Identification of cell type-specific insulin responsive quantitative trait loci in human skeletal muscle

About This Grant

PROJECT SUMMARY/ABSTRACT Type 2 diabetes (T2D) is a complex polygenic disease that results from a multifactorial interaction of environ- ment and lifestyle factors. The estimated heritability of T2D ranges from 30 – 70%, and over 1,000 independ- ent genetic loci have been associated with T2D. However, most loci map to non-coding regions of the genome, leading to challenges elucidating their functional significance. Non-coding genetic variation has the most proxi- mal effect on the molecules bound to DNA (epigenome), which in turn influences the expression of target genes (transcriptome) in a cell-type and context specific manner. A powerful approach to mechanistically link these layers is through identification of quantitative trait loci (QTL) for epigenomic modalities such as chromatin accessibility QTL (caQTL) and gene expression quantitative trait loci (eQTL), followed by testing whether dis- ease associated loci underlie the molecular QTL. In the current study, we will identify cell type-specific and dy- namic molecular response QTLs (rQTLs) in humans in vivo that are relevant to skeletal muscle insulin re- sistance, a core pathophysiologic defect in T2D and related comorbidities. Skeletal muscle accounts for ap- proximately 80% of all glucose uptake in the postprandial state in humans. We and others have shown that skeletal muscle insulin resistance predates glucose intolerance in normoglycemic individuals at high risk of de- veloping T2D, and is evident decades before β-cell failure and overt hyperglycemia develops. In preliminary studies sing single nuclei gene expression (snRNA-Seq) and Assay for Transposase-Accessible Chromatin with Sequencing (ATAC-Seq), we have identified novel response eQTL (r-eQTL) and caQTL (r-caQTL) that are acutely sensitive to insulin during an hyperinsulinemic-euglycemic clamp. These loci include distinct insulin- responsive rQTLs in parenchymal and non-parenchymal cells, including in type 1 and type 2 muscle fiber cells and fibro-adipogenic progenitor cells (FAPs), which are important regulators of muscle homeostasis and regen- eration. In the current application, we build on our pilot data and test the hypothesis that targeted interventional approaches in humans, combined with modern genomic techniques, will uncover novel mechanisms linking common genetic variation to relevant pathophysiological pathways in T2D. In Specific Aim 1, we will Identify cell-type specific insulin responsive molecular QTLs in human skeletal muscle using by collecting muscle biop- sies before and after a hyperinsulinemic-euglycemic insulin clamp (80 mU/m2 ⋅ min). In Specific Aim 2, we will determine acute skeletal muscle insulin resistance molecular QTLs in humans: by using an acute lipotoxicity model of insulin resistance. These studies leverage our unique combined expertise and existing productive col- laboration to integrate whole-body physiological approaches in humans with cutting edge molecular and ge- nomics techniques to reveal dynamic response QTLs that connect disease-relevant metabolic pathways to ge- netic variation.