CSF proteo‐genomic studies identify an interaction between LRRK2 genetic variants and GRN, GPNMB, CTSB, and ENTPD1

Abstract

AbstractBackgroundParkinson’s disease (PD) is a movement disorder characterized by dopaminergic neurodegeneration in the substantia nigra of the brain. Another neurodegenerative disorder, Alzheimer’s disease (AD), is a progressive memory loss disorder with pathological changes mainly at hippocampus and entorhinal cortex. As dementia is also present in late stage of PD, there might be common molecular mechanism between the pathogenesis of AD and PD. Evidence has nominated Leucine Rich Repeat Kinase 2 (LRRK2), Progranulin (GRN), Glycoprotein nonmetastatic melanoma protein B () since these proteins were linked to AD and PD. Identifying genetic variants of 5 proteins will be critical to shed lights on common disrupted pathways shared by AD and PD.MethodTo identify genetic variants associated with these 5 proteins, we performed protein quantitative trait loci (pQTL) analyses of log10 transformed CSF GRN, GPNMB, CTSB, ENTPD1 and LRRK2 assayed in SomaScan platform. We considered ∼11 million sequenced variants from 787 individuals recruited at PPMI in the discovery and ∼4.3 million imputed variants from 799 Knight ADRC samples in replication. Age, sex and 10 principal components were included as covariates. Genome‐wide threshold (5.0×10−8) was used in the meta‐analyses of discovery and replication for significance.ResultOn chromosome 12, exonic missense LRRK2 variant rs33939927 (MAF = 1.4%) was identified as shared pQTL for GRN (P = 7.87×10−10), CTSB (P = 8.99×10−9), GPNMB (P = 3.59×10−9), and ENTPD1 (P = 1.24×10−13). The second LRRK2 exonic missense variant rs34637584 (MAF = 11%) was pQTL consistent for 3 proteins (GRN: P = 2.34×10−8, GPNMB: P = 8.55×10−13, and ENTPD1: P = 1.75×10−13). The third LRRK2 exonic missense variant rs35303786 (MAF = 3.4%) was identified for GPNMB (P = 1.53×10−8) and ENTPD1 (P = 2.31×10−8). The risk allele of 3 SNPs were associated with higher amount of corresponding CSF proteins. No significant LRRK2 pQTL was identified. Additional analyses including colocalisation with AD and PD GWAS results are ongoing.ConclusionTwo low frequency exonic missense LRRK2 variants (rs33939927 and rs35303786) and one common exonic missense LRRK2 variant (rs34637584) were pQTL shared by GRN, CTSB, GPNMB, and ENTPD1. Our findings indicate that the LRRK2 exonic variants are the key genetic regulators of LRRK2 activity and CSF level of GRN, CTSB, GPNMB, and ENTPD1.