Genetically-Regulated Mechanisms of Insulin Resistance in Adipose Tissue

Insulin resistance (IR) is a harbinger of type 2 diabetes (T2D) and partly determined by genetic factors. However, genetically-regulated mechanisms of IR remain poorly understood. Using gene expression, genotype, and insulin sensitivity (S_I and Matsuda index from FSIVGT and OGTT) data from an African American cohort (AAGMEx, N=256), we performed transcript-wide association and expression quantitative trait loci (eQTL) analyses to identify IR-associated cis-regulated transcripts (cis-eGenes) in adipose tissue. Data from a European ancestry cohort (METSIM, N=770) was used for testing replication of Matsuda index-associated cis-eGenes. In vitro genetic silencing studies were performed in a human adipocyte model to define the molecular mechanism of selected genes. Expression level of 2724 transcripts in adipose were negatively (1338) or positively (1386) associated (p<0.001) with Matsuda index in both cohorts. In the AAGMEx cohort, we identified cis-eQTLs (FDR<1%) for 786 Matsuda index-associated transcripts. Cis-eQTLs for 510 Matsuda index-associated genes were identified in both the AAGMEx and METSIM cohorts. These genes were enriched for mitochondrial dysfunction, phagosome maturation, and branched-chain amino acid degradation pathways. The enoyl-CoA hydratase domain-containing 3 (ECHDC3) was the top ranked Matsuda index-associated cis-eGene. ECHDC3 expression level was positively correlated with Matsuda index (r=0.47, p=5.3x10^-15) and rs200943982 was the top ECHDC3 cis-eSNP (p=1.94x10^-9) in AAGMEx. The shRNA-mediated silencing of ECHDC3 in SGBS adipocytes reduced insulin-stimulated Akt phosphorylation. RNA-seq analysis identified 691 differentially-expressed genes in ECHDC3 knockdown cells, which were enriched in γ-linolenate and cholesterol biosynthesis, LXR/RXR activation pathways, and known IR genes.

In summary, variation-based genomic analysis with concurrent in vitro genetic silencing studies identified novel genetic regulatory mechanisms of IR.