{"title":"Identification of pathogenic cell types and shared genetic loci and genes for Alzheimer's disease and inflammatory bowel disease.","authors":"Jingjing Zhang, Yuqing Yan, Liqin Han, Rui Qiao, Xiaohui Niu, Peiluan Li","doi":"10.1093/bfgp/elaf013","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Comorbidities and genetic correlations between gastrointestinal tract diseases and psychiatric disorders have been widely reported, but the underlying intrinsic link between Alzheimer's disease (AD) and inflammatory bowel disease (IBD) is not adequately understood.</p><p><strong>Methods: </strong>To identify pathogenic cell types of AD and IBD and explore their shared genetic architecture, we developed Pathogenic Cell types and shared Genetic Loci (PCGL) framework, which studied AD and IBD and its two subtypes of ulcerative colitis (UC) and Crohn's disease (CD).</p><p><strong>Results: </strong>We found that monocytes and CD8 T cells were the enriched pathogenic cell types of AD and IBDs, respectively. By PCGL framework, there was a significant global genetic correlation between AD and each of IBD, UC, and CD. Especially, local genetic correlations between AD and IBD showed strong signals in chr6. Bidirectional two-sample MR Analyses also validated these. Cross-trait meta-analysis identified two key genetic loci rs660895 (on chr6) and rs917117 (on chr7), which have not been previously reported. Two loci are located on the genes HLA-DRB1 and JAZF1, respectively. MAGMA genome-wide gene-based analysis identified six overlapping genes including HLA-DRB1. Subsequently, for one thing, SMR analyses further validated six shared genes in specific tissues and monocytes. For another, pathway enrichment analysis revealed shared genes were enriched in several natural killer cell mediated cytotoxicity and chemokine signaling pathways.</p><p><strong>Conclusions: </strong>PCGL not only revealed the significant genetic correlations underlying AD and IBDs but also identified enriched pathogenic cell types and new shared loci and genes. We highlighted the mediation of HLA-DRB1 effects in the comorbidity mechanisms.</p>","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":"24 ","pages":""},"PeriodicalIF":2.5000,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12415860/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Briefings in Functional Genomics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/bfgp/elaf013","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Background: Comorbidities and genetic correlations between gastrointestinal tract diseases and psychiatric disorders have been widely reported, but the underlying intrinsic link between Alzheimer's disease (AD) and inflammatory bowel disease (IBD) is not adequately understood.
Methods: To identify pathogenic cell types of AD and IBD and explore their shared genetic architecture, we developed Pathogenic Cell types and shared Genetic Loci (PCGL) framework, which studied AD and IBD and its two subtypes of ulcerative colitis (UC) and Crohn's disease (CD).
Results: We found that monocytes and CD8 T cells were the enriched pathogenic cell types of AD and IBDs, respectively. By PCGL framework, there was a significant global genetic correlation between AD and each of IBD, UC, and CD. Especially, local genetic correlations between AD and IBD showed strong signals in chr6. Bidirectional two-sample MR Analyses also validated these. Cross-trait meta-analysis identified two key genetic loci rs660895 (on chr6) and rs917117 (on chr7), which have not been previously reported. Two loci are located on the genes HLA-DRB1 and JAZF1, respectively. MAGMA genome-wide gene-based analysis identified six overlapping genes including HLA-DRB1. Subsequently, for one thing, SMR analyses further validated six shared genes in specific tissues and monocytes. For another, pathway enrichment analysis revealed shared genes were enriched in several natural killer cell mediated cytotoxicity and chemokine signaling pathways.
Conclusions: PCGL not only revealed the significant genetic correlations underlying AD and IBDs but also identified enriched pathogenic cell types and new shared loci and genes. We highlighted the mediation of HLA-DRB1 effects in the comorbidity mechanisms.
期刊介绍：
Briefings in Functional Genomics publishes high quality peer reviewed articles that focus on the use, development or exploitation of genomic approaches, and their application to all areas of biological research. As well as exploring thematic areas where these techniques and protocols are being used, articles review the impact that these approaches have had, or are likely to have, on their field. Subjects covered by the Journal include but are not restricted to: the identification and functional characterisation of coding and non-coding features in genomes, microarray technologies, gene expression profiling, next generation sequencing, pharmacogenomics, phenomics, SNP technologies, transgenic systems, mutation screens and genotyping. Articles range in scope and depth from the introductory level to specific details of protocols and analyses, encompassing bacterial, fungal, plant, animal and human data.
The editorial board welcome the submission of review articles for publication. Essential criteria for the publication of papers is that they do not contain primary data, and that they are high quality, clearly written review articles which provide a balanced, highly informative and up to date perspective to researchers in the field of functional genomics.
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