Genome-wide gene-environment study identifies glutamate receptor gene GRIN2A as a Parkinson's disease modifier gene via interaction with coffee

Abstract

Our aim was to identify genes that influence the inverse association of coffee with the risk of developing Parkinson's disease (PD). We used genome-wide genotype data and lifetime caffeinated-coffee-consumption data on 1,458 persons with PD and 931 without PD from the NeuroGenetics Research Consortium (NGRC), and we performed a genome-wide association and interaction study (GWAIS), testing each SNP's main-effect plus its interaction with coffee, adjusting for sex, age, and two principal components. We then stratified subjects as heavy or light coffee-drinkers and performed genome-wide association study (GWAS) in each group. We replicated the most significant SNP. Finally, we imputed the NGRC dataset, increasing genomic coverage to examine the region of interest in detail. The primary analyses (GWAIS, GWAS, Replication) were performed using genotyped data. In GWAIS, the most significant signal came from rs4998386 and the neighboring SNPs in GRIN2A. GRIN2A encodes an NMDA-glutamate-receptor subunit and regulates excitatory neurotransmission in the brain. Achieving P(2df) = 10(-6), GRIN2A surpassed all known PD susceptibility genes in significance in the GWAIS. In stratified GWAS, the GRIN2A signal was present in heavy coffee-drinkers (OR = 0.43; P = 6×10(-7)) but not in light coffee-drinkers. The a priori Replication hypothesis that "Among heavy coffee-drinkers, rs4998386_T carriers have lower PD risk than rs4998386_CC carriers" was confirmed: OR(Replication) = 0.59, P(Replication) = 10(-3); OR(Pooled) = 0.51, P(Pooled) = 7×10(-8). Compared to light coffee-drinkers with rs4998386_CC genotype, heavy coffee-drinkers with rs4998386_CC genotype had 18% lower risk (P = 3×10(-3)), whereas heavy coffee-drinkers with rs4998386_TC genotype had 59% lower risk (P = 6×10(-13)). Imputation revealed a block of SNPs that achieved P(2df)<5×10(-8) in GWAIS, and OR = 0.41, P = 3×10(-8) in heavy coffee-drinkers. This study is proof of concept that inclusion of environmental factors can help identify genes that are missed in GWAS. Both adenosine antagonists (caffeine-like) and glutamate antagonists (GRIN2A-related) are being tested in clinical trials for treatment of PD. GRIN2A may be a useful pharmacogenetic marker for subdividing individuals in clinical trials to determine which medications might work best for which patients.

Figure 1. Manhattan Plot and QQ Plot of GWAIS.

Panel A depicts the Manhattan plot for the GWAIS (joint test of association and interaction with coffee, 2df, adjusted for sex, age, PC1 and PC2). The novel spike on chromosome 16 corresponds to 12 GRIN2A SNPs that were genotyped. Imputed SNPs achieved P_2df<5×10⁻⁸ (see Table 4). Additive model is shown here, Dominant and Recessive are in Figure S1. Dominant and Additive models yielded similar results for top hits (see Table 1). Panel B is the QQ plot where the observed P values (red line) are plotted against the expected P values under no association (straight black line). The plots were made first by including all genotyped SNPs (red), then excluding those in the SNCA, HLA and MAPT regions (green) and finally by excluding GRIN2A (blue).

Figure 2. GWAS in heavy coffee-drinkers.

Panel A depicts GWAS in heavy coffee drinkers with GRIN2A achieving the lowest P values. The P values in stratified GWAS are for genotyped SNP's main effect on PD risk, adjusted for sex, age, PC1 and PC2. Imputed SNPs (not shown here) achieved P = 3×10⁻⁸ (see Table 4). Additive model is shown here; see Figure S1 for Dominant model. Dominant and additive models yielded similar results for top hits (see Table 2). Panel B is the QQ plot for heavy coffee drinkers where the observed P values (red line) are plotted against the expected P values under no association (straight black line). The plots were made first by including all SNPs (red), then excluding SNCA, HLA and MAPT (green) and finally by excluding GRIN2A (blue). Unlike the QQ plot for GWAIS, the effects of SNCA, HLA and MAPT are unnoticeable. The only deviation is seen at the extreme <10⁻⁵ which is primarily due to GRIN2A.

Figure 3. GWAS in light coffee-drinkers.

Neither the Manhattan plot (Panel A) nor the QQ plot (Panel B) exhibit evidence of association between GRIN2A and PD among individuals who drink little or no coffee.