ArticleScientific reports2025
Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles.
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Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4citing papers in PubMed
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Who cites it
4 citing papers in PubMed.
- Pan-cancer analysis identifies KANSL2 as a cell-cycle-associated regulator of tumor progression and immunity in liver hepatocellular carcinoma.Clinical and experimental medicine · 2026Article
- RFX5 in cancer: context-dependent molecular functions and emerging translational relevance.Frontiers in immunology · 2026Review
- Cancer complexity: why we need a novel cancer research strategy.Frontiers in oncology · 2025Article
- Tumor-infiltrating lymphocytes and tumor-associated macrophages in cancer immunoediting: a targetable therapeutic axis.Frontiers in immunology · 2025Review
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Authors and funding
51 authors.
Bhavneet BhinderEnglander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
Verena FriedlBiomolecular Engineering Department, School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.
Sunantha SethuramanDivision of Oncology, Department of Medicine, Washington University in St. Louis, 4515 McKinley Dr, St. Louis, MO, 63110, USA.
Davide RissoDepartment of Statistical Sciences, University of Padova, Via C. Battisti 241, 35121, Padua, Italy.
Kami E ChiottiDepartment of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA.
R Jay MashlDivision of Oncology, Department of Medicine, Washington University in St. Louis, 4515 McKinley Dr, St. Louis, MO, 63110, USA.
Kyle P EllrottDepartment of BioMedical Engineering, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA.
Jordan A LeeDepartment of BioMedical Engineering, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA.
Christopher K WongBiomolecular Engineering Department, School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.
Kofi GyanEnglander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
Aditya DeshpandeEnglander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
Marcin ImielinskiEnglander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
Rohan BarejaEnglander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
Josh StuartUC Santa Cruz Genomics Institute, Santa Cruz, CA, 95064, USA.
Myron PetoDepartment of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA.
Katherine A HoadleyLineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
Alexander J LazarDepartments of Pathology, Genomics Medicine, Dermatology, & Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd-Unit 85, Houston, TX, 77030, USA.
Andrew D CherniackBroad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
Jingchun ZhuUC Santa Cruz Genomics Institute, Santa Cruz, CA, 95064, USA.
Shaolong CaoDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX, 77030, USA.
Mark RubinDepartment for BioMedical Research, University of Bern, Bern, 3012, Switzerland.
Wenyi WangDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX, 77030, USA.
Oliver F BatheDivision of Surgical Oncology, Tom Baker Cancer Centre, 1331 - 29Th St NW, Calgary, AB, T2N 4N2, Canada.
Nicolas RobineNew York Genome Center, Computational Biology, 101 Avenue of the Americas, New York, NY, 10013, USA.
Li DingDivision of Oncology, Department of Medicine, Washington University in St. Louis, 4515 McKinley Dr, St. Louis, MO, 63110, USA.
Peter W LairdVan Andel Institute, 333 Bostwick AVE NE, Grand Rapids, MI, 49503, USA.
Wanding ZhouVan Andel Institute, 333 Bostwick AVE NE, Grand Rapids, MI, 49503, USA.
Hui ShenVan Andel Institute, 333 Bostwick AVE NE, Grand Rapids, MI, 49503, USA.
Vésteinn ThorssonInstitute for Systems Biology, 401 Terry Avenue N, Seattle, WA, 98109, USA.
Jen Jen YehDepartment of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
Matthew H BaileyDivision of Oncology, Department of Medicine, Washington University in St. Louis, 4515 McKinley Dr, St. Louis, MO, 63110, USA.
Daniel Cui ZhouDivision of Oncology, Department of Medicine, Washington University in St. Louis, 4515 McKinley Dr, St. Louis, MO, 63110, USA.
Xianlu L PengDepartment of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
Mary GoldmanUC Santa Cruz Genomics Institute, Santa Cruz, CA, 95064, USA.
Yongsheng LiDepartment of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
Anil KorkutDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX, 77030, USA.
Nidhi SahniDepartment of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Rd 1C, Smithville, TX, 78957, USA.
D Neil HayesUniversity of Tennessee Health Sciences Center, Memphis, TN, 38103, USA.
Michael K A MensahNational Cancer Institute, 31 Center Dr, 3A20, Bethesda, MD, 20892, USA.
Ina FelauNational Cancer Institute, 31 Center Dr, 3A20, Bethesda, MD, 20892, USA.
Anab KemalNational Cancer Institute, 31 Center Dr, 3A20, Bethesda, MD, 20892, USA.
Samantha Caesar-JohnsonNational Cancer Institute, 31 Center Dr, 3A20, Bethesda, MD, 20892, USA.
John A DemchokNational Cancer Institute, 31 Center Dr, 3A20, Bethesda, MD, 20892, USA.
Liming YangNational Cancer Institute, 31 Center Dr, 3A20, Bethesda, MD, 20892, USA.
Martin L FergusonNational Cancer Institute, 31 Center Dr, 3A20, Bethesda, MD, 20892, USA.
Roy TarnuzzerNational Cancer Institute, 31 Center Dr, 3A20, Bethesda, MD, 20892, USA.
Zhining WangNational Cancer Institute, 31 Center Dr, 3A20, Bethesda, MD, 20892, USA.
Jean C ZenklusenNational Cancer Institute, 31 Center Dr, 3A20, Bethesda, MD, 20892, USA.
Cancer Genome Atlas Analysis Network
Paul Spellman *Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA. spellmap@ohsu.edu.
Olivier Elemento *Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA. ole2001@med.cornell.edu.
Funding
Statistical methods for genomic analysis of heterogeneous tumorsR01CA268380 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Wenyi Wang · 2022 to 2026
$2.4MIntegrative Cancer Epigenomic Data Analysis Center (ICE-DAC)U24CA264023 · NCI · VAN ANDEL RESEARCH INSTITUTE · PI LAIRD, PETER W, SHEN, HUI · 2021 to 2025
$2.2MGDANII_DLBCL cohort analysis and cloud costsU24CA264024 · NCI · BROAD INSTITUTE, INC. · PI GAD A GETZ, Esther Rheinbay · 2021 to 2026
$2.1MThe MSK Genomic Data Analysis Center for Tumor EvolutionU24CA264028 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI SCHULTZ, NIKOLAUS, SHAH, SOHRAB P · 2021 to 2025
$2.1MThe joint WCM-NYGC Center for Functional and Clinical Interpretation of Tumor ProfilesU24CA264032 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI ELEMENTO, OLIVIER, ROBINE, NICOLAS · 2021 to 2025
$2.0MCenter for the Comprehensive Analysis of Cancer Somatic Copy-Number Alterations, Rearrangements, and Long-Read Sequencing DataU24CA264029 · NCI · BROAD INSTITUTE, INC. · PI BEROUKHIM, RAMEEN, CHERNIACK, ANDREW DAVID · 2021 to 2025
$1.9MUCSC-Buck Genome Data Analysis Center for the Genomic Data Analysis Network v2.0U24CA264009 · NCI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI BENZ, CHRISTOPHER, STUART, JOSHUA MICHAEL · 2021 to 2025
$1.9MA Genome Data Analysis Center Focused on Batch Effect Analysis and Data IntegrationU24CA264006 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI AKBANI, REHAN, WEINSTEIN, JOHN N · 2021 to 2025
$1.9MDeep exploration of drivers, evolution, and microenvironment toward discovering principal themes in cancerU24CA264010 · NCI · WASHINGTON UNIVERSITY · PI DING, LI, GOVINDAN, RAMASWAMY · 2021 to 2025
$1.8MOHSU Center for Specialized Data Analysis as part of the GDANU24CA264007 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI ELLROTT, KYLE, SPELLMAN, PAUL T. · 2021 to 2025
$1.8MSpecialized RNA analysis center for integrative genomic analysesU24CA264021 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAYES, DAVID N, HOADLEY, KATHERINE A. · 2021 to 2025
$1.7MPathway, Network and Spatiotemporal Integration of Cancer Genomics DataU24CA264027 · NCI · PRINCETON UNIVERSITY · PI RAPHAEL, BENJAMIN, YEH, JEN JEN · 2021 to 2025
$1.5MNCI NIH HHS R01 CA268380NCI NIH HHS U24 CA264006NCI NIH HHS U24 CA264007NCI NIH HHS U24 CA264009NCI NIH HHS U24 CA264010NCI NIH HHS U24 CA264021NCI NIH HHS U24 CA264023NCI NIH HHS U24 CA264024NCI NIH HHS U24 CA264027NCI NIH HHS U24 CA264028NCI NIH HHS U24 CA264029NCI NIH HHS U24 CA264032
Abstract
Traditional gene expression deconvolution methods assess a limited number of cell types, therefore do not capture the full complexity of the tumor microenvironment (TME). Here, we integrate nine deconvolution tools to assess 79 TME cell types in 10,592 tumors across 33 different cancer types, creating the most comprehensive analysis of the TME. In total, we found 41 patterns of immune infiltration and stroma profiles, identifying heterogeneous yet unique TME portraits for each cancer and several new findings. Our findings indicate that leukocytes play a major role in distinguishing various tumor types, and that a shared immune-rich TME cluster predicts better survival in bladder cancer for luminal and basal squamous subtypes, as well as in melanoma for RAS-hotspot subtypes. Our detailed deconvolution and mutational correlation analyses uncover 35 therapeutic target and candidate response biomarkers hypotheses (including CASP8 and RAS pathway genes).
Indexed as
MutationNeoplasmsTumor MicroenvironmentBiomarkers, TumorGene Expression ProfilingGene Expression Regulation, NeoplasticHumansPrognosisStromal CellsBiomarkers, TumorCell type estimationDeconvolutionImmune cellsIntegrated scoresiScoresPan-cancer analysisSomatic mutationsStromaSurvivalTumor microenvironmentTumor progression
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