Identification of Candidate Parkinson Disease Genes by Integrating Genome-Wide Association Study, Expression, and Epigenetic Data Sets

Importance Substantial genome-wide association study (GWAS) work in Parkinson disease (PD) has led to the discovery of an increasing number of loci shown reliably to be associated with increased risk of disease. Improved understanding of the underlying genes and mechanisms at these loci will be key to understanding the pathogenesis of PD. / Objective To investigate what genes and genomic processes underlie the risk of sporadic PD. / Design and Setting This genetic association study used the bioinformatic tools Coloc and transcriptome-wide association study (TWAS) to integrate PD case-control GWAS data published in 2017 with expression data (from Braineac, the Genotype-Tissue Expression [GTEx], and CommonMind) and methylation data (derived from UK Parkinson brain samples) to uncover putative gene expression and splicing mechanisms associated with PD GWAS signals. Candidate genes were further characterized using cell-type specificity, weighted gene coexpression networks, and weighted protein-protein interaction networks. / Main Outcomes and Measures It was hypothesized a priori that some genes underlying PD loci would alter PD risk through changes to expression, splicing, or methylation. Candidate genes are presented whose change in expression, splicing, or methylation are associated with risk of PD as well as the functional pathways and cell types in which these genes have an important role. / Results Gene-level analysis of expression revealed 5 genes (WDR6 [OMIM 606031], CD38 [OMIM 107270], GPNMB [OMIM 604368], RAB29 [OMIM 603949], and TMEM163 [OMIM 618978]) that replicated using both Coloc and TWAS analyses in both the GTEx and Braineac expression data sets. A further 6 genes (ZRANB3 [OMIM 615655], PCGF3 [OMIM 617543], NEK1 [OMIM 604588], NUPL2 [NCBI 11097], GALC [OMIM 606890], and CTSB [OMIM 116810]) showed evidence of disease-associated splicing effects. Cell-type specificity analysis revealed that gene expression was overall more prevalent in glial cell types compared with neurons. The weighted gene coexpression performed on the GTEx data set showed that NUPL2 is a key gene in 3 modules implicated in catabolic processes associated with protein ubiquitination and in the ubiquitin-dependent protein catabolic process in the nucleus accumbens, caudate, and putamen. TMEM163 and ZRANB3 were both important in modules in the frontal cortex and caudate, respectively, indicating regulation of signaling and cell communication. Protein interactor analysis and simulations using random networks demonstrated that the candidate genes interact significantly more with known mendelian PD and parkinsonism proteins than would be expected by chance. / Conclusions and Relevance Together, these results suggest that several candidate genes and pathways are associated with the findings observed in PD GWAS studies

Identification of sixteen novel candidate genes for late onset Parkinson’s disease

Background Parkinson’s disease (PD) is a neurodegenerative movement disorder affecting 1–5% of the general population for which neither effective cure nor early diagnostic tools are available that could tackle the pathology in the early phase. Here we report a multi-stage procedure to identify candidate genes likely involved in the etiopathogenesis of PD. Methods The study includes a discovery stage based on the analysis of whole exome data from 26 dominant late onset PD families, a validation analysis performed on 1542 independent PD patients and 706 controls from different cohorts and the assessment of polygenic variants load in the Italian cohort (394 unrelated patients and 203 controls). Results Family-based approach identified 28 disrupting variants in 26 candidate genes for PD including PARK2, PINK1, DJ-1(PARK7), LRRK2, HTRA2, FBXO7, EIF4G1, DNAJC6, DNAJC13, SNCAIP, AIMP2, CHMP1A, GIPC1, HMOX2, HSPA8, IMMT, KIF21B, KIF24, MAN2C1, RHOT2, SLC25A39, SPTBN1, TMEM175, TOMM22, TVP23A and ZSCAN21. Sixteen of them have not been associated to PD before, were expressed in mesencephalon and were involved in pathways potentially deregulated in PD. Mutation analysis in independent cohorts disclosed a significant excess of highly deleterious variants in cases (p = 0.0001), supporting their role in PD. Moreover, we demonstrated that the co-inheritance of multiple rare variants (≥ 2) in the 26 genes may predict PD occurrence in about 20% of patients, both familial and sporadic cases, with high specificity (> 93%; p = 4.4 × 10− 5). Moreover, our data highlight the fact that the genetic landmarks of late onset PD does not systematically differ between sporadic and familial forms, especially in the case of small nuclear families and underline the importance of rare variants in the genetics of sporadic PD. Furthermore, patients carrying multiple rare variants showed higher risk of manifesting dyskinesia induced by levodopa treatment. Conclusions Besides confirming the extreme genetic heterogeneity of PD, these data provide novel insights into the genetic of the disease and may be relevant for its prediction, diagnosis and treatment

An open-access database and analysis tool for perovskite solar cells based on the FAIR data principles

AbstractLarge datasets are now ubiquitous as technology enables higher-throughput experiments, but rarely can a research field truly benefit from the research data generated due to inconsistent formatting, undocumented storage or improper dissemination. Here we extract all the meaningful device data from peer-reviewed papers on metal-halide perovskite solar cells published so far and make them available in a database. We collect data from over 42,400 photovoltaic devices with up to 100 parameters per device. We then develop open-source and accessible procedures to analyse the data, providing examples of insights that can be gleaned from the analysis of a large dataset. The database, graphics and analysis tools are made available to the community and will continue to evolve as an open-source initiative. This approach of extensively capturing the progress of an entire field, including sorting, interactive exploration and graphical representation of the data, will be applicable to many fields in materials science, engineering and biosciences.</jats:p

Redox stratification of an ancient lake in Gale crater, Mars

Gale crater on Mars was once a lake fed by rivers and groundwater. Hurowitz et al. analyzed 3.5 years of data from the Curiosity rover’s exploration of Gale crater to determine the chemical conditions in the ancient lake. Close to the surface, there were plenty of oxidizing agents and rocks formed from large, dense grains, whereas the deeper layers had more reducing agents and were formed from finer material. This redox stratification led to very different environments in different layers, which provides evidence for Martian climate change. The results will aid our understanding of where and when Mars was once habitable

Mineralogy of an ancient lacustrine mudstone succession from the Murray formation, Gale crater, Mars

The Mars Science Laboratory Curiosity rover has been traversing strata at the base of Aeolis Mons (informally known as Mount Sharp) since September 2014. The Murray formation makes up the lowest exposed strata of the Mount Sharp group and is composed primarily of finely laminated lacustrine mudstone intercalated with rare crossbedded sandstone that is prodeltaic or fluvial in origin. We report on the first three drilled samples from the Murray formation, measured in the Pahrump Hills section. Rietveld refinements and FULLPAT full pattern fitting analyses of X-ray diffraction patterns measured by the MSL CheMin instrument provide mineral abundances, refined unit-cell parameters for major phases giving crystal chemistry, and abundances of X-ray amorphous materials. Our results from the samples measured at the Pahrump Hills and previously published results on the Buckskin sample measured from the Marias Pass section stratigraphically above Pahrump Hills show stratigraphic variations in the mineralogy; phyllosilicates, hematite, jarosite, and pyroxene are most abundant at the base of the Pahrump Hills, and crystalline and amorphous silica and magnetite become prevalent higher in the succession. Some trace element abundances measured by APXS also show stratigraphic trends; Zn and Ni are highly enriched with respect to average Mars crust at the base of the Pahrump Hills (by 7.7 and 3.7 times, respectively), and gradually decrease in abundance in stratigraphically higher regions near Marias Pass, where they are depleted with respect to average Mars crust (by more than an order of magnitude in some targets). The Mn stratigraphic trend is analogous to Zn and Ni, however, Mn abundances are close to those of average Mars crust at the base of Pahrump Hills, rather than being enriched, and Mn becomes increasingly depleted moving upsection. Minerals at the base of the Pahrump Hills, in particular jarosite and hematite, as well as enrichments in Zn, Ni, and Mn, are products of acid-sulfate alteration on Earth. We hypothesize that multiple influxes of mildly to moderately acidic pore fluids resulted in diagenesis of the Murray formation and the observed mineralogical and geochemical variations. The preservation of some minerals that are highly susceptible to dissolution at low pH (e.g., mafic minerals and fluorapatite) suggests that acidic events were not long-lived and that fluids may not have been extremely acidic (pH>2). Alternatively, the observed mineralogical variations within the succession may be explained by deposition in lake waters with variable Eh and/or pH, where the lowermost sediments were deposited in an oxidizing, perhaps acidic lake setting, and sediments deposited in the upper Pahrump Hills and Marias Pass were deposited lake waters with lower Eh and higher pH