNA is caused by haploinsufficiency of the first protein or the first functional RNA, the method comprising:
• administering a pharmaceutical composition to the subject, wherein the pharmaceutical composition comprises (i) an antisense oligomer (ASO) or a vector encoding the ASO and (ii) a pharmaceutically acceptable excipient;
• wherein the ASO binds to targeted region of a retained-intron-containing pre-mRNA (MC pre-mRNA) that comprises a retained intron, an exon flanking a 5′ splice site of the retained intron, and an exon flanking a 3′ splice site of the retained intron, and wherein the RIC pre-mRNA encodes a target protein or a target functional RNA;
• wherein the first protein is different from the target protein and the first functional RNA is different from the target functional RNA;
• wherein the ASO increases splicing efficiency of the RIC pre-mRNA by modulating splicing of the retained intron from the RIC pre-mRNA in a cell of the subject as compared to a cell of a subject with the disease or condition that has not been administered the pharmaceutical composition.

A method for identifying from among a set of antisense oligomers (ASOs) an ASO that increases an amount of mRNA encoding a target protein or a target functional RNA by inducing constitutive splicing of a retained intron from a retained-intron-containing pre-mRNA (RIC pre-mRNA) that comprises at least one retained intron and that encodes the target protein or the target functional RNA, wherein the ASOs in the set are tiled every 1 to 5 nucleotides, and wherein each ASO in the set of ASOs hybridizes to a target region of the RIC pre-mRNA that is about 100 nucleotides upstream of the 5′ splice site of the at least one retained intron to about 100 nucleotides downstream of the 5′ splice site of the at least one retained intron;

• or
• about 100 nucleotides upstream of the 3′ splice site of the at least one retained intron to about 100 nucleotides downstream of the 3′ splice site of the at least one retained intron;
• the method comprising:
• (a) delivering a first ASO in the set of ASOs to a cell comprising the RIC pre-mRNA;
• (b) measuring an amount of the RIC pre-mRNA and measuring an amount of mRNA encoding the target protein or the target functional RNA in the cell to which the first ASO was delivered;
• (c) measuring an amount of the RIC pre-mRNA and measuring an amount of mRNA encoding a target protein or a target functional RNA in a control cell;
• and (d) comparing the amounts of the RIC pre-mRNA and the mRNA measured in (b) and (c);
• wherein the first ASO is identified as an ASO that increases an amount of mRNA encoding the target protein or the target functional RNA by inducing constitutive splicing of the at least one retained intron from the RIC pre-mRNA based on an observed decrease in the amount of the RIC pre-mRNA and an observed increase in the amount of mRNA encoding the target protein or the target functional RNA in the cell to which the first ASO was delivered compared to a control cell;
• and repeating steps (a) through (d) with additional ASOs in the set of ASOs as needed to identify an ASO that increases an amount of mRNA from a gene in a cell by inducing constitutive splicing of a retained intron from the RIC pre-mRNA.