Identification Of Common Risk Genes Between Parkinson’s Disease(PD) And Related Diseases And PD Functionally Related Genes Based On Genetic Pleiotropy

Background and objective: With the ever-changing environment and lifestyles and the increasing aging population,many complex diseases,such as Parkinson’s disease(PD),inflammatory bowel disease(IBD),Alzheimer’s disease(AD)and amyotrophic lateral sclerosis(ALS),are posing a huge threat to human health.The complex diseases have highly complicated pathogenesis,involving the interaction between genetic and environmental factors.In recent years,exploring the underlying mechanisms of complex diseases has long been a field of interest for clinicians,geneticist and bioinformaticians.Genome-wide association studies(GWAS)have been widely applied to identify the susceptibility genes for most complex diseases and have achieved a series of research results,which provide an important basis for further research on clarifying the likely mechanisms in complex diseases.However,GWAS has several notable limitations,and the causal genetic variants identified by GWAS can only explain a small proportion of the heritability of most complex diseases.More efforts are needed to improve the detection of additional variants that may underlie the “missing heritability”.Genetic pleiotropy is the phenomenon where a single locus affects two or more apparently unrelated phenotypic traits.A growing number of cross-phenotype associations indicate that genetic pleiotropy is widespread in complex diseases.The possible explanation for this phenomenon is that pleiotropic genes are more prone to be hub genes involved into key physiological mechanisms.The "omnigenic" model proposed by Boyle et al explain that pleiotropic genes may ultimately affect disease specific core genes through regulatory networks,thereby affecting disease susceptibility.Therefore,the identification of pleiotropic genes among diseases or complex traits provides a new insight into the missing heritability of complex diseases,and can also help us understand the shared etiology among diseases,which is likely to be the drug target to prevent and treat multiple diseases in the near future.However,as far as we know,there has been limited systematic study performed to investigate the common genes among diseases of interest for our study.Herein,due to the phenomenon of genetic pleiotropy,we systematically identified common risk genes between PD and IBD,and among three common neurodegenerative diseases including PD,AD and ALS based on existing GWAS datasets by combining multivariate analysis and univariate analysis.In addition,the majority of diseaseassociated SNPs also showed a correlation with altered gene expression or DNA methylation,which is also a form of pleiotropic effects.Using the summary data-based Mendelian randomization method,we integrated summary statistics from PD GWAS,expression quantitative trait loci(e QTL)and methylation quantitative trait loci(m QTL)studies of the large sample to prioritize functionally-related genes for PD,which may provide a novel theoretical basis for setting up further experimental studies,rapid diagnosis,targeted therapy and drug research for PD.Methods:1.We used the Linux operating system and the python scripts to merge and intersect the GWAS datasets from different diseases,and subsequently carried out gene annotation,linkage disequilibrium(LD)-prune analysis and standardized regression coefficients.2.We designed two separate analysis strategies: one was to identify pleiotropic genes by multivariate analysis(meta CCA)combined with gene expression profile data from GEO database,and the other was to analyze pleiotropic genes among diseases by different gene-level association analysis(VEGAS2,Meta Xcan and MAGMA).3.Gene ontology(GO)annotation,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses and a proteinprotein interaction network(PPIN)analysis were conducted to explore the shared biological mechanism among different diseases.4.The summary data-based Mendelian randomization(SMR)was used to analyze the association of gene expression or DNA methylation with PD.5.We used the WGCNA R package to construct the coexpression network for potential caual genes identified by SMR and the known PDrelated genes,and we identified the genes that significantly co-express with the known PD-related genes,which may have similar biological functions.6.GO Biological Pathways enrichments were obtained to explore the potential biological functions of these genes in the pathogenesis of PD.Results:1.Identification of common risk genes for PD and IBD: Using two analysis strategies,a total of 64 pleiotropic genes were identified that were significantly associated with PD and IBD.After searching the public databases including GWAS catalog and Pubmed,we found that 19 genes were reported to be associated with PD and IBD,and 25 were reported to be associated with only one disease,and 20 have not been previously reported to be associated with PD or IBD.By GO annotation,KEGG pathway enrichment analysis and PPIN analysis,Th1 and Th2 cell differentiation(ko04658)pathway was the most significant one(P=3.62E-11)with the greatest number of enriched genes(15/64),and JAK2 was significantly enriched in four KEGG pathways,and highly interacted with more than three proteins(interaction score≥0.9).In addition,novel pleiotropic genes including ADAM15,EFNA1,GBA and SLC50A1 were associated with PD and IBD in two univariate gene-level association analyses,significantly being enriched among multiple biological pathways.2.Identification of common risk genes for PD,AD and ALS: A total of 18 pleiotropic genes were identified that were significantly associated with PD,AD and ALS.Among them,2 genes were previously reported in all three neurodegenerative diseases,and 4 have been reported to be associated with two of the three diseases,and 9 have been reported to be associated with only one of the three diseases,and 3 have not been reported in the three diseases.By GO annotation and PPIN analyses,adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains process(GO:0002460)was the most significant(P=2.80E-06)and enriched with greatest number of pleiotropic genes.HLA-DRB1,HLA-DQA1 and HLADQB1 were significantly associated with PD and AD by MAGMA or(and)Meta Xcan analyes,being significantly enriched in the adaptive immune response related pathway.In the PPIN,there were interactions among HLA-DQA1,HLA-DQB1 and HLA-DRB1.In addition,C9orf72,APOC2 and TOMM40,which are previously reported to be associated with at least two neurodegenerative diseases,were significantly enriched in the macroautophagy pathway.The autophagy dysregulation has been confirmed to play a key role in most neurodegenerative diseases.The novel pleiotropic genes—PVRL2 and CLPTM1 were highly correlated with three neurodegenerative diseases in the meta CCA analysis results,and were significantly enriched in multiple biological processes(P<0.05),and highly interacted with multiple proteins.3.Identification of PD function-related genes: Through SMR and WGCNA analyses,a total of 29 causative genes were significantly associated with PD,and a co-expression relationship was observed between these genes and 16 known PD causative or susceptibility genes.GO-biological process enrichment results showed that regulation of mitochondrial fission(GO:0090140)was enriched with the most pleiotropic genes(14/29),and MAPT,STK39,KANSL1,SH3GL2 and STX1 B were previously reported to be associated with PD,and NCOR1,TTC19 and FDFT1 were identified as novel PD candidate genes.The vesicle-mediated transport in synapse(GO:0099003)was the most significant(P=4.61E-11),and CPLX1,STX1 B and SH3GL2 have been reported to be associated with PD,and SNX17 was identified as a novel PD candidate gene.In the SMR results,the expression of SNX17 was associated with PD in blood and the brain tissues.The other novel PD candidate genes such as KAT8 gene,whose expression was also associated with PD across multiple brain tissues.Conclusion:1.This study validated 19 pleiotropic genes that have been reported to be associated with PD and IBD,and firstly identified 45 pleiotropic genes associated with PD and IBD.Th1 and Th2 cell differentiation pathway may play an important role in the pathogenesis of PD and IBD.The JAK2 may be a key pleiotropic gene in PD and IBD.The novel pleiotropic genes ADAM15,EFNA1,GBA and SLC50A1 warrant further intensive investigation.2.This study validated 6 pleiotropic genes that were previously associated with more than two neurodegenerative diseases,and firstly identified 12 pleiotropic genes associated with PD,AD and ALS.Adaptive immune-mediated inflammation and autophagy pathways may play important roles in the pathogenesis of neurodegenerative diseases.HLA-DQA1,HLA-DQB1,HLA-DRB1,C9orf72,TOMM40 and APOC2 genes may be key pleiotropic genes of these neurodegenerative diseases.Further experiments need to be designed to explore the biological functions of the novel pleiotropic genes including PVRL2 and CLPTM1 in neurodegenerative diseases.3.The PD candidate genes identified by SMR and WGCNA analyses indicated that the regulation of mitochondrial fission may be the key pathophysiological mechanism of PD.MAPT,STK39,KANSL1,SH3GL2,STX1 B,NCOR1,TTC19 and FDFT1 may be the key genes in the regulation of mitochondrial fission.The vesicle-mediated transport in synapse may play an important role in the etiology of PD.The SNX17 and KAT8 identified in our study underlines endosomal sorting and histone acetylation may be involved in the pathophysiological mechanisms of PD.