Type 2 diabetes (T2D) associated polymorphisms regulate expression of adjacent transcripts in transformed lymphocytes, adipose, and muscle from Caucasian and African-American subjects

Abstract

Context: Genome-wide association scans (GWAS) have identified novel single nucleotide polymorphisms (SNPs) that increase T2D susceptibility and indicated the role of nearby genes in T2D pathogenesis.

Objective: We hypothesized that T2D-associated SNPs act as cis-regulators of nearby genes in human tissues and that expression of these transcripts may correlate with metabolic traits, including insulin sensitivity (S(I)).

Design, settings, and patients: Association of SNPs with the expression of their nearest transcripts was tested in adipose and muscle from 168 healthy individuals who spanned a broad range of S(I) and body mass index (BMI) and in transformed lymphocytes (TLs). We tested correlations between the expression of these transcripts in adipose and muscle with metabolic traits. Utilizing allelic expression imbalance (AEI) analysis we examined the presence of other cis-regulators for those transcripts in TLs.

Results: SNP rs9472138 was significantly (P = 0.037) associated with the expression of VEGFA in TLs while rs6698181 was detected as a cis-regulator for the PKN2 in muscle (P = 0.00027) and adipose (P = 0.018). Significant association was also observed for rs17036101 (P = 0.001) with expression of SYN2 in adipose of Caucasians. Among 19 GWAS-implicated transcripts, expression of VEGFA in adipose was correlated with BMI (r = -0.305) and S(I) (r = 0.230). Although only a minority of the T2D-associated SNPs were validated as cis-eQTLs for nearby transcripts, AEI analysis indicated presence of other cis-regulatory polymorphisms in 54% of these transcripts.

Conclusions: Our study suggests that a small subset of GWAS-identified SNPs may increase T2D susceptibility by modulating expression of nearby transcripts in adipose or muscle.

Fig. 1.

Genotypic association of SNP rs6698181 with the expression of protein kinase N2 (PKN2) transcript in human adipose and muscle. The box plot shows transcript level expression of PKN2 for different genotypes for SNP rs6698181. PKN2 expression is shown after 18S normalization and ln transformation. N = no. of samples. The box represents the interquartile range, which contains 50% of the values. The whiskers are lines that extend the box to the highest and lowest values, excluding outliers. A line across the box indicates the median.

Fig. 2.

Expression of vascular endothelial growth factor A (VEGFA) in adipose and muscle is correlated with metabolic traits. VEGFA expression is shown after 18S normalization and ln transformation. Insulin sensitivity [S_I (×10⁻⁴ · min⁻¹ [μU/ml]⁻¹)] and body mass index (kg/m²) data are shown after ln transformation. Sc. adipose, sc adipose; Sk. muscle, skeletal muscle; r, partial correlation coefficient; p, statistical significance of correlation.

Fig. 3.

rs1043681 is a cis-regulatory SNP for DNAJC11 expression in transformed lymphocyte. SNP rs1043681 in 3′UTR of the DNAJC11 gene allelic expression imbalance in both Caucasian and African-American TLs (A) and also regulates total expression of DNAJC11 (B). A, Allelic ratio of G and A alleles of rs1043681 in genomic DNA (gDNA) and cDNA from heterozygous individuals are shown as evidence of allelic expression imbalance. B, The box plot shows transcript level expression of DNAJC11 for different genotypes for SNP rs1043681. DNAJC11 expression is shown after 18S normalization and ln transformation. N = no. of samples. The box represents the interquartile range, which contains 50% of the values. The whiskers are lines that extend the box to the highest and lowest values, excluding outliers. A line across the box indicates the median.