The impact of rare variants in lysosomal genes in the pathogenesis of Parkinson disease
Molecular Biology and Physiology of Neurons and Glial Cells
Final Report Abstract
Genetically complex Parkinson disease (PD) is pathologically characterized by intraneuronal proteinaceous inclusions containing aggregated α-Synuclein. Impaired lysosomal degradation of α-Synuclein and other cellular constituents plays an important role in the pathogenesis. Genetic variants in the lysosomal glucocerebrosidase gene (GBA) are robustly associated with PD. In the project Impact of rare variants in lysosomal genes in the pathogenesis of Parkinson disease, we examined the association between rare genetic variants in 23 lysosomal candidate genes and PD. We investigated 4096 PD patients and an equal number of controls by pooled targeted nextgeneration-sequencing. Single-variant association and genewise burden tests were performed, each with and without Bonferroni multiple testing correction. Multiple testingcorrected single variant associations were found for variants in GBA, TMEM175, NEDD4 and VPS13C. Genewise multiple testing-corrected results confirmed the association of rare GBA variants with PD even after removal of a single PD-associated variant and demonstrate association between rare variants in the ATP13A2 gene and PD. Without multiple testing correction, we find suggestive evidence for an association between variants in SMPD1, LAMP1, LAMP3 and VPS13C and PD. We experienced several difficulties in the implementation of the project. (1) The performance of the HaloPlex kit was insufficient (predicted coverage of the targeted genetic region: 99%, true coverage: 88%). (2) Due to failure in capturing target DNA-probe hybrids using streptavidin-coated magnetic beads, we lost a considerable proportion of PCR products leading to a second amplification effort. (3) Due to insufficient sequencing quality and the ‘cross-over’ design of this study, there was limited reliability to control the results by Sanger sequencing. Fortunately, at least, the sequencing quality was not dependent on case / control status. (4) These difficulties lead to a significantly greater bioinformatics effort to evaluate the sequencing data. In agreement with previous studies, we conclude that variants in specific lysosomal genes but not in lysosomal genes per se are associated with PD. Furthermore, we identified statistically significant associations between PD and moderately frequent and private variants in PRKN. We found no significant association between PD and variants in PINK1 or PARK7.
