Diabetes Metab J.  2021 Mar;45(2):241-250. 10.4093/dmj.2019.0204.

Enhancer-Gene Interaction Analyses Identified the Epidermal Growth Factor Receptor as a Susceptibility Gene for Type 2 Diabetes Mellitus

• Yang Y
• Yao S
• Ding JM
• Chen W
• Guo Y

• KMID: 2514200
• DOI: http://doi.org/10.4093/dmj.2019.0204

Abstract

Genetic interactions are known to play an important role in the missing heritability problem for type 2 diabetes mellitus (T2DM). Interactions between enhancers and their target genes play important roles in gene regulation and disease pathogenesis. In the present study, we aimed to identify genetic interactions between enhancers and their target genes associated with T2DM.

We performed genetic interaction analyses of enhancers and protein-coding genes for T2DM in 2,696 T2DM patients and 3,548 controls of European ancestry. A linear regression model was used to identify single nucleotide polymorphism (SNP) pairs that could affect the expression of the protein-coding genes. Differential expression analyses were used to identify differentially expressed susceptibility genes in diabetic and nondiabetic subjects.

We identified one SNP pair, rs4947941×rs7785013, significantly associated with T2DM (combined P=4.84×10⁻¹⁰). The SNP rs4947941 was annotated as an enhancer, and rs7785013 was located in the epidermal growth factor receptor (EGFR) gene. This SNP pair was significantly associated with EGFR expression in the pancreas (P=0.033), and the minor allele “A” of rs7785013 decreased EGFR gene expression and the risk of T2DM with an increase in the dosage of “T” of rs4947941. EGFR expression was significantly upregulated in T2DM patients, which was consistent with the effect of rs4947941×rs7785013 on T2DM and EGFR expression. A functional validation study using the Mouse Genome Informatics (MGI) database showed that EGFR was associated with diabetes-relevant phenotypes.

Genetic interaction analyses of enhancers and protein-coding genes suggested that EGFR may be a novel susceptibility gene for T2DM.

Keyword

Diabetes mellitus, type 2; Epistasis, genetic; ErbB receptors; Gene regulatory networks

Figure

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  Fig. 1 Association of the minor allele “A” of rs7785013 with type 2 diabetes mellitus in subjects carrying different genotypes of rs4947941 in the Gene Environment Association Studies (GENEVA) and Institute of Personalized Medicine (IPM) datasets. The odds ratios (ORs) of the association analyses results are shown in the y-axis. TT, subjects carrying “TT” of rs4947941; TC, subjects carrying “TC” of rs4947941; CC, subjects carrying “CC” of rs4947941.

• 

  Fig. 2 Epigenetic annotation for the region surrounding rs4947941 and rs7785013. The topologically associating domain (TAD) data in the GM12878 cell line were downloaded from the Gene Expression Omnibus (GEO) data, GSE63525. TAD-like domains were identified using promoter capture Hi-C in human pancreatic islets. Chromatin interaction data in multiple cell lines were downloaded from the 4DGenome Database. Active histone modifications, including H3k4me1, H3k4me3, and H3k27ac, in pancreatic islets were obtained from the Roadmap Project using the WashU EpiGenome Browser. EGFR, epidermal growth factor receptor.

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  Fig. 3 Association of the minor allele “A” of rs7785013 with the expression of the epidermal growth factor receptor (EGFR) in the pancreas of subjects carrying different genotypes of rs4947941 in the GTEx Pilot Project. The beta values of the association analyses results are shown in the y-axis. CC, subjects carrying “CC” of rs4947941; TC, subjects carrying “TC” of rs4947941; TT, subjects carrying “TT” of rs4947941.

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  Fig. 4 The results of the differential expression analyses of the epidermal growth factor receptor (EGFR) in diabetic and nondiabetic subjects in the (A) GSE76894, (B) GSE25724, (C) GSE12643, and (D) GSE9006 datasets.

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