Identification of functional non-coding variants affecting Alzheimer's disease risk by Massively Parallel Reporter Assay

The majority of genetic risk variants for late-onset Alzheimers disease (LOAD) reside within non-coding genomic regions, suggesting they exert pathogenic effects by disrupting transcriptional regulatory programs. To systematically identify functional variants, we performed an unbiased, high-throughput Massively Parallel Reporter Assay (MPRA) in the THP-1 human monocytic cell line, screening 2,231 SNPs across 24 LOAD GWAS loci. We identified 62 variants exhibiting significant allele-specific transcriptional regulatory output, including rs636317 in the MS4A locus. The risk allele of rs636317 disrupts a CTCF binding motif, altering fine-scale chromatin looping. To validate these findings, we employed CRISPR/Cas9 to generate an allele-specific deletion of the rs636317 T allele in H9 human embryonic stem cells. Monocytes differentiated from these edited cells displayed increased expression of MS4A4E, MS4A6A, and TREM2, along with highly elevated levels of soluble TREM2 (sTREM2). These results provide a mechanistic link between a non-coding genetic variant, transcriptional regulation of the MS4A family, and TREM2-mediated immune responses in Alzheimers disease pathogenesis.