TRANSCRIPTOME ANALYSIS IN BLOOD AND BRAIN IDENTIFIES GENE EXPRESSION REGULATION AND CORRESPONDING QUANTITATIVE TRAIT LOCI IN ALZHEIMER’S DISEASE

Abstract

Over 25 genetic risk loci for Alzheimer's disease (AD) have currently been identified. Many of the identified risk variants are located in intergenic or intronic regions, indicating an effect on gene expression regulation. We performed transcriptome-wide RNA-sequencing and complementary DNA sequencing to elucidate the functional correlation of genetic risk factors with transcriptome regulation in AD. Differential expression signatures are further investigated by transcriptome-wide RNA-sequencing of frontal cortex and hippocampus in AD patients and control individuals. We performed Truseq stranded mRNA selection followed by Illumina sequencing of lymphoblast cell line RNA in 58 AD patients and 19 control individuals and hippocampal and frontal cortex RNA in 10 AD patients and 10 control individuals, generating ∼140*106 reads per sample. DNA sequencing of AD risk genes CD2AP, PICALM, BIN1, ABCA7, CD33, CLU, MS4A and EPHA1 was performed using HaloPlex target enrichment technology followed by Illumina sequencing. DNA sequencing of deregulated genes in lymphoblasts was performed by parallel exon amplification followed by Illumina sequencing. Gene expression quantification and differential expression analysis was performed using RSEM software and the DESeq2 R package. Expression quantitative trait loci (eQTL) analysis was performed using the MatrixEQTL and SQTLseekeR R packages. Differential expression analysis identified 67 genes differentially expressed in lymphoblasts. Among deregulated genes were several genes implicated in the brain-derived neurotrophic factor signaling pathway, including the BDNF receptor trkB and its signalling activator PTPRF. EQTL analysis in AD risk genes identified expression regulation of transcript isoforms, including preferential expression of a 2143bp BIN1 transcript over a 1832bp transcript in carriers of a BIN1 variant associated with decreased risk of AD (nominal p-value 0.005, OR 0.52, 95% CI (0.33–0.82)). Replication of identified expression signatures and associated eQTLs in hippocampal and frontal cortex RNA is currently ongoing. Combining transcriptome and DNA sequencing identified genetic factors directly regulating gene transcript and isoform expression, providing a comprehensive overview of expression regulation in risk genes for AD. Comparison of differential gene expression patterns in lymphoblast cell and brain RNA will further provide an indication of tissue-specific and cross-tissue regulatory effects and their associated eQTLs in AD.