Late-onset Alzheimer disease risk variants mark brain regulatory loci

Abstract

Objective: To investigate the top late-onset Alzheimer disease (LOAD) risk loci detected or confirmed by the International Genomics of Alzheimer's Project for association with brain gene expression levels to identify variants that influence Alzheimer disease (AD) risk through gene expression regulation.

Methods: Expression levels from the cerebellum (CER) and temporal cortex (TCX) were obtained using Illumina whole-genome cDNA-mediated annealing, selection, extension, and ligation assay (WG-DASL) for ∼400 autopsied patients (∼200 with AD and ∼200 with non-AD pathologies). We tested 12 significant LOAD genome-wide association study (GWAS) index single nucleotide polymorphisms (SNPs) for cis association with levels of 34 genes within ±100 kb. We also evaluated brain levels of 14 LOAD GWAS candidate genes for association with 1,899 cis-SNPs. Significant associations were validated in a subset of TCX samples using next-generation RNA sequencing (RNAseq).

Results: We identified strong associations of brain CR1, HLA-DRB1, and PILRB levels with LOAD GWAS index SNPs. We also detected other strong cis-SNPs for LOAD candidate genes MEF2C, ZCWPW1, and SLC24A4. MEF2C and SLC24A4, but not ZCWPW1 cis-SNPs, also associate with LOAD risk, independent of the index SNPs. The TCX expression associations could be validated with RNAseq for CR1, HLA-DRB1, ZCWPW1, and SLC24A4.

Conclusions: Our results suggest that some LOAD GWAS variants mark brain regulatory loci, nominate genes under regulation by LOAD risk variants, and annotate these variants for their brain regulatory effects.

Figure 1. Kernel density plots

(A) CR1 TCX, (B) HLA-DRB1 TCX and (C) CER, (D) PILRB (ILMN_1723984) TCX and (E) CER gene expression residuals by relevant index SNP. Distribution of brain gene expression level residuals from all patients obtained after adjustment for all covariates is shown. Green line indicates distribution of gene expression residuals for homozygous minor individuals (Min); blue line indicates the same for heterozygotes (Het); red line indicates the same for major homozygotes (Maj). The number of individuals with each genotype is indicated on the plot (#). CER = cerebellum; SNP = single nucleotide polymorphism; TCX = temporal cortex.

Figure 2. LocusZoom plots

(A) CR1 TCX expression levels cis-SNP associations, (B) HLA-DRB1 CER expression levels cis-SNP associations, and (C) PILRB (ILMN_1723984) TCX expression levels cis-SNP associations. Square points indicate β <0 (i.e., minor allele associated with lower expression levels); circle points indicate β >0 (i.e., minor allele associated with higher expression levels). Relevant index LOAD GWAS SNP is indicated with a red asterisk below point on plot. LD based on HapMap2 build hg18. r² values plotted relative to the most significant cis-SNP indicated by purple marker. HLA-DRB1 locus index LOAD GWAS SNP rs9271192 is the most significant cis-SNP. Region displayed = candidate gene ±110 kb. CER = cerebellum; GWAS = genome-wide association study; LOAD = late-onset Alzheimer disease; SNP = single nucleotide polymorphism; TCX = temporal cortex.

Figure 3. LocusZoom plots

(A) MEF2C CER expression levels cis-SNP associations, (B) ZCWPW1 TCX expression levels cis-SNP associations, and (C) SLC24A4 cerebellum expression levels cis-SNP associations. See figure 2 legend for description of other features. CER = cerebellum; SNP = single nucleotide polymorphism; TCX = temporal cortex.