{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T15:29:53Z","timestamp":1789658993388,"version":"4.0.1"},"reference-count":39,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Natural Science Foundation of China","award":["82274511"],"award-info":[{"award-number":["82274511"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Natural Science Foundation of China","award":["82575002"],"award-info":[{"award-number":["82575002"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]},{"award":["82274511"],"award-info":[{"award-number":["82274511"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"award":["82575002"],"award-info":[{"award-number":["82575002"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Xiyuan Hospital","award":["XYZX0204-03"],"award-info":[{"award-number":["XYZX0204-03"]}],"id":[{"id":"https:\/\/ror.org\/02y0vze35","id-type":"ROR","asserted-by":"crossref"}]},{"award":["XYZX0204-03"],"award-info":[{"award-number":["XYZX0204-03"]}],"id":[{"id":"https:\/\/ror.org\/02y0vze35","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background:\u00a0Helicobacter pylori (H. pylori) infection is a well-established risk factor for gastric cancer; however, evidence on the associations between antigen-specific antibody traits, host methylation, and gastric cancer risk remains limited. Methods: Using a forward two-sample Mendelian randomization (MR) design, we integrated methylation quantitative trait loci (mQTLs), external cohorts, The Cancer Genome Atlas\u2013Stomach Adenocarcinoma (TCGA-STAD), and functional annotations through a three-stage framework (antibody trait screening, CpG prioritization, and external replication) to evaluate a two-step pathway from host antibody response to gastric cancer via DNA methylation. Results: Among six H. pylori antigens, antibody response to outer membrane protein (OMP) showed the strongest positive association with gastric cancer risk (OR = 1.186, 95% CI: 1.079\u20131.304, raw p = 4.08 \u00d7 10\u22124). CpG-level prioritization identified cg24290947 (annotated to HLA-DMA) as a methylation site linked to gastric cancer susceptibility, with an inverse MR association (beta = \u22120.2347, 95% CI: \u22120.3980 to \u22120.0713, raw p = 0.00487). External exploration showed that cg24290947 methylation was elevated in H. pylori-positive gastric mucosa; however, its direct tumor\u2013normal difference in a 12-pair cohort was not significant, although regional methylation perturbations were observed. HLA-DMA and MHC-II expression were consistently higher in tumor versus normal tissues across three cohorts, whereas TCGA-STAD did not support a stable linear relationship between cg24290947 methylation and HLA-DMA\/MHC-II expression; three of six composition-adjusted models showed nominal significance but were model-dependent. These signals were enriched in antigen processing and presentation pathways. Conclusions: cg24290947\/HLA-DMA represents a hypothesis-generating regional methylation candidate for further investigation rather than a confirmed linear transcriptional regulator. The MR evidence is based on European-ancestry summary data; its generalizability and any clinical predictive value warrant independent evaluation.<\/jats:p>","DOI":"10.3390\/genes17091125","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T18:23:53Z","timestamp":1789496633000},"page":"1125","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["H. pylori Outer Membrane Protein Antibody Response, MHC\/HLA-DMA Methylation, and Gastric Cancer Risk: A Multi-Layer Evidence Integration Study Using Mendelian Randomization"],"prefix":"10.3390","volume":"17","author":[{"given":"Yangxi","family":"Fu","sequence":"first","affiliation":[{"name":"Graduate School, Beijing University of Chinese Medicine, Beijing 100029, China"},{"name":"Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Zheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Shan","family":"Liu","sequence":"additional","affiliation":[{"name":"Beijing Traditional Chinese Medicine Research Institute Co., Ltd., Beijing 100011, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Lin","family":"Liu","sequence":"additional","affiliation":[{"name":"Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]},{"given":"Xudong","family":"Tang","sequence":"additional","affiliation":[{"name":"Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"project-administration","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,15]]},"reference":[{"key":"ref_1","first-page":"229","article-title":"Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"74","author":"Bray","year":"2024","journal-title":"CA Cancer J. Clin."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"49565","DOI":"10.18632\/oncotarget.10391","article-title":"Clinical significance and diagnostic value of serum CEA, CA19-9 and CA72-4 in patients with gastric cancer","volume":"7","author":"Liang","year":"2016","journal-title":"Oncotarget"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"He, X., Qi, W., Wang, Q., and Zhao, S. (2024). Knowledge and practice of early gastric cancer screening among adults aged \u226545 years in China: A cross-sectional study. BMC Public Health, 24.","DOI":"10.1186\/s12889-024-20558-x"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1053\/j.gastro.2023.12.022","article-title":"Global Prevalence of Helicobacter pylori Infection and Incidence of Gastric Cancer Between 1980 and 2022","volume":"166","author":"Chen","year":"2024","journal-title":"Gastroenterology"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"e888","DOI":"10.1016\/S2468-2667(21)00164-X","article-title":"The relative and attributable risks of cardia and non-cardia gastric cancer associated with Helicobacter pylori infection in China: A case-cohort study","volume":"6","author":"Yang","year":"2021","journal-title":"Lancet Public Health"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1093\/ije\/dyad007","article-title":"Helicobacter pylori multiplex serology and risk of non-cardia and cardia gastric cancer: A case-cohort study and meta-analysis","volume":"52","author":"Yao","year":"2023","journal-title":"Int. J. Epidemiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e12881","DOI":"10.1111\/hel.12881","article-title":"Association between Helicobacter pylori antibodies determined by multiplex serology and gastric cancer risk: A meta-analysis","volume":"27","author":"Wang","year":"2022","journal-title":"Helicobacter"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1007\/s10120-016-0650-0","article-title":"Mechanisms for the induction of gastric cancer by Helicobacter pylori infection: Aberrant DNA methylation pathway","volume":"20","author":"Maeda","year":"2017","journal-title":"Gastric Cancer"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/s41576-024-00760-8","article-title":"DNA methylation in mammalian development and disease","volume":"26","author":"Smith","year":"2025","journal-title":"Nat. Rev. Genet."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1158\/1078-0432.CCR-05-2096","article-title":"High levels of aberrant DNA methylation in Helicobacter pylori-infected gastric mucosae and its possible association with gastric cancer risk","volume":"12","author":"Maekita","year":"2006","journal-title":"Clin. Cancer Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1430","DOI":"10.1158\/0008-5472.CAN-09-2755","article-title":"Inflammatory processes triggered by Helicobacter pylori infection cause aberrant DNA methylation in gastric epithelial cells","volume":"70","author":"Niwa","year":"2010","journal-title":"Cancer Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2034","DOI":"10.1002\/ijc.28219","article-title":"Changes in aberrant DNA methylation after Helicobacter pylori eradication: A long-term follow-up study","volume":"133","author":"Shin","year":"2013","journal-title":"Int. J. Cancer"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1410","DOI":"10.1136\/gutjnl-2025-335039","article-title":"Precision risk stratification of primary gastric cancer after eradication of H. pylori by a DNA methylation marker: A multicentre prospective study","volume":"74","author":"Yamada","year":"2025","journal-title":"Gut"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"104844","DOI":"10.1016\/j.ebiom.2023.104844","article-title":"Integrated environmental, lifestyle, and epigenetic risk prediction of primary gastric neoplasia using the longitudinally monitored cohorts","volume":"98","author":"Usui","year":"2023","journal-title":"eBioMedicine"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"ofaa450","DOI":"10.1093\/ofid\/ofaa450","article-title":"Genetic Determinants of Antibody-Mediated Immune Responses to Infectious Diseases Agents: A Genome-Wide and HLA Association Study","volume":"7","author":"Kreuzer","year":"2020","journal-title":"Open Forum Infect. Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e34408","DOI":"10.7554\/eLife.34408","article-title":"The MR-Base platform supports systematic causal inference across the human phenome","volume":"7","author":"Hemani","year":"2018","journal-title":"eLife"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1038\/s41588-021-00923-x","article-title":"Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation","volume":"53","author":"Min","year":"2021","journal-title":"Nat. Genet."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"D138","DOI":"10.1093\/nar\/gkad965","article-title":"NCBI GEO: Archive for gene expression and epigenomics data sets: 23-year update","volume":"52","author":"Clough","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Cancer Genome Atlas Research Network (2014). Comprehensive molecular characterization of gastric adenocarcinoma. Nature, 513, 202\u2013209.","DOI":"10.1038\/nature13480"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2612","DOI":"10.1038\/ncomms3612","article-title":"Inferring tumour purity and stromal and immune cell admixture from expression data","volume":"4","author":"Yoshihara","year":"2013","journal-title":"Nat. Commun."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Chen, E.Y., Tan, C.M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G.V., Clark, N.R., and Ma\u2019ayan, A. (2013). Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-128"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: Tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"D672","DOI":"10.1093\/nar\/gkae909","article-title":"KEGG: Biological systems database as a model of the real world","volume":"53","author":"Kanehisa","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"D672","DOI":"10.1093\/nar\/gkad1025","article-title":"The Reactome Pathway Knowledgebase 2024","volume":"52","author":"Milacic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/s41571-023-00747-0","article-title":"Global burden of gastric cancer: Epidemiological trends, risk factors, screening and prevention","volume":"20","author":"Thrift","year":"2023","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1002\/mc.23650","article-title":"Helicobacter pylori infection associated DNA methylation in primary gastric cancer significantly correlates with specific molecular and clinicopathological features","volume":"63","author":"Tahara","year":"2024","journal-title":"Mol. Carcinog."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Capparelli, R., and Iannelli, D. (2022). Epigenetics and Helicobacter pylori. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23031759"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1038\/s41419-025-08042-9","article-title":"Helicobacter pylori-induced aberrant methylation of ID4 mediated by DNMT3B drives gastric cancer progression via DEC1-SHH signaling pathway","volume":"16","author":"Luan","year":"2025","journal-title":"Cell Death Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/s41419-025-08029-6","article-title":"Hypermethylation-mediated HNF4A silencing by Helicobacter pylori infection drives gastric cancer by disrupting epithelial cell polarity and activating EMT signaling","volume":"16","author":"Li","year":"2025","journal-title":"Cell Death Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1093\/ije\/dyu176","article-title":"Network Mendelian randomization: Using genetic variants as instrumental variables to investigate mediation in causal pathways","volume":"44","author":"Burgess","year":"2015","journal-title":"Int. J. Epidemiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1097\/EDE.0000000000000081","article-title":"Methodological Challenges in Mendelian Randomization","volume":"25","author":"VanderWeele","year":"2014","journal-title":"Epidemiology"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"lqaa028","DOI":"10.1093\/nargab\/lqaa028","article-title":"MR-LDP: A two-sample Mendelian randomization for GWAS summary statistics accounting for linkage disequilibrium and horizontal pleiotropy","volume":"2","author":"Cheng","year":"2020","journal-title":"NAR Genom. Bioinform."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"R37","DOI":"10.1186\/gb-2014-15-2-r37","article-title":"The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts","volume":"15","author":"Wagner","year":"2014","journal-title":"Genome Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1186\/s12943-024-02100-0","article-title":"Unraveling the key role of chromatin structure in cancer development through epigenetic landscape characterization of oral cancer","volume":"23","author":"Xue","year":"2024","journal-title":"Mol. Cancer"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"808","DOI":"10.3350\/cmh.2025.1370","article-title":"FOXM1 influences DNA methylation to augment TACC3 alternative splicing directed by KAT2A in hepatocellular carcinoma","volume":"32","author":"Zhao","year":"2026","journal-title":"Clin. Mol. Hepatol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/j.tig.2020.01.008","article-title":"Advances in the Evolutionary Understanding of MHC Polymorphism","volume":"36","author":"Radwan","year":"2020","journal-title":"Trends Genet."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.1600-065X.1999.tb01371.x","article-title":"The impact of the non-classical MHC proteins HLA-DM and HLA-DO on loading of MHC class II molecules","volume":"172","author":"Kropshofer","year":"1999","journal-title":"Immunol. Rev."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/s41423-018-0181-1","article-title":"Distinct editing functions of natural HLA-DM allotypes impact antigen presentation and CD4+ T cell activation","volume":"17","author":"Morrison","year":"2020","journal-title":"Cell. Mol. Immunol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/368554a0","article-title":"HLA-DMA and -DMB genes are both required for MHC class II\/peptide complex formation in antigen-presenting cells","volume":"368","author":"Fling","year":"1994","journal-title":"Nature"}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/9\/1125\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T04:19:34Z","timestamp":1789618774000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/9\/1125"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,15]]},"references-count":39,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["genes17091125"],"URL":"https:\/\/doi.org\/10.3390\/genes17091125","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,15]]}}}