Parkinson's Disease Risk Enhancers in Microglia [RNA-seq]
Genome-wide association studies (GWAS) have uncovered thousands of single nucleotide polymorphisms (SNPs) that are associated with Parkinson's disease (PD) risk. The functions of most of these SNPs, including the cell type they influence, and how they affect PD etiology remain largely unknown. To identify functional SNPs, we aligned PD risk SNPs within active regulatory regions of DNA in microglia, a cell type implicated in PD development. Out of 6,749 'SNPs of interest' from the most recent PD GWAS metanalysis, 73 were located in open regulatory chromatin as determined by both ATAC-seq and H3K27ac ChIP-seq.  We identified an active enhancer in microglia in intron two of SNCA that overlaps two PD risk SNPs, rs2737004 and rs2619356. In iPSC-derived microglia, CRISPR/Cas9 deletion of the open chromatin encompassing these SNPs caused reduced expression of multiple genes including SNCA and the adjacent gene MMRN1. Loss of the enhancer also led to upregulation of genes involved in glucose metabolism, a process that is known to be altered in PD patients. Our work expands the role of SNCA in Parkinson's Disease and provides a connection between PD-associated genetic variants and underlying biology that points to a risk mechanism in microglia. Overall design: To assess the functionality of a PD risk enhancer in intron 2 of SNCA, RNA-seq was performed at three time-points across differentiation, (1) iPSCs (2) hematopoietic progenitors (HPCs) and (3) microglia, in wild-type cells and two clones generated via CRISPR/Cas9 deletion of 439 base pairs of the open chromatin region at the enhancer. [contributor] Van Andel Institute Genomics Core