ArticleCell2024
Pan-cancer proteogenomics characterization of tumor immunity.
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Article in Cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65citing papers in PubMed
22.0field-weighted citation impact, top 1% of its field
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
65 citing papers in PubMed, 78 citations in OpenAlex.
- Proteogenomic analysis of the CALGB 40601 (Alliance) HER2+ breast cancer neoadjuvant trial reveals resistance biomarkers.Cell reports. Medicine · 2025Trial
- Post‑translational modification‑governed immune states in cancer immunity: Biomarker implications for checkpoint competence, tumor visibility and immunotherapy resistance (Review).International journal of oncology · 2026Review
- Multi-omics analysis reveals comprehensive aberrant protein and phosphorylation characteristics in breast cancer and paired metastatic lymph nodes.Protein & cell · 2026Article
- ITPRIPL1: A tumor immune-associated biomarker with prognostic and therapeutic implications in gastrointestinal cancer.Scientific reports · 2026Article
- pH-neutralization strategy to suppress GPCR68 spatiotemporally activates T cells and enhances anti-tumor immunity.Bioactive materials · 2026Article
- Proteomic health archetypes identified in disease-free adults enable risk assessment for diverse chronic diseases.Genome medicine · 2026Article
- PathTIGR: A pathway topology-informed graph representation learning framework for immunotherapy response prediction.Science advances · 2026Article
- Gallic acid chemoprevention of oral carcinogenesis is associated with HSD11β2 upregulation and immune remodeling.Scientific reports · 2026Article
- Discovering proteo-transcriptomic networks via biologically informed heterogeneous graph learning.Nucleic acids research · 2026Article
- Review
- Proteogenomics: decoding cancer in multiple dimensions.MedScience · 2026Review
- Hijacking emergency granulopoiesis: Neutrophil ontogeny and reprogramming in cancer.Molecular oncology · 2026Review
- Human Systems Immunology in the Omics Era: Challenges, Methods, and Emerging Directions.European journal of immunology · 2026Review
- Integrative multi-omics profiling deciphers tumor microenvironment heterogeneity and immunotherapy vulnerabilities in lung neuroendocrine carcinomas.Journal of advanced research · 2026Article
- Article
- Single-cell omics in tumor lymph node metastasis: mechanisms and therapeutic implications.Molecular cancer · 2026Review
- Deciphering RNA and protein expression discordance identifies TOP2A as a prognostic biomarker and potential therapeutic target in lung adenocarcinoma.Discover oncology · 2026Article
- Genome-wide screenings identify BAP1 as a synthetic-lethality target with CDK4/6 inhibitors.Science advances · 2026Article
- Panorama: a database for the oncogenic evaluation of somatic mutations in pan-cancer.Database : the journal of biological databases and curation · 2026Article
- Redox-metabolic circuits as a central regulator of T cell-based immunotherapy.Frontiers in immunology · 2026Review
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
59 authors at 16 institutions in 4 countries.
Francesca PetraliaDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: francesca.petralia@mssm.edu.
Weiping MaDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Tomer M YaronMeyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Francesca Pia CarusoBIOGEM Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy; Department of Electrical Engineering and Information Technologies, University of Naples "Federico II", Naples, Italy.
Nicole TignorDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Joshua M WangInstitute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
Daniel CharytonowiczDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Jared L JohnsonMeyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
Emily M HuntsmanMeyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA.
Giacomo B MarinoDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Anna CalinawanDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
John Erol EvangelistaDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Myvizhi Esai SelvanDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Shrabanti ChowdhuryDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Dmitry RykunovDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Azra KrekDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Xiaoyu SongInstitute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Berk TurhanDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Karen E ChristiansonBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
David A LewisDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Eden Z DengDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Daniel J B ClarkeDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Jeffrey R WhiteakerTranslational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Jacob J KennedyTranslational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Lei ZhaoTranslational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Rossana Lazcano SeguraDepartments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Harsh BatraDepartment of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Maria Gabriela RasoDepartment of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Edwin Roger ParraDepartment of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Rama SoundararajanDepartment of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Ximing TangDepartment of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Yize LiDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
Xinpei YiLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Shankha SatpathyBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Ying WangInstitute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
Maciej WiznerowiczDepartment of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland; Department of Oncology, Heliodor Swiecicki Clinical Hospital, 60-203 Poznań, Poland.
Tania J González-RoblesInstitute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
Antonio IavaroneDepartment of Neurological Surgery, Department of Biochemistry, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA.
Sara J C GoslineBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
Boris RevaDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Ana I RoblesOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.
Alexey I NesvizhskiiDepartments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
D R ManiBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Michael A GilletteBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
Robert J KleinDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Marcin CieslikDepartments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Bing ZhangLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Amanda G PaulovichTranslational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Robert SebraDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Zeynep H GümüşDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Galen HostetterPathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
David FenyöInstitute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
Gilbert S OmennDepartments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, & Environmental Health, University of Michigan, Ann Arbor, MI 48109, USA.
Lewis C CantleyMeyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
Avi Ma'ayanDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Alexander J LazarDepartments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Michele CeccarelliSylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA; Department of Public Health Sciences, University of Miami, Miami, FL, USA.
Pei WangDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: pei.wang@mssm.edu.
Clinical Proteomic Tumor Analysis Consortium
Icahn School of Medicine at Mount Sinai · USThe University of Texas MD Anderson Cancer Center · USBaylor College of Medicine · USBroad Institute · USNew York University · USFred Hutch Cancer Center · USUniversity of Miami · USUniversity of Michigan · USCornell University · USHarvard University · USBiogem · ITCancer Clinic · USJames S. McDonnell Foundation · USPacific Northwest National Laboratory · USPoznan University of Medical Sciences · PLVan Andel Institute · US
Funding
Strategic Vision & Impact on Environmental HealthP30ES017885 · NIEHS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Marie Sylvia O'Neill · 2011 to 2026
$21.3MProject 3: The Evolving Role of Regional Lymph Nodes in Melanoma ProgressionU54CA263001 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Kelly Valentine Ruggles · 2022 to 2026
$11.6MRole of Phosphoinositides and Protein Kinases in the control of Cancer MetabolismR35CA197588 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI LEWIS C. CANTLEY · 2016 to 2026
$10.2MProteogenomic Studies aimed at understanding ovarian tumor responses to agents targeting the DNA damage response and translating this knowledge into clinical benefitU01CA214114 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI BIRRER, MICHAEL, PAULOVICH, AMANDA G · 2017 to 2021
$8.4MMICROSCALED PROTEOGENOMICS FOR CANCER CLINICAL TRIALSU01CA214125 · NCI · BAYLOR COLLEGE OF MEDICINE · PI ANURAG, MEENAKSHI, CARR, STEVEN A · 2017 to 2021
$7.0MProteogenomic Translational Research Center for Clinical ProteomicU01CA214116 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI DRUKER, BRIAN J, RODLAND, KARIN D · 2017 to 2021
$6.8MMount Sinai Medical Scientist Training ProgramT32GM146636 · NIGMS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Talia H Swartz · 2022 to 2026
$6.8MCenter for Advanced Multi-Omic Characterization of CancerU24CA271012 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI Tao Liu · 2022 to 2026
$6.6MCenter of Excellence for High Throughput Proteogenomic CharacterizationU24CA210986 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, GILLETTE, MICHAEL A · 2016 to 2020
$6.4MCenter of Excellence for High Throughput Proteogenomic CharacterizationU24CA270823 · NCI · BROAD INSTITUTE, INC. · PI STEVEN A CARR, MICHAEL A GILLETTE · 2022 to 2026
$5.3MThe Comprehensive Proteome Characterization Center at Johns Hopkins: High Precision Discovery and Confirmation of Genoproteomic TargetsU24CA210985 · NCI · JOHNS HOPKINS UNIVERSITY · PI CHAN, DANIEL WANYUI, ZHANG, HUI · 2016 to 2020
$5.3MPNNL Proteome Characterization CenterU24CA210955 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI LIU, TAO, SMITH, RICHARD D · 2016 to 2020
$5.3MNCI NIH HHS F30 CA265288NCI NIH HHS F30 CA271622NCI NIH HHS HHSN261201500003CNCI NIH HHS HHSN261201500003INCI NIH HHS R33 CA263705NCI NIH HHS R35 CA197588NCI NIH HHS U01 CA214114NCI NIH HHS U01 CA214116NCI NIH HHS U01 CA214125NCI NIH HHS U24 CA210954NCI NIH HHS U24 CA210955NCI NIH HHS U24 CA210967NCI NIH HHS U24 CA210972NCI NIH HHS U24 CA210979NCI NIH HHS U24 CA210985NCI NIH HHS U24 CA210986NCI NIH HHS U24 CA210993NCI NIH HHS U24 CA224260NCI NIH HHS U24 CA264250NCI NIH HHS U24 CA270823NCI NIH HHS U24 CA271012NCI NIH HHS U24 CA271037NCI NIH HHS U24 CA271075NCI NIH HHS U24 CA271114NCI NIH HHS U54 CA263001NIEHS NIH HHS P30 ES017885NIGMS NIH HHS T32 GM136542NIGMS NIH HHS T32 GM146636
Abstract
Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data. We identified seven distinct immune subtypes based on integrative learning of cell type compositions and pathway activities. We then thoroughly categorized unique genomic, epigenetic, transcriptomic, and proteomic changes associated with each subtype. Further leveraging the deep phosphoproteomic data, we studied kinase activities in different immune subtypes, which revealed potential subtype-specific therapeutic targets. Insights from this work will facilitate the development of future immunotherapy strategies and enhance precision targeting with existing agents.
Indexed as
NeoplasmsProteogenomicsCombined Modality TherapyGenomicsHumansProteomicsTumor Escapehistopathologyimmune subtypeimmunotherapykinase activitymultiomic deconvolutionproteogenomicstumor immunity
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