Functional Evaluation of a Parkinson’s Disease Risk Enhancer in Microglia

• Main Author: Booms, Alix N
• Format: Dissertation
• Language: English
• Published: ProQuest Dissertations & Theses 01-01-2024
• Subjects: Cellular biology; Molecular biology; Neurosciences
• ISBN: 9798381693768

Genome-wide association studies (GWAS) have uncovered thousands of low penetrant single nucleotide polymorphisms (SNPs) that associate with increased risk for Parkinson’s disease (PD). Although most of them have unknown function, a portion, located in enhancers, are known to have allele-specific effects on gene regulation via binding to transcription factors together with promoters during transcription initiation. These interactions result in the enhancement of mRNA levels and are important for driving cell-type-specific gene expression. Microglia, the brain resident immune cells, show enrichment of PD risk variants within open chromatin at some of the enhancers around genes that are important for microglia function. Altered microglia function has been linked to PD, but the genetic mechanisms are not well understood. To investigate the impact of PD risk SNPs on microglia function, we first sought to identify those that overlap active regulatory chromatin in microglia, mapped using ATAC and ChIP-seq data from human iPSC-derived and primary microglia. Out of 6,749 PD risk SNPs, 73 overlapped active regulatory DNA in microglia. One of the top candidate functional risk SNPs resides in an intragenic enhancer at SNCA, a well-known PD risk gene. To identify the target genes/gene network of this SNCA “risk enhancer,” we used CRISPR-Cas9 to delete the open chromatin region encompassing two SNPs. Loss of the enhancer resulted in decreased expression of SNCA, the adjacent gene MMRN1, and a small subset of other genes. A portion of differentially expressed genes are involved in cell cycle regulation and glucose metabolism, two linked processes that are known to be dysfunctional in PD patients. This work provides a connection between PD-associated genetic variation and potential biological mechanisms that may contribute to PD risk in microglia.