Novel late-onset Alzheimer disease loci variants associate with brain gene expression

Abstract

Objective: Recent genome-wide association studies (GWAS) of late-onset Alzheimer disease (LOAD) identified 9 novel risk loci. Discovery of functional variants within genes at these loci is required to confirm their role in Alzheimer disease (AD). Single nucleotide polymorphisms that influence gene expression (eSNPs) constitute an important class of functional variants. We therefore investigated the influence of the novel LOAD risk loci on human brain gene expression.

Methods: We measured gene expression levels in the cerebellum and temporal cortex of autopsied AD subjects and those with other brain pathologies (∼400 total subjects). To determine whether any of the novel LOAD risk variants are eSNPs, we tested their cis-association with expression of 6 nearby LOAD candidate genes detectable in human brain (ABCA7, BIN1, CLU, MS4A4A, MS4A6A, PICALM) and an additional 13 genes ±100 kb of these SNPs. To identify additional eSNPs that influence brain gene expression levels of the novel candidate LOAD genes, we identified SNPs ±100 kb of their location and tested for cis-associations.

Results: CLU rs11136000 (p = 7.81 × 10(-4)) and MS4A4A rs2304933/rs2304935 (p = 1.48 × 10(-4)-1.86 × 10(-4)) significantly influence temporal cortex expression levels of these genes. The LOAD-protective CLU and risky MS4A4A locus alleles associate with higher brain levels of these genes. There are other cis-variants that significantly influence brain expression of CLU and ABCA7 (p = 4.01 × 10(-5)-9.09 × 10(-9)), some of which also associate with AD risk (p = 2.64 × 10(-2)-6.25 × 10(-5)).

Conclusions: CLU and MS4A4A eSNPs may at least partly explain the LOAD risk association at these loci. CLU and ABCA7 may harbor additional strong eSNPs. These results have implications in the search for functional variants at the novel LOAD risk loci.

Figure 1. Box plots of the residuals for the preprocessed expression values for ABCA7, CLU, and MS4A4A genes in the (A) temporal cortex and (B) cerebellum

Residuals were obtained following adjustment for age at death, gender, APOE ε4 dose, PCR plate, RNA Integrity Number (RIN), adjusted RIN², and diagnosis in all subjects included in the analysis, for each genotype (0, 1, or 2 alleles) of the targeted SNP (rs#) in a linear regression model. Median values are represented by a thick, black, horizontal line within the box, while the box represents the upper and lower quartiles. The whiskers represent the maximum and minimum values (excluding outliers) defined as 1.5 times the interquartile range. Outliers are represented as circles. The subject counts for each genotype are indicated (N =) above each box.