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.
