{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T16:25:47Z","timestamp":1793463947306,"version":"4.5.0"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T00:00:00Z","timestamp":1748563200000},"content-version":"vor","delay-in-days":29,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"DAAD Ta\u2019ziz project GJRC-IH: German-Jordanian Research Cluster in Intelligent Healthcare Informatics","award":["57747902"],"award-info":[{"award-number":["57747902"]}]},{"name":"GARN-CLS: German Arab Research Network for Computational Life Science","award":["57682181"],"award-info":[{"award-number":["57682181"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Helicobacter pylori infection is one of the most common gastric pathogens; however, the molecular mechanisms driving its progression to gastric cancer remain poorly understood. This study aimed to identify the key transcriptomic drivers and therapeutic targets of H. pylori\u2013associated gastric cancer through an integrative transcriptomic analysis. This analysis integrates microarray and RNA-seq datasets to identify significant differentially expressed genes (DEGs) involved in the progression of H. pylori\u2013associated gastric cancer. In addition to independent analyses, data were integrated using ComBat to detect consistent expression patterns of hub genes. This approach revealed distinct clustering patterns and stage-specific transcriptional changes in common DEGs across disease progression, including H. pylori infection, gastritis, atrophy, and gastric cancer. Genes such as TPX2, MKI67, EXO1, and CTHRC1 exhibited progressive upregulation from infection to cancer, highlighting involvement in cell cycle regulation, DNA repair, and extracellular matrix remodeling. These findings provide insights into molecular shifts linking inflammation-driven infection to malignancy. Furthermore, network analysis identified hub genes, including CXCL1, CCL20, IL12B, and STAT4, which are enriched in immune pathways such as chemotaxis, leukocyte migration, and cytokine signaling. This emphasizes their role in immune dysregulation and tumor development. Expression profiling demonstrated the upregulation of hub genes in gastric cancer and stage-specific changes correlating with disease progression. Finally, drug\u2013gene interaction analysis identified therapeutic opportunities, with hub genes interacting with approved drugs like abatacept and zoledronic acid, as well as developmental drugs such as adjuvant and relapladib. These findings highlight the key role of these hub genes as biomarkers and therapeutic targets, providing a foundation for advancing precision medicine in H. pylori\u2013associated gastric cancer. Overall, this study paves the way for advancing precision medicine in H. pylori\u2013associated gastric cancer by providing insights into the development of early detection biomarkers, risk stratification, and targeted therapies. This supports the clinical translation of precision medicine strategies in H. pylori\u2013associated gastric cancer.<\/jats:p>","DOI":"10.1093\/bib\/bbaf241","type":"journal-article","created":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T08:52:13Z","timestamp":1747817533000},"source":"Crossref","is-referenced-by-count":15,"title":["Multi-omics analysis of\n                    <i>Helicobacter pylori<\/i>\n                    \u2013associated gastric cancer identifies hub genes as a novel therapeutic biomarker"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1379-6493","authenticated-orcid":false,"given":"Sara H","family":"Mohamed","sequence":"first","affiliation":[{"name":"Department of Microbiology, Egyptian Drug Authority (EDA), formerly National Organization for Drug Control and Research (NODCAR) , Giza 14281,","place":["Egypt"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9102-8839","authenticated-orcid":false,"given":"Mohamed","family":"Hamed","sequence":"additional","affiliation":[{"name":"Institute for Biostatistics and Informatics in Medicine and Ageing Research (IBIMA), Rostock University Medical Center , Rostock 18057 ,","place":["Germany"]},{"name":"Faculty of Media Engineering and Technology, German University in Cairo , Cairo 11835 ,","place":["Egypt"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hussain A","family":"Alamoudi","sequence":"additional","affiliation":[{"name":"Radiation Oncology Department, Oncology Center in East Jeddah Hospital (Jeddah First Health Cluster) , Rabigh ,","place":["Saudi Arabia"]},{"name":"Center of Nanotechnology, King Abdulaziz University , Jeddah 21589 ,","place":["Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zayd","family":"Jastaniah","sequence":"additional","affiliation":[{"name":"Center of Nanotechnology, King Abdulaziz University , Jeddah 21589 ,","place":["Saudi Arabia"]},{"name":"Department of Internal Medicine, Faculty of Medicine, King Abdulaziz University , Rabigh ,","place":["Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5349-7960","authenticated-orcid":false,"given":"Fadhl M","family":"Alakwaa","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Division of Nephrology, University of Michigan , Ann Arbor, MI ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3887-8196","authenticated-orcid":false,"given":"Asmaa","family":"Reda","sequence":"additional","affiliation":[{"name":"Center of Nanotechnology, King Abdulaziz University , Jeddah 21589 ,","place":["Saudi Arabia"]},{"name":"Zoology Department, Computational Biology and Bioinformatics Division, Faculty of Science, Benha University , Benha 12613,","place":["Egypt"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,5,30]]},"reference":[{"key":"2025053008014905700_ref1","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1038\/nrmicro1658","article-title":"Helicobacter pylori evolution and phenotypic diversification in a changing host","volume":"5","author":"Suerbaum","year":"2007","journal-title":"Nat Rev Microbiol"},{"key":"2025053008014905700_ref2","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1016\/S2468-1253(23)00070-5","article-title":"Global prevalence of helicobacter pylori infection between 1980 and 2022: a systematic review and meta-analysis","volume":"8","author":"Li","year":"2023","journal-title":"Lancet Gastroenterol 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