Dissecting GWAS Identified Risk Variants in Parkinson's Disease – Functional Role of GPNMB in the Pathogenesis of PD

点击翻译按钮获取中文摘要

ABSTRACT Parkinson’s Disease (PD) is the second most common chronic progressive neurodegenerative disease. Epide- miology and population genetics suggest that sporadic PD (>95% of cases) results from a complex interaction between genetic risk, aging, and environmental factors. A detailed understanding of the genetic risk is the first step to elucidating this complex interaction. Genome wide association studies (GWAS) have identified numer- ous risk variants (e.g., single nucleotide polymorphisms [SNPs]) present in 78 genomic regions associated with an increased risk of developing PD. However, there is little insight regarding which and how these SNPs mech- anistically contribute to the development and progression of PD. Since most of the functional SNPs are highly enriched in non-coding regulatory DNA elements such as distal enhancers, the prevailing theory is that cis- acting effects of the functional non-coding SNPs on gene expression play a significant role in the development of complex diseases. To compile a list of probable causal SNPs in brain enhancers, we integrated GWAS-iden- tified PD-risk variants with epigenomic data identifying brain-specific enhancers and gene expression datasets in primary brain tissue. This analysis revealed multiple candidate PD-risk variants in a microglia-specific en- hancer element in the glycoprotein nonmetastatic melanoma protein B (GPNMB) locus. GPNMB is a type 1 transmembrane protein known to be upregulated in the substantia nigra of PD patients. Very little is known re- garding its molecular function and how the dysregulation of GPNMB contributes to PD. Our preliminary analy- sis of changes in the cellular transcriptome after GPNMB gene deletion in hPSC-derived microglia identified alterations in expression levels of multiple key genes associated with CNS inflammation (i.e. NLRP2, NLRP12). In addition, there is compelling evidence indicating a role for GPNMB in autophagy (macroautoph- agy, mitophagy, and CMA). Based on previous literature and our preliminary data, I speculate that the cis-act- ing effect of a PD-risk associated sequence variant in a microglia-specific GPNMB enhancer leads to in- creased GPNMB expression, resulting in autophagy dysregulation and ultimately culminating in the activation of inflammatory pathways in microglia which contribute to the neurodegeneration observed in PD. To test this hypothesis this project aims to: (1) to identify the causal risk variant present in this upstream enhancer of GPNMB and characterize the molecular mechanisms by which the causal risk variant dysregulates GPNMB expression in microglia using CRISPR/Cas9-risk variant edited hPSCs, (2) characterize the functional effects of gain and loss of GPNMB on microglial inflammation associated with microglial activation and neurodegener- ation associated-inducers, and (3) characterize the functional effect of GPNMB on autophagy and determine if autophagy is an intermediate mechanism by which GPNMB influences inflammation. This work will provide in- valuable insight into the novel link between non-coding PD risk variants, GPNMB, autophagy, and inflamma- tion.