Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes

Abstract

Objective: Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired β-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology.

Research design and methods: We have conducted a meta-analysis of genome-wide association tests of ∼2.5 million genotyped or imputed single nucleotide polymorphisms (SNPs) and fasting proinsulin levels in 10,701 nondiabetic adults of European ancestry, with follow-up of 23 loci in up to 16,378 individuals, using additive genetic models adjusted for age, sex, fasting insulin, and study-specific covariates.

Results: Nine SNPs at eight loci were associated with proinsulin levels (P < 5 × 10(-8)). Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has been associated with fasting glucose, one (PCSK1) has been implicated in obesity, and four (TCF7L2, SLC30A8, VPS13C/C2CD4A/B, and ARAP1, formerly CENTD2) increase T2D risk. The proinsulin-raising allele of ARAP1 was associated with a lower fasting glucose (P = 1.7 × 10(-4)), improved β-cell function (P = 1.1 × 10(-5)), and lower risk of T2D (odds ratio 0.88; P = 7.8 × 10(-6)). Notably, PCSK1 encodes the protein prohormone convertase 1/3, the first enzyme in the insulin processing pathway. A genotype score composed of the nine proinsulin-raising alleles was not associated with coronary disease in two large case-control datasets.

Conclusions: We have identified nine genetic variants associated with fasting proinsulin. Our findings illuminate the biology underlying glucose homeostasis and T2D development in humans and argue against a direct role of proinsulin in coronary artery disease pathogenesis.

FIG. 1.

Manhattan plot of the association P values for fasting proinsulin adjusted for fasting insulin. Directly genotyped and imputed SNPs are plotted with their meta-analysis P values (as −log10 values) as a function of genomic position (NCBI Build 36). The SNPs that achieved genome-wide significance (P < 5 × 10⁻⁸) on follow-up are shown in red. Insert: Quantile-quantile (Q-Q) plot for fasting proinsulin adjusted for fasting insulin. The expected null distribution is plotted along the diagonal, the entire distribution of observed P values is plotted in blue, and a distribution that excludes the nine novel findings is plotted in red.

FIG. 2.

Regional plots of eight genomic regions containing novel genome-wide significant associations. For each region, directly genotyped and imputed SNPs are plotted with their meta-analysis P values (as −log10 values) as a function of genomic position (NCBI Build 36). In each panel, the stage 1 discovery SNP taken forward to stage 2 follow-up is represented by a purple diamond (with global meta-analysis P value), with its stage 1 discovery P value denoted by a red diamond with bolded borders. Estimated recombination rates (taken from HapMap) are plotted to reflect the local LD structure around the associated SNPs and their correlated proxies (according to a white to red scale from r² = 0 to 1, based on pairwise r² values from HapMap CEU). Gene annotations were taken from the University of California Santa Cruz genome browser. A: ARAP1 region; B: MADD region; C: PCSK1 region; D: TCF7L2 region; E: VPS13C/C2CD4A/B region; F: SLC30A8 region; G: LARP6 region; H: SGSM2 region.

FIG. 3.

Expression profiles of biologically plausible genes within each associated locus across a range of human tissue types, including islet preparations from three donors. Expression levels determined with respect to the geometric mean of three endogenous control assays. A: ARAP1 region; B: MADD region; C: VPS13C/C2CD4A/B region; D: LARP6 region; E: SGSM2 region. F: Expression levels of genes near the proinsulin-associated variants in human FAC-sorted β-cells. Data are expression means ± SD of the relative expression measured by quantitative PCR obtained from three human nondiabetic donors.