Transcript Variants of Genes Involved in Neurodegeneration Are Differentially Regulated by the Apoe and Mapt Haplotypes

Abstract

Genetic variations at the Apolipoprotein E (ApoE) and microtubule-associated protein tau (MAPT) loci have been implicated in multiple neurogenerative diseases, but their exact molecular mechanisms are unclear. In this study we performed transcript level linear modelling using the blood whole transcriptome data and genotypes of the 570 subjects in the Parkinson’s progression markers initiative (PPMI) cohort. ApoE, MAPT haplotypes and two SNPs at the SNCA locus (rs356181, rs3910105) were used to detect expression quantitative trait loci eQTLs associated with the transcriptome and differential usage of transcript isoforms. As a result, we identified 151 genes associated with the genotypic variations, 29 cis and 122 trans eQTL positions. Profound effect with genome-wide significance of ApoE e4 haplotype on the expression of TOMM40 transcripts was identified. This finding potentially explain in part the frequently established genetic association with the APOE e4 haplotypes in neurodegenerative diseases. Moreover, MAPT haplotypes had significant differential impact on 23 transcripts from the 17q21.31 and 17q24.1 loci. MAPT haplotypes had also the largest (256) and smallest (-178) effect sizes measured as beta values on two different transcripts from the same gene (LRRC37A2). Intronic SNP in the SNCA gene, rs3910105, differentially induces expression of three SNCA isoforms. In conclusion, this study established clear association between well-known haplotypic variance and transcript specific regulation in the blood. APOE e4 and MAPT H1/H2 haplotypic variants are associated with the expression of several genes related to the neurodegeneration.

APOE Allele Frequency in Southern Greece: Exploring the Role of Geographical Gradient in the Greek Population

“…Interestingly, the TOMM 40 gene is known to be downregulated in the brain and blood of patients with AD. Studies suggest that TOMM 40 implication to AD onset synergistically lies with the APOE gene by relating to similar genome regions [75,76]. Hence, future studies investigating the frequencies of TOMM40 SNPs across different geographical latitudes including northern and southern regions in Greece would be of particular interest, especially in combination with the frequencies of APOE alleles.…”