An Alzheimer's disease-associated common regulatory variant in a PTK2B intron alters microglial function

Identifying and functionally validating the causal variants at genome-wide association study (GWAS) loci is very challenging and has only been achieved for very few variants. Here, we validate a single-nucleotide polymorphism (SNP) associated with increased Alzheimer's disease (AD) risk in an intronic enhancer of PTK2B, by engineering it into human induced pluripotent stem cells (hiPSCs). Upon differentiation to macrophages and microglia, the variant increases chromatin accessibility at the enhancer and binding of transcription factor CEBPB but causes only subtle effects on PTK2B or CLU expression. Nonetheless, this variant affects both the transcriptome and phenotype of the cells: interferon gamma-responsive genes are downregulated, secreted chemokine levels are reduced, and microglial chemotaxis is affected. We propose the variant acts by altering microglial reactivity, consistent with the established role of these cells in AD progression. This work demonstrates the power of isogenic hiPSC models for functionally validating GWAS-identified common regulatory variants.