{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T03:44:02Z","timestamp":1775619842933,"version":"3.50.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,2,12]],"date-time":"2024-02-12T00:00:00Z","timestamp":1707696000000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Health Medical Research Fund","award":["07182016"],"award-info":[{"award-number":["07182016"]}]},{"name":"Research Fund Secretariat in Hong Kong"},{"name":"Theme-based Research Scheme"},{"name":"Hong Kong Research Grants Council","award":["T12-703\/22-R"],"award-info":[{"award-number":["T12-703\/22-R"]}]},{"DOI":"10.13039\/501100003452","name":"Innovation and Technology Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003452","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Neoantigens are derived from somatic mutations in the tumors but are absent in normal tissues. Emerging evidence suggests that neoantigens can stimulate tumor-specific T-cell-mediated antitumor immune responses, and therefore are potential immunotherapeutic targets. We developed ImmuneMirror as a stand-alone open-source pipeline and a web server incorporating a balanced random forest model for neoantigen prediction and prioritization. The prediction model was trained and tested using known immunogenic neopeptides collected from 19 published studies. The area under the curve of our trained model was 0.87 based on the testing data. We applied ImmuneMirror to the whole-exome sequencing and RNA sequencing data obtained from gastrointestinal tract cancers including 805 tumors from colorectal cancer (CRC), esophageal squamous cell carcinoma (ESCC) and hepatocellular carcinoma patients. We discovered a subgroup of microsatellite instability-high (MSI-H) CRC patients with a low neoantigen load but a high tumor mutation burden (&amp;gt;\u200910 mutations per Mbp). Although the efficacy of PD-1 blockade has been demonstrated in advanced MSI-H patients, almost half of such patients do not respond well. Our study identified a subset of MSI-H patients who may not benefit from this treatment with lower neoantigen load for major histocompatibility complex I (P\u2009&amp;lt;\u20090.0001) and II (P\u2009=\u20090.0008) molecules, respectively. Additionally, the neopeptide YMCNSSCMGV-TP53G245V, derived from a hotspot mutation restricted by HLA-A02, was identified as a potential actionable target in ESCC. This is so far the largest study to comprehensively evaluate neoantigen prediction models using experimentally validated neopeptides. Our results demonstrate the reliability and effectiveness of ImmuneMirror for neoantigen prediction.<\/jats:p>","DOI":"10.1093\/bib\/bbae024","type":"journal-article","created":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T08:38:30Z","timestamp":1705394310000},"source":"Crossref","is-referenced-by-count":18,"title":["ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction"],"prefix":"10.1093","volume":"25","author":[{"given":"Gulam Sarwar","family":"Chuwdhury","sequence":"first","affiliation":[{"name":"Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China"},{"name":"University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China"}]},{"given":"Yunshan","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Yale School of Public Health , New Haven, Connecticut , USA"}]},{"given":"Chi-Leung","family":"Chiang","sequence":"additional","affiliation":[{"name":"Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China"},{"name":"University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China"}]},{"given":"Ka-On","family":"Lam","sequence":"additional","affiliation":[{"name":"Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China"},{"name":"University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China"}]},{"given":"Ngar-Woon","family":"Kam","sequence":"additional","affiliation":[{"name":"Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China"},{"name":"University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China"},{"name":"Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park , Shatin , Hong Kong"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3048-9823","authenticated-orcid":false,"given":"Zhonghua","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Columbia University , New York, NY , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5558-0685","authenticated-orcid":false,"given":"Wei","family":"Dai","sequence":"additional","affiliation":[{"name":"Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China"},{"name":"University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China"},{"name":"University of Hong Kong-Shenzhen Hospital , Shenzhen , P. R. China"}]}],"member":"286","published-online":{"date-parts":[[2024,2,10]]},"reference":[{"issue":"6334","key":"2024021207292433400_ref1","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1126\/science.aak9510","article-title":"Landscape of immunogenic tumor antigens in successful immunotherapy of virally induced epithelial cancer","volume":"356","author":"Stevanovi\u0107","year":"2017","journal-title":"Science"},{"issue":"30","key":"2024021207292433400_ref2","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2025570118","article-title":"Characterization of neoantigen-specific T cells in cancer resistant to immune checkpoint therapies","volume":"118","author":"Li","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"2024021207292433400_ref3","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.cels.2018.05.014","article-title":"MHCflurry: open-source class I MHC binding affinity 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