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Item Genome-wide case-only analysis of gene-gene interactions with known Parkinson's disease risk variants reveals link between LRRK2 and SYT10(Springer Nature, 2023-06-29) Aleknonytė-Resch, Milda; Trinh, Joanne; Leonard, Hampton; Delcambre, Sylvie; Leitão, Elsa; Lai, Dongbing; Smajić, Semra; Orr-Urtreger, Avi; Thaler, Avner; Blauwendraat, Cornelis; Sharma, Arunabh; Makarious, Mary B.; Kim, Jonggeol Jeff; Lake, Julie; Rahmati, Pegah; Freitag-Wolf, Sandra; Seibler, Philip; Foroud, Tatiana; Singleton, Andrew B.; The International Parkinson Disease Genomics Consortium; Grünewald, Anne; Kaiser, Frank; Klein, Christine; Krawczak, Michael; Dempfle, Astrid; Medical and Molecular Genetics, School of MedicineThe effects of one genetic factor upon Parkinson’s disease (PD) risk may be modified by other genetic factors. Such gene-gene interaction (G×G) could explain some of the ‘missing heritability’ of PD and the reduced penetrance of known PD risk variants. Using the largest single nucleotide polymorphism (SNP) genotype data set currently available for PD (18,688 patients), provided by the International Parkinson’s Disease Genomics Consortium, we studied G×G with a case-only (CO) design. To this end, we paired each of 90 SNPs previously reported to be associated with PD with one of 7.8 million quality-controlled SNPs from a genome-wide panel. Support of any putative G×G interactions found was sought by the analysis of independent genotype-phenotype and experimental data. A total of 116 significant pairwise SNP genotype associations were identified in PD cases, pointing towards G×G. The most prominent associations involved a region on chromosome 12q containing SNP rs76904798, which is a non-coding variant of the LRRK2 gene. It yielded the lowest interaction p-value overall with SNP rs1007709 in the promoter region of the SYT10 gene (interaction OR = 1.80, 95% CI: 1.65–1.95, p = 2.7 × 10−43). SNPs around SYT10 were also associated with the age-at-onset of PD in an independent cohort of carriers of LRRK2 mutation p.G2019S. Moreover, SYT10 gene expression during neuronal development was found to differ between cells from affected and non-affected p.G2019S carriers. G×G interaction on PD risk, involving the LRRK2 and SYT10 gene regions, is biologically plausible owing to the known link between PD and LRRK2, its involvement in neural plasticity, and the contribution of SYT10 to the exocytosis of secretory vesicles in neurons.Item Role of Lysosomal Gene Variants in Modulating GBA-Associated Parkinson's Disease Risk(Wiley, 2022) Straniero, Letizia; Rimoldi, Valeria; Monfrini, Edoardo; Bonvegna, Salvatore; Melistaccio, Giada; Lake, Julie; Soldà, Giulia; Aureli, Massimo; Shankaracharya; Keagle, Pamela; Foroud, Tatiana; Landers, John E.; Blauwendraat, Cornelis; Zecchinelli, Anna; Cilia, Roberto; Di Fonzo, Alessio; Pezzoli, Gianni; Duga, Stefano; Asselta, Rosanna; Medical and Molecular Genetics, School of MedicineBackground: To date, variants in the GBA gene represent the most frequent large-effect genetic factor associated with Parkinson's disease (PD). However, the reason why individuals with the same GBA variant may or may not develop neurodegeneration and PD is still unclear. Objectives: Therefore, we evaluated the contribution of rare variants in genes responsible for lysosomal storage disorders (LSDs) to GBA-PD risk, comparing the burden of deleterious variants in LSD genes in PD patients versus asymptomatic subjects, all carriers of deleterious variants in GBA. Methods: We used a custom next-generation sequencing panel, including 50 LSD genes, to screen 305 patients and 207 controls (discovery cohort). Replication and meta-analysis were performed in two replication cohorts of GBA-variant carriers, of 250 patients and 287 controls, for whom exome or genome data were available. Results: Statistical analysis in the discovery cohort revealed a significantly increased burden of deleterious variants in LSD genes in patients (P = 0.0029). Moreover, our analyses evidenced that the two strongest modifiers of GBA penetrance are a second variation in GBA (5.6% vs. 1.4%, P = 0.023) and variants in genes causing mucopolysaccharidoses (6.9% vs. 1%, P = 0.0020). These results were confirmed in the meta-analysis, where we observed pooled odds ratios of 1.42 (95% confidence interval [CI] = 1.10-1.83, P = 0.0063), 4.36 (95% CI = 2.02-9.45, P = 0.00019), and 1.83 (95% CI = 1.04-3.22, P = 0.038) for variants in LSD genes, GBA, and mucopolysaccharidosis genes, respectively. Conclusion: The identification of genetic lesions in lysosomal genes increasing PD risk may have important implications in terms of patient stratification for future therapeutic trials. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson Movement Disorder Society.