Combinatorial multiomic analysis from a pedigree of Sox10Dom Hirschsprung mice implicates Dach1 as a modifier of Enteric Nervous System development

BackgroundHirschsprung disease (HSCR) is characterized by absence of enteric ganglia (aganglionosis) along variable lengths of the distal intestine. This disorder results from deficient colonization of fetal intestine by enteric neural crest-derived cells (ENCDCs). HSCR exhibits complex, multifactorial inheritance with penetrance and severity varying widely even within a family. SOX10 is among causal genes that predispose to aganglionosis. Yet, how gene interactions influence severity of HSCR aganglionosis is not understood. We previously used an F1-intercross strategy to map genetic modifiers of aganglionosis in the Sox10Dom HSCR mouse. Here we employ an extended pedigree mapping approach and complementary omics analyses of the developing Enteric Nervous System (ENS) to identify modifier loci that affect severity of HSCR aganglionosis. ResultsTo identify loci that modify aganglionosis extent we undertook genome-wide association study (GWAS) of an extended pedigree of Sox10Dommice on a mixed C57BL/6J x C3HeBFeJLe-a/a background. GWAS uncovered genetic modifiers of aganglionosis severity in this cohort. Within each modifier interval, we prioritize candidate genes based on gene expression in the developing ENS, proximity to open chromatin regions in ENCDCs, and presence of conserved SOX10 binding motifs. This strategy identified known genes in ENS development as well as multiple novel genes. Dach1 emerged as a top priority gene for modifying ENCDCs migration and thus influencing aganglionosis severity. ConclusionsThis study identifies genome intervals and intrinsic genes that modify Sox10Dom aganglionosis severity and that are candidate modifiers of human HSCR severity. AUTHOR SUMMARYHirschsprung disease is a complex genetic neurodevelopmental disorder that causes loss of neurons in the distal bowel. The length of gut lacking neurons, called "aganglionosis", in HSCR patients can vary widely even between affected siblings. Multiple genes are Mendelian causative for HSCR, but little is known about the gene interactions responsible for the notable variation in aganglionosis severity. In this study, we use a mouse model of HSCR to identify genomic regions, "modifiers", associated with length of aganglionosis. Genes active within these regions are then identified in RNA-sequencing and open chromatin data from progenitor cells, which form the enteric nervous system. These omics approaches identify both known and novel genes that can affect enteric neuron development and may underly HSCR severity in patients. Dach1, already known for effects on neuronal progenitor proliferation and migration in other aspects of the nervous system, emerged as the top priority gene. The findings greatly expand the gene network that influences HSCR aganglionosis.