Cell type‐specific enhancer‐promoter connectivity maps in the human brain and associations with Alzheimer’s disease risk

Background There is no clear genetic cause for most cases of late‐onset Alzheimer’s disease (AD), however, genome‐wide association studies have identified multiple genetic variants associated with increased risk of AD. These AD‐risk variants are often located in non‐coding DNA regulatory regions called enhancers, which upon transcription factor binding, modulate the expression of nearby genes. One of the major challenges facing the field of AD research is the assignment of cell‐type specificity and functionality to these genetic variants. Method Nuclei of microglia, neurons, astrocytes and oligodendrocytes were isolated from frozen human cortical tissue. Sorted nuclei were processed using chromatin immunoprecipitation and sequencing (ChIP‐seq) to define cell type promoter and enhancer regions. The assay for transposase accessible chromatin sequencing (ATAC‐seq) was used to define open chromatin regions, which indicates likely transcription factor binding sites. Proximity Ligation‐Assisted ChIP‐seq (PLAC‐seq) is a chromatin conformation assay that was used to link distal enhancers to target genes. Enhancers were validated by CRISPR‐mediated deletion of putative regions in induce‐pluripotent stem cells (iPSCs) that were derived into neurons, microglia and astrocytes followed by gene expression analysis. Result Genetic variants associated with increased risk of AD were largely confined to microglia enhancers, whereas genetic variants for psychiatric disorders such as autism and schizophrenia were enriched in neuronal enhancers. Enhancer‐promoter interactome maps connected disease‐risk variants located in enhancers to gene promoters. Integrative analysis of promoter‐enhancer interactome maps has not only revised and expanded the gene repertoire influenced by AD‐risk variants but has also revealed the probable cell types in which they function. Lastly, the BIN1 locus, the second highest putative AD‐risk gene after APOE, has a microglia‐specific enhancer that harbors AD‐risk variants. CRISPR‐deletion of the microglia BIN1 enhancer in iPSCs ablated BIN1 gene expression in iPSC‐derived microglia and not neurons or astrocytes. Conclusion There has been intense interest in elucidating mechanisms that link human non‐coding genetic variation to risk of neurodegenerative and psychiatric diseases. Towards this effort, enhancer‐promoter connectivity maps in the human brain has enabled an initial cell‐type‐specific interpretation of human genetic variation associated with disease risk for AD and other brain disorders.