A Genetic Study of Cerebral Atherosclerosis Reveals Novel Associations with NTNG1 and CNOT3

Abstract

Cerebral atherosclerosis is a leading cause of stroke and an important contributor to dementia. Yet little is known about its genetic basis. To examine the association of common single nucleotide polymorphisms with cerebral atherosclerosis severity, we conducted a genomewide association study (GWAS) using data collected as part of two community-based cohort studies in the United States, the Religious Orders Study (ROS) and Rush Memory and Aging Project (MAP). Both studies enroll older individuals and exclude participants with signs of dementia at baseline. From our analysis of 1325 participants of European ancestry who had genotype and neuropathologically assessed cerebral atherosclerosis measures available, we found a novel locus for cerebral atherosclerosis in NTNG1. The locus comprises eight SNPs, including two independent significant SNPs: rs6664221 (β = -0.27, 95% CI = (-0.35, -0.19), p = 1.29 × 10^-10) and rs10881463 (β = -0.20, 95% CI = (-0.27, -0.13), p = 3.40 × 10^-8). We further found that the SNPs may influence cerebral atherosclerosis by regulating brain protein expression of CNOT3. CNOT3 is a subunit of CCR4-NOT, which has been shown to be a master regulator of mRNA stability and translation and an important complex for cholesterol homeostasis. In summary, we identify a novel genetic locus for cerebral atherosclerosis and a potential mechanism linking this variation to cerebral atherosclerosis progression. These findings offer insights into the genetic effects on cerebral atherosclerosis.

Keywords: cerebral atherosclerosis; genome-wide association; mediation.

Figure A1

Quantile-Quantile plot of observed p-value distribution. Gray shading shows 95% confidence intervals for 1000 most significant p-values expected under the null hypothesis.

Figure A2

Power analysis. Plots shows power at p-value < 5 × 10⁻⁸ for a range of effect size (β) values across the full range of MAF values. Overall, the results for the ROS/MAP discovery analysis suggest above 50% power to detect alleles with effects size of 0.25 down to ~25% MAF (panel A). The effect size of significant SNPs in ROS/MAP ranged from β values of −0.27 to −0.20 for alleles with approximately 20% MAF; thus, panel B suggests essentially no power to detect those SNPs in the Banner dataset whereas panel C suggests ~32–90% power to detect those SNPs in ADGC.

Figure 1

GWAS results. (A) Manhattan plot of p-values per SNP plotted by genomic position. Dotted line marks genome-wide significance threshold (p < 5 × 10⁻⁸). A locus on chromosome 1 reached genome-wide significance. (B) Genomic locations, allele information, and β estimates for the eight significant SNPs. The reported population allele frequencies were estimated from the 1000G CEU samples. For all eight SNPs, the minor allele was the tested allele. Independent SNPs are highlighted in bold. (C) Detail of significant locus and surrounding genomic region, including intron-exon diagram for NTNG1. The diamond indicates the top SNP, and color of round points indicates the level of linkage disequilibrium (measured as r²) with the top SNP, estimated from the 1000G EUR reference population.

Figure 2

CNOT3 partially mediates the effect of variation at rs6664221 on cerebral atherosclerosis. The effects for rs10881463 are similar.