278-OR: Single-Nucleus Multiomics Profiling across 49 Individuals of Hispanic Ancestry Reveals Cell-Specific Skeletal Muscle Insulin-Responsive Gene Regulatory Signatures

More than 1,000 genome-wide association study (GWAS) signals have been identified for type 2 diabetes (T2D) and related metabolic traits. 90% of these map to non-coding regions. This has obfuscated efforts to establish mechanisms, partly because some variants may impact disease risk in stimulatory rather than basal contexts. To identify these context-specific mechanisms, we performed single-nucleus RNA and ATAC (snRNA, snATAC) profiling on paired vastus lateralis skeletal muscle biopsies before and after four-hour euglycemic hyperinsulinemic clamp in 49 individuals of Hispanic ancestry.

After rigorous quality control, we jointly clustered 62,642 RNA and 91,734 ATAC nuclei (154,376 total) with LIGER from 47 individuals. We identified 15 cell types ranging from type 1 fibers (30.4% of nuclei) to T cells (0.4% of nuclei). We analyzed type 2a fibers (27.1% of nuclei)-a representative, intermediate muscle fiber type. Of 11,228 tested genes, 31.4% (n=3,526) were significantly differentially expressed (FDR <5%), using DESeq2 and adjusting for batch and individual factors. This dramatic transcriptomic response was significantly enriched (FDR <5%) for response to hormone stimulus. Further, of 619,445 tested ATAC peaks, 7.3% (n=45,474) were significantly differentially accessible (FDR <5%). Curiously, these differentially accessible regions (DARs) were enriched for T2D-related GWAS signals such as Stumvoll insulin sensitivity index (ISI) and waist-to-hip ratio, adjusted for BMI-but only in type 2a, and not other muscle fiber types. As an example, the rs12303671-T-G ISI GWAS signal lies in a type 2a-specific DAR, suggesting cell-type-specific regulation under stimulatory contexts at a disease-relevant GWAS signal. We are currently performing expression and chromatin accessibility QTL mapping. These analyses may nominate testable cell- and context-specific mechanisms of T2D risk in skeletal muscle.