TRANSCRIPTIONAL REGULATION OF GENES AT THE ALZHEIMER'S DISEASE RISK LOCI

We previously identified genetic associations with brain levels of genes at the late-onset Alzheimer's disease (LOAD) risk GWAS loci ABCA7, BIN1, CLU, CR1 and MS4A4A with cis SNPs, including some of the top AD risk variants. We further investigated the association of the CLU locus variants with the long (CLU1) and short (CLU2) isoforms of CLU and determined that these two isoforms have opposite direction of association. These results highlight the importance of evaluating gene expression associations for specific gene isoforms. In this study, we evaluate the association of specific isoforms of the genes at the top 20 LOAD risk GWAS loci from large meta-analysis. We obtained gene expression measures of ∼24,000 transcripts in two brain regions (temporal cortex and cerebellum) for ∼200 AD subjects and ∼200 subjects with other pathologies using Illumina's WG-DASL array. To evaluate associations between isoforms of genes at the top 20 LOAD risk GWAS loci with cis SNPs, we designed isoform-specific assays to implement in the NanoString nCounter™ technology for ∼200 brain RNA samples. The associations of gene isoforms with cis SNPs will be evaluated using multivariable linear regression analyses controlling for appropriate covariates. The isoform associations from NanoString will be compared with gene expression associations from our previous WG-DASL microarray study. Our expression studies using WG-DASL microarray approach demonstrated associations of cis SNPs at LOAD risk GWAS loci with levels of nearby genes. Our subsequent findings in CLU using isoform-specific qPCR assays showed differential associations with two isoforms of this gene. Given these results, we expect that our isoform-specific assays will provide an in-depth assessment of the expression associations we previously detected at the LOAD GWAS loci and may also uncover novel associations for specific gene isoforms. Many genes at the LOAD GWAS loci associate with cis SNPs, some of which are the top LOAD risk SNPs. This suggests that many LOAD GWAS variants confer risk by transcriptional regulation of genes at these loci. Some of these variants may influence alternative splicing of exons and therefore levels of specific isoforms. Dissection of this transcriptional regulation is expected to have implications for LOAD pathophysiology.