{"title":"一项大规模的多组学多基因风险评分分析确定了与类风湿关节炎相关的候选风险位点。","authors":"Jingni Hui, Dan He, Chen Liu, Panxing Shi, Ruixue Zhou, Meijuan Kang, Ye Liu, Yifan Gou, Bingyi Wang, Shiqiang Cheng, Xuena Yang, Chuyu Pan, Wenming Wei, Feng Zhang","doi":"10.1016/j.jbspin.2024.105841","DOIUrl":null,"url":null,"abstract":"<p><strong>Objective: </strong>This study aimed to investigate the associations of multi-omics polygenic risk score (PRS) and rheumatoid arthritis (RA) to identify potential genes/proteins and biological pathways.</p><p><strong>Methods: </strong>Based on multi-omics data from 48,813 participants in the INTERVAL cohort, we calculated multi-omics PRS for 13,646 mRNAs (RNASeq), 308 proteins (Olink), 2380 proteins (SomaScan), 726 metabolites (Metabolon), and 141 metabolites (Nightingale). Using the generalized linear model, we first evaluated the associations between multi-omics PRS and RA in 58,813 UK Biobank participants. The Gene Ontology (GO) project and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to identify the functional pathways in RA. Furthermore, differential gene expression profile datasets were used to validate the identified genes/proteins in our study.</p><p><strong>Results: </strong>We identified 59 transcriptomics PRS and 29 proteomics PRS significantly associated with RA. Both proteomics and transcriptomic PRS identified HLA-DQA2 (RNASeq: OR=1.19, P=1.18×10<sup>-24</sup>; SomaScan: OR=1.24, P=4.43×10<sup>-27</sup>) and AGER (RNASeq: OR=0.91, P=4.18×10<sup>-4</sup>; SomaScan: OR=0.93, P=3.97×10<sup>-3</sup>) were significantly associated with RA. Proteomic PRS from different profiling platforms (SomaScan and Olink) identified a consistent association between TFF3 (SomaScan: OR=0.90, P=4.08×10<sup>-6</sup>; Olink: OR=0.93, P=4.87×10<sup>-3</sup>) and RA. The identified gene/proteins were mainly enriched in the NF-kappa B signaling pathway (hsa04064, P=5.06×10<sup>-5</sup>) and Cytokine-cytokine receptor interaction (hsa04060, P=2.49×10<sup>-4</sup>). In addition, a total of 12 candidate genes in our study were verified in two independent GEO datasets, such as FLOT1 and ABCF1.</p><p><strong>Conclusion: </strong>Our findings provide novel insights into the involvement of identified genes/proteins and pathways in the pathogenesis of RA from multi-omics levels.</p>","PeriodicalId":54902,"journal":{"name":"Joint Bone Spine","volume":" ","pages":"105841"},"PeriodicalIF":3.8000,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"A large-scale multi-omics polygenic risk score analysis identified candidate risk locus associated with rheumatoid arthritis.\",\"authors\":\"Jingni Hui, Dan He, Chen Liu, Panxing Shi, Ruixue Zhou, Meijuan Kang, Ye Liu, Yifan Gou, Bingyi Wang, Shiqiang Cheng, Xuena Yang, Chuyu Pan, Wenming Wei, Feng Zhang\",\"doi\":\"10.1016/j.jbspin.2024.105841\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Objective: </strong>This study aimed to investigate the associations of multi-omics polygenic risk score (PRS) and rheumatoid arthritis (RA) to identify potential genes/proteins and biological pathways.</p><p><strong>Methods: </strong>Based on multi-omics data from 48,813 participants in the INTERVAL cohort, we calculated multi-omics PRS for 13,646 mRNAs (RNASeq), 308 proteins (Olink), 2380 proteins (SomaScan), 726 metabolites (Metabolon), and 141 metabolites (Nightingale). Using the generalized linear model, we first evaluated the associations between multi-omics PRS and RA in 58,813 UK Biobank participants. The Gene Ontology (GO) project and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to identify the functional pathways in RA. Furthermore, differential gene expression profile datasets were used to validate the identified genes/proteins in our study.</p><p><strong>Results: </strong>We identified 59 transcriptomics PRS and 29 proteomics PRS significantly associated with RA. Both proteomics and transcriptomic PRS identified HLA-DQA2 (RNASeq: OR=1.19, P=1.18×10<sup>-24</sup>; SomaScan: OR=1.24, P=4.43×10<sup>-27</sup>) and AGER (RNASeq: OR=0.91, P=4.18×10<sup>-4</sup>; SomaScan: OR=0.93, P=3.97×10<sup>-3</sup>) were significantly associated with RA. Proteomic PRS from different profiling platforms (SomaScan and Olink) identified a consistent association between TFF3 (SomaScan: OR=0.90, P=4.08×10<sup>-6</sup>; Olink: OR=0.93, P=4.87×10<sup>-3</sup>) and RA. The identified gene/proteins were mainly enriched in the NF-kappa B signaling pathway (hsa04064, P=5.06×10<sup>-5</sup>) and Cytokine-cytokine receptor interaction (hsa04060, P=2.49×10<sup>-4</sup>). In addition, a total of 12 candidate genes in our study were verified in two independent GEO datasets, such as FLOT1 and ABCF1.</p><p><strong>Conclusion: </strong>Our findings provide novel insights into the involvement of identified genes/proteins and pathways in the pathogenesis of RA from multi-omics levels.</p>\",\"PeriodicalId\":54902,\"journal\":{\"name\":\"Joint Bone Spine\",\"volume\":\" \",\"pages\":\"105841\"},\"PeriodicalIF\":3.8000,\"publicationDate\":\"2024-12-26\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Joint Bone Spine\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1016/j.jbspin.2024.105841\",\"RegionNum\":3,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"RHEUMATOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Joint Bone Spine","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1016/j.jbspin.2024.105841","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"RHEUMATOLOGY","Score":null,"Total":0}
A large-scale multi-omics polygenic risk score analysis identified candidate risk locus associated with rheumatoid arthritis.
Objective: This study aimed to investigate the associations of multi-omics polygenic risk score (PRS) and rheumatoid arthritis (RA) to identify potential genes/proteins and biological pathways.
Methods: Based on multi-omics data from 48,813 participants in the INTERVAL cohort, we calculated multi-omics PRS for 13,646 mRNAs (RNASeq), 308 proteins (Olink), 2380 proteins (SomaScan), 726 metabolites (Metabolon), and 141 metabolites (Nightingale). Using the generalized linear model, we first evaluated the associations between multi-omics PRS and RA in 58,813 UK Biobank participants. The Gene Ontology (GO) project and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to identify the functional pathways in RA. Furthermore, differential gene expression profile datasets were used to validate the identified genes/proteins in our study.
Results: We identified 59 transcriptomics PRS and 29 proteomics PRS significantly associated with RA. Both proteomics and transcriptomic PRS identified HLA-DQA2 (RNASeq: OR=1.19, P=1.18×10-24; SomaScan: OR=1.24, P=4.43×10-27) and AGER (RNASeq: OR=0.91, P=4.18×10-4; SomaScan: OR=0.93, P=3.97×10-3) were significantly associated with RA. Proteomic PRS from different profiling platforms (SomaScan and Olink) identified a consistent association between TFF3 (SomaScan: OR=0.90, P=4.08×10-6; Olink: OR=0.93, P=4.87×10-3) and RA. The identified gene/proteins were mainly enriched in the NF-kappa B signaling pathway (hsa04064, P=5.06×10-5) and Cytokine-cytokine receptor interaction (hsa04060, P=2.49×10-4). In addition, a total of 12 candidate genes in our study were verified in two independent GEO datasets, such as FLOT1 and ABCF1.
Conclusion: Our findings provide novel insights into the involvement of identified genes/proteins and pathways in the pathogenesis of RA from multi-omics levels.
期刊介绍：
Bimonthly e-only international journal, Joint Bone Spine publishes in English original research articles and all the latest advances that deal with disorders affecting the joints, bones, and spine and, more generally, the entire field of rheumatology.
All submitted manuscripts to the journal are subjected to rigorous peer review by international experts: under no circumstances does the journal guarantee publication before the editorial board makes its final decision. (Surgical techniques and work focusing specifically on orthopedic surgery are not within the scope of the journal.)Joint Bone Spine is indexed in the main international databases and is accessible worldwide through the ScienceDirect and ClinicalKey platforms.
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