Insomnia is a pervasive sleep disorder affecting up to one-third of the adult U.S. population. An extensive amount of genetic association data from genome wide association studies (GWAS) has uncovered hundreds of loci associated with insomnia and other sleep traits, yet few of these targets have undergone full characterization and their contribution to sleep traits remain poorly understood. Additionally, GWAS does not necessarily determine the true effector gene(s) at a given locus, leading to frequent mischaracterization and misinterpretation of genotype-phenotype interactions.
Our group has developed a variant-to-gene mapping approach that integrates existing insomnia GWAS loci with a combination of ATAC-seq and promoter-focused Capture C-derived data in human induced pluripotent stem cell-derived neural progenitor cells. We identified candidate genes with accessible promoter regions that were contacted at high resolution by insomnia-associated SNPs residing in open chromatin. Target genes with known orthologs and available Drosophila RNAi lines were then subjected to deep phenotyping of sleep traits. Candidate genes producing greater than 20 percent change in sleep duration in Drosophila were then screened in a vertebrate zebrafish model using CRISPR/Cas9 mutagenesis in F0 larvae.
This pipeline revealed fifteen genes producing robust sleep phenotypes with more than a 20 percent change in sleep duration in Drosophila. Of the candidate genes screened thus far in zebrafish, we found that disruption of pigq expression significantly (p>0.05) increased sleep duration in both zebrafish and Drosophila through regulation of sleep bout length and frequency, revealing a conserved, yet novel regulator of sleep duration. Additionally, CRISPR mutations in cbx1b and meis1b in zebrafish resulted in reduced sleep duration similar to results in Drosophila.
This pipeline uses cutting-edge genomic and behavioral approaches to perform high-throughput screening of existing GWAS-identified insomnia loci. This genotype-to-phenotype approach emphasizes the importance of behavioral validation following large cohort studies and narrowed the candidate gene list from more than 200 to fewer than 20 providing a more tractable set of gene targets for further molecular characterization. Cross-species validation also improves our understanding of the conservation of sleep characteristics throughout evolution.
Support (If Any)
NIH grants R01 HL143790, P01 HL094307, T32 HL07953