Genetic determinants of TF binding in pooled microglia

PROJECT SUMMARY Alzheimer's disease (AD) is an age-related neurodegenerative disease characterized by progressive cognitive decline and dementia. Genetic studies of AD have identified 75 loci associated with susceptibility. Accumulating evidence indicates that AD risk loci (both common and rare variants) are enriched for myeloid cell (monocytes and microglia) expressed genes. We have previously demonstrated that AD susceptibility alleles affect myeloid function by altering gene expression, splicing or chromatin. These AD-associated noncoding variants are highly enriched in myeloid cell enhancers, but whether they affect enhancer function and binding of myeloid transcription factors—and if so, how—remains largely unknown. The overall objective of this study is therefore to identify the AD-associated common genetic variants that alters the binding of AD-relevant TFs in myeloid cells. In Aim 1, we will perform Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) by pooling microglia samples to generate genome-wide profiles of PU.1, CEBPβ, MEF2C, BCL11A, BHLHE41, and CTCF, and histone H3 lysine 27 acetylation (H3K27ac) (TFs prioritized by AD genetics and functional genomics studies). In aim 2, we will use a pooling-based approach to map transcription factor binding quantitative trait loci (bQTL). TF binding profiles combined with RNA-seq (eQTL) and ATAC-seq (caQTL) data being generated from the same samples will allow us to identify genetic effects on chromatin that propagate to gene expression. We will perform colocalization analysis to identify AD susceptibility alleles that affect binding of TFs. The combined analyses of data on multiple types of regulatory mechanisms will allow us to understand the basis for concerted changes in regulatory outputs, and prioritize functional variants among statistically equivalent genetic associations. Finally, in aim 3, we will validate the regulatory effect of binding-disrupting functional variants using massively parallel reporter assays (MPRA) in human induced pluripotent stem cells (iPSCs) into induced microglia-like cells (iMGL). Together these studies will not only further our understanding how AD risk variants affect disease process but also provide key information bridging AD genetics to molecular mechanisms in microglia, setting the stage for future mechanistic studies.