Host: The Japanese Society of Toxicology
Aberrant alternative RNA splicing regulation is a major cause of genetic diseases, as a recent estimate points out involvement of ~35% of reported mutations in induction of mis-splicing events. Although currently available information for pathogenic mutations are mostly limited to exonic sequences and their vicinity sites owing to a technical limitation of exome sequencing, recent advances in whole genome sequencing shed a light to mutations within deep-intronic sites. Deepintronic mutations may create “pseudo exon”, in which a particular intronic sequence is recognized as an exon due to a cryptic splice site or splice enhancer introduced as a consequence of deepintronic mutations. Inclusion of a pseudo exon induces frameshift and creation of premature stop codon to inhibit expression of a specific gene, leading to pathogenesis. While such pseudo exonic mutations are speculated as major cases for undiagnostic patients of genetic diseases, so far there is no comprehensive investigation for disease-related deep-intronic mutations, and thus their diagnostic applications remain to be achieved. Moreover, pathogenesis-related alternative RNA splicing recently regarded as an attractive therapeutic target, especially after approval of Nusinersen, and characterization of pseudo exonic mutations may also provide a novel therapeutic opportunity. A large scale resources for whole genome sequences, such as Tohoku Medical Megabank Organization (ToMMo), The 1,000 Genome Project, and The GenomeAsia 100K Project, have been developed recently, and current advances in artificial intelligence (AI) technology made it feasible to conduct functional computation for numerous datasets of whole genome sequencing. In this proposal, by taking advantage of whole genome sequence resources and application of AI, we are developing data-driven high-throughput assay system for a comprehensive characterization of deep-intronic mutations, in which AI-based survey for pseudo exonic deep-intronic mutations from ~7,500 whole genome datasets are connected with wet validation in a corresponding donor cells obtained through ToMMo or genome editing. Identified mutations are deposited in a database, and further assessed for diagnostic use by a pseudo exonic mutation array, as well as drug target by a splice-targeting small molecule compounds or antisense nucleotide drugs.
