An integrative transethnic approach to identify novel functional genes in Parkinson's disease using in silico and in vivo experiments

Interpretation of GWAS results for PD have to date been very challenging. It is now well established that the vast majority of variants with a functional role in PD and other complex diseases are likely to be non-coding and regulatory. As a result, the actual implicated functional genes remain largely undefined. This study encompasses both in silico and in vivo experiments with the aim of dissecting the genetic aetiology of PD. With regards to in silico analyses, our research group has made important progress in this field by using genetic maps to effectively integrate high-resolution in silico data at disease loci to infer function. The multi-marker mapping method we use obtains replicated estimates for precise causal locations based on population-specific genetic maps that have distances expressed in additive Linkage Disequilibrium (LD) Units (LDU maps). These maps are constructed for the same population from which the GWAS data was collected. Thus the mapping location analysis takes directly into account the patterns of LD that are specific to that population. Our work demonstrates that replicated disease-associated loci located on LDU maps can be effectively combined with expression data, as well as specific regulatory annotation to help localise the potential functional genetic variants and identify the genes that the loci perturb. Our proposal is to apply the same computational methods to the analysis of genomic and transcriptomic data to advance the identification of the functionally implicated genes and pathways related to PD. The most promising disease transethnic loci and corresponding implicated functional genes will be screened and validated using two well-established Drosophila models of PD. Our proposal provides the unique opportunity to use both in silico mapping and follow up with in vivo functional experiments in order to obtain greater insights into the genetics of PD. The identification and functional elucidation of PD susceptibility genes holds great promise for the discovery of new therapeutic targets and treatment strategies in PD.

The complex causal chain between a gene and its effect on disease susceptibility cannot be unravelled until we have a full understanding of the regulatory genetic architecture that underpins PD, and until the causal changes have been localised in the DNA sequence. We will use powerful gene mapping tools to obtain refined location estimates for all known PD loci and to identify novel replicated loci. The location estimates for all PD disease loci will be analysed further using expression data across tissues/cells (e.g. brain, monocytes) to investigate whether the PD disease loci are also regulatory loci (expression Quantitative Trait Loci, eQTLs). The precision in co-locating PD and eQTL loci on the high-resolution LDU maps will help us identify the functionally implicated cis- and trans- genes and the corresponding pathways that are dysregulated by PD-eQTL-associated loci. All implicated cis- and trans-genes will be independently validated for differential expression and association with PD using expression case/control data. Pathway and gene set enrichment analyses (GSEA) will be used to assess the role of mitochondrial dysfunction in PD pathogenesis. All PD-eQTL associated loci will be characterised in detail using in silico functional analyses and investigated for overlap with relevant functional annotation, including epigenetic marks (brain tissue). The most promising disease loci and corresponding implicated functional genes will be further investigated using well-established Drosophila models of PD. The proposed integrated approach will enable us to move rapidly from lists of putative risk loci to in vivo validation of their potential aetiological role in PD. The identification and functional elucidation of PD susceptibility genes holds great promise for the discovery of new therapeutic targets and treatment strategies in PD.