ArticleCell reports. Medicine2026
A 15-layer multi-omics analysis of gastric cancer ecotypes provides therapeutic insights.
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Article in Cell reports. Medicine, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2citing papers in PubMed
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Who cites it
2 citing papers in PubMed.
- Phosphorylation shapes antigen presentation and immune recognition: mechanistic insights and translational perspectives.Frontiers in immunology · 2026Review
- Gastric bacterial microbiota and gastric carcinogenesis: from dysbiosis to immune remodeling and therapeutic opportunities.Frontiers in immunology · 2026Review
Corrections and comments
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Authors and funding
61 authors.
Yuefan WangDepartment of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Lindsey K OlsenLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Fenglong JiaoDepartment of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA.
Chenwei WangLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Kevin X JiangDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Yongchao DouLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Yingwei HuDepartment of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Liyuan JiaoDepartment of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Wenrong ChenLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
John M ElizarrarasLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Pratik KhareGigantest, Baltimore, MD, USA.
Nengneng YuDepartment of Computer Science, University of Maryland, College Park, MD, USA.
Huili ZhuDepartment of Gastrointestinal Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Lijun ChenDepartment of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Tung-Shing M LihDepartment of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Pınar Ö EserCancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Fernanda Martins RodriguesDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA.
Zhiao ShiLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Cissy ZhangGigantest, Baltimore, MD, USA.
Clinton YuDepartment of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA.
David I HeimanCancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Yuxing LiaoLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Paul W ShaferLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Seunghyuk ChoiLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Jong Min ChoiLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Sara R SavageLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Eric J JaehnigLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Jonathan T LeiLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Yanling SunLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Chien-Wei PengDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA.
Zhenyu SunDepartment of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Paul MorenkovDepartment of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA.
Kevin ZhangDepartment of Neuroscience, Krieger School of Arts and Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Yifat GeffenCancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Julian HessCancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Chandan Kumar-SinhaDepartment of Pathology, University of Michigan, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.
D R ManiBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Li DingDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
Gad GetzCancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; Krantz Family Center for Cancer Research and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
Qing Kay LiDepartment of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Gilbert S OmennDepartments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and Environmental Health, University of Michigan, Ann Arbor, MI, USA.
Anne LeGigantest, Baltimore, MD, USA.
Galen HostetterVan Andel Research Institute, Grand Rapids, MI, USA.
Chelsea J NewtonVan Andel Research Institute, Grand Rapids, MI, USA.
Shuang CaiICF, 530 Gaither Road Suite 500, Rockville, MD, USA.
Karen A KetchumICF, 530 Gaither Road Suite 500, Rockville, MD, USA.
Ana I RoblesOffice of Cancer Clinical Proteomics Research, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.
Mehdi MesriOffice of Cancer Clinical Proteomics Research, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.
Parham MinooDepartment of Pathology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
M Constanza CamargoDivision of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
Eunkyung AnOffice of Cancer Clinical Proteomics Research, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.
Ralph H HrubanDepartment of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Zaoxing LiuDepartment of Computer Science, University of Maryland, College Park, MD, USA.
Mathangi ThiagarajanFrederick National Laboratory for Cancer Research, Frederick, MD, USA.
Anders B DohlmanDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Ramon U JinDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA; Division of Oncology and Gastroenterology, Washington University School of Medicine, St. Louis, MO, USA.
Lan HuangDepartment of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA.
Daniel W ChanDepartment of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Hui ZhangDepartment of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Electronic address: huizhang@jhu.edu.
Bing ZhangLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. Electronic address: bing.zhang@bcm.edu.
Clinical Proteomic Tumor Analysis Consortium
Funding
Center for Advanced Multi-Omic Characterization of CancerU24CA271012 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI Tao Liu · 2022 to 2026
$6.6MProteogenomic Characterization of Tumor Tissues and Preclinical Models with High PrecisionU24CA271079 · NCI · JOHNS HOPKINS UNIVERSITY · PI DANIEL Wanyui CHAN, Hui Zhang · 2022 to 2026
$6.6MProteogenomic characterization of early and late resistance mechanisms in acute myeloid leukemiaU01CA271412 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI BRIAN J DRUKER, Paul D Piehowski · 2022 to 2026
$5.8MProteogenomic studies to understand mechanisms and drivers of resistance to immunotherapiesU01CA271407 · NCI · FRED HUTCHINSON CANCER CENTER · PI Diwakar Davar, AMANDA G PAULOVICH · 2022 to 2026
$5.6MCenter of Excellence for High Throughput Proteogenomic CharacterizationU24CA270823 · NCI · BROAD INSTITUTE, INC. · PI STEVEN A CARR, MICHAEL A GILLETTE · 2022 to 2026
$5.3MMayo Clinic Center for Clinical ProteomicsU01CA271410 · NCI · MAYO CLINIC ROCHESTER · PI Rafael Fonseca, AKHILESH PANDEY · 2022 to 2026
$5.3MProteogenomic translator for cancer biomarker discovery towards precision medicineU24CA271114 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Avi Ma'ayan, Pei Wang · 2022 to 2026
$5.0MProteogenomic Predictors of Recurrence in Non-small Cell Lung CancerU01CA271402 · NCI · WASHINGTON UNIVERSITY · PI STEVEN A CARR, MICHAEL A GILLETTE · 2022 to 2026
$5.0MTranslating Pediatric Cancer Proteogenomic Data into Biological and Clinical InsightsU24CA271076 · NCI · BAYLOR COLLEGE OF MEDICINE · PI Bing Zhang · 2022 to 2026
$5.0MMichigan Center for Translational Cancer Proteogenomics-Diversity SupplementU24CA271037 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Saravana Mohan Dhanasekaran, Alexey I Nesvizhskii · 2022 to 2026
$4.4MCenter for comprehensive proteogenomic data analysisU24CA271075 · NCI · BROAD INSTITUTE, INC. · PI GAD A GETZ, Denkanikota R Mani · 2022 to 2026
$3.9MNCI NIH HHS U01 CA271402NCI NIH HHS U01 CA271407NCI NIH HHS U01 CA271410NCI NIH HHS U01 CA271412NCI NIH HHS U24 CA270823NCI NIH HHS U24 CA271012NCI NIH HHS U24 CA271037NCI NIH HHS U24 CA271075NCI NIH HHS U24 CA271076NCI NIH HHS U24 CA271079NCI NIH HHS U24 CA271114
Abstract
Gastric cancer is marked by profound molecular and microenvironmental heterogeneity that limits therapeutic progress. Here, we present a 15-layer multi-omics atlas that integrates genomics, epigenomics, transcriptomics, proteomics, multiple post-translational modifications (PTMs), protein-protein interactions, metabolomics, and microbiome profiles from 159 primary gastric adenocarcinomas and 30 matched normal adjacent tissues. Using cell-state deconvolution, we define tumor ecotypes that refine genomic and histological subtypes by capturing distinct tumor microenvironment architectures linked to clinical outcomes and potential associations with immunotherapy response. Multi-omics integration prioritizes genomic and epigenomic aberrations and their associated vulnerabilities; defines ecotype-specific transcriptional programs, signaling pathways, PTMs, protein interaction networks, and metabolic regulation; and identifies microbiome features linked to ecotypes and resistance pathways. We further prioritize ecotype-, genomic subtype-, and cell type-specific targetable proteins using proteomic and PTM analyses within a tumor microenvironment context. This comprehensive atlas provides a systems-level blueprint for decoding gastric cancer heterogeneity and advancing precision oncology.
Indexed as
Stomach NeoplasmsGene Expression Regulation, NeoplasticGenomicsHumansMetabolomicsMicrobiotaMultiomicsProtein Interaction MapsProtein Processing, Post-TranslationalProteomicsTumor Microenvironmentgastric cancermetabolomicsmicrobiomemulti-omicspost-translational modificationsprecision oncologyprotein-protein interactionsproteogenomicstherapeutic targetstumor ecotypestumor microenvironment
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.