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Identification of differential regulation of European versus African local ancestry haplotypes surrounding ApoEε4
Author(s) -
Vasquez Marina Lipkin,
Celis Katrina,
Van Booven Derek,
Hofmann Natalia K.,
Rajabli Farid,
Griswold Anthony J.,
Brown Christopher D.,
PericakVance Margaret A,
Nuytemans Karen,
Vance Jeffery M.
Publication year - 2020
Publication title -
alzheimer's and dementia
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 6.713
H-Index - 118
eISSN - 1552-5279
pISSN - 1552-5260
DOI - 10.1002/alz.046016
Subject(s) - apolipoprotein e , haplotype , enhancer , genetics , allele , biology , coding region , gene , disease , medicine , transcription factor , pathology
Background The risk for late‐onset Alzheimer disease (AD) in ApoEε4 carriers differs between ancestral groups. ApoEε4 Non‐Hispanic White (NHW) homozygotes have an odds ratio of 14.9 while the risk is much lower in Africans (AF) (OR 2.2‐5.7). Local ancestry (LA) analyses in ApoEε4 carrier populations have shown the protective effect in Africans relative to NHW is due to factors lying in the LA surrounding ApoEε4 . No coding differences between genes in the LA have been observed between AF and NHW ancestries. Thus regulatory differences in LA non‐coding regions are most likely involved in the protective factor(s) lowering the risk for AF carriers of ApoEε4 . Enhancers are the most common regulatory element, and thus we sought to identify if any of these variants had functional enhancer effects between the two ancestries. Little functional characterization of genetic regulation in AF ancestries has been investigated. Method We identified 56 significant sequence differences among AF and ApoEε4 haplotypes from the 1000 genomes in a topologically associated area (56kb) surrounding ApoE . None of these differences were identified to be protein coding. We applied Massively Parallel Reporter Assay (MPRA) supplemented with single variant reporter assays using Promega Dual Glo‐Luciferase System in AD relevant cell lines to identify the regulatory potential of these variants and their surrounding regions and to assess the differential effect sizes of the variant alleles on enhancer activity. Result For MPRA and complementary single variants reporter assays, we generated ∼900bp PCR fragments surrounding these variants to ensure full representation of potential regulatory elements. MPRA vector library or single reporter vectors were transfected in three cell lines (SHY‐SY5Y neuronal cells, U‐118 astrocytes and HMC3 microglia). We identified evidence for differential regulation between AF and EU variant haplotypes in intron 5 of PVRL2 , TOMM40 intronic regions and a large region located 3’ of APOC1 . The latter encompasses a putative enhancer identified through ENCODE analyses in brains with NHW ancestry. Conclusion Our results indicate several areas of differential regulation in this LA region on ApoEε4 haplotypes. Follow‐up of the identified regulatory regions is currently ongoing using publicly available data and in‐house iPSC derived cell lines.