High‐resolution, genome‐wide, promoter‐focused Capture C in astrocytes implicates causal genes for Alzheimer’s disease

Abstract

AbstractBackgroundPrevious studies of Alzheimer’s Disease (AD) have primarily implicated neurons and microglia as disease‐conferring cell types due to obvious links with degeneration and inflammation, respectively. However, astrocytes may also play a role in AD pathogenesis, but have been less studied in this context. Indeed, genome‐wide association studies (GWAS) have identified multiple genomic variants that reside near genes with astrocyte‐related functions, such as lipid processing and synaptic function. However, GWAS only reports genomic variants associated with a given trait and not necessarily the precise localization of culprit genes. High resolution chromatin conformation capture‐based techniques detect 3D genomic interactions between GWAS‐implicated signals and their effector genes, and allow for the characterization of non‐coding variants in the context of their regulatory activity.MethodTo improve on the low resolution of available Hi‐C data, we employed a high resolution DpnII‐based Capture‐C method to simultaneously characterize the physical genome‐wide interactions of 36,691 baited regions covering human promoters genome‐wide (including non‐coding transcripts) ‐ which we applied to a human primary astrocyte line (NHA, Lonza). Following sequencing, we investigated significant interactions at two different resolutions (1‐fragment and 4‐fragment resolutions; median fragment size = 265bp and 1,441bp, respectively). In parallel, we generated ATAC‐seq open chromatin maps to filter for informative (r2>0.7) proxy single nucleotide polymorphisms (SNPs) for each of the 45 AD independent signals reported to date.ResultATAC‐seq fine‐mapping yielded 100 candidate SNPs in open chromatin for 30 of these loci. By further constraining on our promoter Capture C data in astrocytes, at both one and four DpnII fragment resolution (median distance between interacting regions 9kb and 71kb, respectively), we observed contacts to “open” promoters for 6 putative target genes, corresponding to 6 of the original GWAS loci. These included PICALM, FERMT2, CASS4, and CLU. ConclusionWe observed informative contacts between proxy SNPs and putative effector genes in the human astrocyte context for ∼13% of AD GWAS loci. Further efforts in other relevant cell types, where many of the other loci may in fact be principally operating, should shed light on additional signals. Follow‐up functional studies are warranted to validate these findings.