244-OR: Single Nuclei Chromatin and Transcriptome Profiling across Human and Rat Skeletal Muscle Identifies Regulatory Elements, Genes, and Cell Types Associated with Diabetes GWAS Signals

Abstract

Skeletal muscle is the largest organ, by weight (>40%), in the human body; insulin resistance in this and other peripheral tissues is a hallmark of type 2 diabetes (T2D). Recent genome wide association study (GWAS) results show significant enrichment for fasting insulin single nucleotide polymorphisms (SNPs) in skeletal muscle tissue chromatin-defined regulatory regions. The next steps towards mechanistic translation are identification of causal variants, the target genes these variants regulate, and the specific cell populations in which they function. To accomplish this, we optimized and performed single-nuclei resolution chromatin (snATAC-seq) and transcriptome (snRNA-seq) profiling across human and rat frozen skeletal muscle, collectively measuring ’omic profiles on 38,386 nuclei. We used integrative non-negative matrix factorization for data fusion across ’omics modalities and species, revealing seven distinct clusters that range in abundance from 58% to 2.1% of all nuclei. The clusters are consistent across independent human and rat samples and across ’omic modalities. We find heterogeneity in fasting insulin GWAS enrichment across snATAC peaks for the muscle cell types (2/7 significantly enriched), one of which is mesenchymal stem cells (∼4% of nuclei). We use genetically fine-mapped SNPs from the largest T2D GWAS and find the highest posterior probability 99% credible set SNP (rs702634) out of three at the ARL15 locus resides in a muscle mesenchymal stem cell-specific snATAC peak. We are nearly finished snRNA+snATAC profiling across 400 additional samples, which will enable muscle cell-specific e/chromQTL analyses and GWAS colocalization reports for the ADA meeting. This work represents a unique resource for the genetic signature of skeletal muscle biology at unprecedented epigenomic, transcriptomic, and cellular scales. Disclosure S. Parker: None. Funding American Diabetes Association (1-14-INI-07 to S.P.); National Institutes of Health (R01DK117960)