Integration of Alzheimer's disease genetics and myeloid genomics identifies disease risk regulatory elements and genes [ATAC-seq]

Genome-wide association studies (GWAS) have identified more than 40 loci associated with Alzheimer’s disease (AD), but the causal variants, regulatory elements, genes and pathways remain largely unknown, impeding a mechanistic understanding of AD pathogenesis. Previously, we showed that AD risk alleles are enriched in myeloid-specific epigenomic annotations. Here, we show that they are specifically enriched in active enhancers of monocytes, macrophages and microglia. We integrated AD GWAS with myeloid epigenomic and transcriptomic datasets using analytical approaches to link myeloid enhancer activity to target gene expression regulation and AD risk modification. We identify AD risk enhancers and nominate candidate causal genes among their likely targets (including AP4E1, AP4M1, APBB3, BIN1, MS4A4A, MS4A6A, PILRA, RABEP1, SPI1, TP53INP1, and ZYX) in twenty loci. Fine-mapping of these enhancers nominates candidate functional variants that likely modify AD risk by regulating gene expression in myeloid cells. In the MS4A locus we identified a single candidate functional variant and validated it in human induced pluripotent stem cell (hiPSC)-derived microglia and brain. Taken together, this study integrates AD GWAS with multiple myeloid genomic datasets to investigate the mechanisms of AD risk alleles and nominates candidate functional variants, regulatory elements and genes that likely modulate disease susceptibility.

全基因组关联分析（Genome-wide association studies, GWAS）已发现超过40个与阿尔茨海默病（Alzheimer's disease, AD）相关的基因座，但其中的因果变异、调控元件、相关基因及通路仍未明确，这阻碍了学界对AD发病机制的机制性阐释。此前我们的研究表明，AD风险等位基因富集于髓系特异性表观基因组注释区域。本研究进一步发现，此类等位基因特异性富集于单核细胞、巨噬细胞及小胶质细胞的活性增强子区域内。我们通过多种分析方法，将AD全基因组关联分析数据与髓系表观基因组、转录组数据集进行整合，以建立髓系增强子活性与靶基因表达调控及AD风险修饰之间的关联。我们在20个基因座中鉴定出AD风险增强子，并从其潜在靶基因（涵盖AP4E1、AP4M1、APBB3、BIN1、MS4A4A、MS4A6A、PILRA、RABEP1、SPI1、TP53INP1及ZYX）中筛选出候选因果基因。对上述增强子进行精细定位后，我们筛选出候选功能性变异，此类变异或通过调控髓系细胞内的基因表达来改变AD发病风险。在MS4A基因座中，我们鉴定出单个候选功能性变异，并在人类诱导多能干细胞（induced pluripotent stem cell, hiPSC）分化获得的小胶质细胞及脑组织样本中对该变异进行了验证。综上，本研究将AD全基因组关联分析数据与多套髓系基因组数据集进行整合，以探究AD风险等位基因的作用机制，并筛选出或可调控疾病易感性的候选功能性变异、调控元件及相关基因。