ArticleCancer cell2021
Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma.
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In one paragraph
Article in Cancer cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 245 papers, 1 of them a synthesis that pooled it.
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245citing papers in PubMed, 1 pooled it
24.0field-weighted citation impact, top 1% of its field
What it found
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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
245 citing papers in PubMed, 1 synthesis or guideline pooled it, 368 citations in OpenAlex.
- Single-cell meta-analysis of T cells reveals clonal dynamics of response to checkpoint immunotherapy.Cell genomics · 2025Pooled it
- FGF/FGFR Alteration Type as a Candidate Enrichment Biomarker for Gunagratinib in Recurrent or Metastatic Head and Neck Cancer: An Exploratory Analysis of Two Early-Phase Trials.Targeted oncology · 2026Trial
- Palbociclib, a Selective CDK4/6 Inhibitor, Administered Before and After Chemoradiotherapy for Human Papillomavirus-Negative, Locally Advanced Head and Neck Squamous Cell Carcinoma: A Single-Arm, Phase II Trial.JCO precision oncology · 2025Trial
- RhoA WT allele loss unleashes the cancer driver function of RhoA E40Q.The Journal of clinical investigation · 2026Article
- Targeting MDA-9/syntenin-1 (SDCBP) as a strategy to eliminate head and neck squamous cell carcinoma stem cells.Cancer letters · 2026Article
- Complex assembly and activity states as multifaceted protein attributes explaining phenotypic variability.Molecular systems biology · 2026Article
- Effective tumor kinetics inferred from single routine H&E biopsies enable counterfactual virtual radiotherapy trials.medRxiv : the preprint server for health sciences · 2026Article
- Identifying head and neck squamous cell carcinoma: HPV-associated signature by integrating bulk and single-cell sequencing data.Medicine · 2026Article
- Proteogenomic characterization of pulmonary large-cell neuroendocrine carcinoma identifies molecular features and therapeutic strategy.Science advances · 2026Article
- Spatially resolved proteomics provides insights into the normal-dysplasia-tumor continuum in oral squamous cell carcinoma.BMC oral health · 2026Article
- Bimodality in pan-cancer proteomics reveals new opportunities for biomarker discovery.Genome biology · 2026Article
- Biomarkers Predictive of Immunotherapy Efficacy in Head and Neck Squamous Cell Carcinoma: Current Insights and Future Perspectives.World journal of otorhinolaryngology - head and neck surgery · 2026Review
- Molecular and Immune Landscape of Recurrent and/or Distant Metastatic Squamous Cell Carcinoma of the Head and Neck: An EORTC/IMMUCAN Project.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Multivariate Random Forests for Cross-Modal Multi-Omics Integration.bioRxiv : the preprint server for biology · 2026Article
- Mass Spectrometric Detected Cancer Proteins as Resources for Cancer Research.Journal of proteome research · 2026Article
- Region-Resolved Integrative Multi-Omic Characterization Reveals Diverse Tumor and Microenvironment Features of Pituitary Neuroendocrine Tumors.Molecular & cellular proteomics : MCP · 2026Article
- Transcriptional states define dependencies and therapeutic vulnerabilities in head and neck cancer.NPJ precision oncology · 2026Article
- RAPTOR Silencing Inhibits Head and Neck Squamous Cell Carcinoma Progression via Regulation of S100A8/A9 and Urokinase Plasminogen Activator.Medical science monitor : international medical journal of experimental and clinical research · 2026Article
- MultiOmicsXplorer, a tool to browse, access and analyse multi-omics data.BMC bioinformatics · 2026Article
- Global impact of germline structural variation on the cancer proteome.Nature communications · 2026Article
185 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
70 authors at 19 institutions in 2 countries.
Chen HuangLester 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.
Lijun ChenDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
Sara R SavageLester 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.
Rodrigo Vargas EguezDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
Yongchao DouLester 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.
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.
Felipe da Veiga LeprevostDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Eric J JaehnigLester 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.
Jonathan T LeiLester 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.
Bo WenLester 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.
Michael SchnaubeltDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
Karsten KrugBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Xiaoyu SongTisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Marcin CieślikDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Hui-Yin ChangDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Matthew A WyczalkowskiDepartment 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.
Kai LiLester 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.
Antonio ColapricoSylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
Qing Kay LiDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
David J ClarkDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
Yingwei HuDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
Liwei CaoDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
Jianbo PanDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University, Baltimore, MD 21231, USA.
Yuefan WangDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
Kyung-Cho ChoDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
Zhiao ShiLester 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.
Yuxing LiaoLester 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.
Wen JiangLester 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.
Meenakshi AnuragLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
Jiayi JiTisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Seungyeul YooDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Daniel Cui ZhouDepartment 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.
Wen-Wei LiangDepartment 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.
Michael WendlDepartment 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.
Pankaj VatsMichigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Steven A CarrBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
D R ManiBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Zhen ZhangDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
Jiang QianDepartment of Ophthalmology, Johns Hopkins University, Baltimore, MD 21231, USA.
Xi S ChenSylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
Alexander R PicoInstitute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA.
Pei WangDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Arul M ChinnaiyanDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Karen A KetchumESAC, Inc., Rockville, MD 20850, United States.
Christopher R KinsingerOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA.
Ana I RoblesOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA.
Eunkyung AnOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA.
Tara HiltkeOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA.
Mehdi MesriOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA.
Mathangi ThiagarajanLeidos Biomedical Research Inc., Frederick NaVonal Laboratory for Cancer Research, Frederick, MD 21702, USA.
Alissa M WeaverDepartment of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
Andrew G SikoraDepartment of Head and Neck Surgery, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
Jan LubińskiDepartment of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, 71-252 Szczecin, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland.
Małgorzata WierzbickaPoznań University of Medical Sciences, 61-701 Poznań, Poland; Institute of Human Genetics Polish Academy of Sciences, 60-479 Poznań, Poland.
Maciej WiznerowiczInternational Institute for Molecular Oncology, 60-203 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland.
Shankha SatpathyBroad 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.
George MilesLester 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.
Matthew J EllisLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
Gilbert S OmennDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Henry RodriguezOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA.
Emily S BojaOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA.
Saravana M DhanasekaranDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Li DingDepartment 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.
Alexey I NesvizhskiiDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Adel K El-NaggarDepartment of Pathology, Division of Pathology and Laboratory Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA.
Daniel W ChanDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA. Electronic address: dchan@jhmi.edu.
Hui ZhangDepartment of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA. Electronic address: huizhang@jhu.edu.
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. Electronic address: bing.zhang@bcm.edu.
Clinical Proteomic Tumor Analysis Consortium
Johns Hopkins University · USBaylor College of Medicine · USNational Cancer Institute · USUniversity of Michigan–Ann Arbor · USWashington University in St. Louis · USIcahn School of Medicine at Mount Sinai · USBroad Institute · USMassachusetts Institute of Technology · USInternational Institute for Molecular Oncology · PLJames S. McDonnell Foundation · USMichigan Center for Translational Pathology · USThe University of Texas MD Anderson Cancer Center · USUniversity of Miami · USEnterprise Science and Computing (United States) · USGladstone Institutes · USLeidos Biomedical Research Inc. (United States)Poznan University of Medical Sciences · PLSylvester Comprehensive Cancer Center · USVanderbilt University · US
Funding
UNC-CH CENTER FOR ENVIRONMENTAL HEALTH &SUSCEPTIBILITYP30ES010126 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Stephanie Engel · 2001 to 2026
$36.3MMICROSCALED PROTEOGENOMICS FOR CANCER CLINICAL TRIALSU01CA214125 · NCI · BAYLOR COLLEGE OF MEDICINE · PI ANURAG, MEENAKSHI, CARR, STEVEN A · 2017 to 2021
$7.0MCenter of Excellence for High Throughput Proteogenomic CharacterizationU24CA210986 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, GILLETTE, MICHAEL A · 2016 to 2020
$6.4MThe 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
$5.3MiPGDAC, An Integrative Proteogenomic Data Analysis Center for CPTACU24CA210954 · NCI · BAYLOR COLLEGE OF MEDICINE · PI ZHANG, BING · 2016 to 2020
$4.9MSystems Biology based Proteogenomic Translator for Cancer Marker Discovery towards Precision MedicineU24CA210993 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI SCHADT, ERIC E, WANG, PEI · 2016 to 2020
$4.6MIntegrated high throughput proteogenomic data analysis center for CPTACU24CA210979 · NCI · BROAD INSTITUTE, INC. · PI BIRGER, CHET, GETZ, GAD A · 2016 to 2020
$4.4MUniversity of Michigan Proteogenomics Data Analysis CenterU24CA210967 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CHINNAIYAN, ARUL M, DHANASEKARAN, SARAVANA M · 2016 to 2020
$4.1MProteogenomic Data Analysis for Cancer Systems Biology and Clinical TranslationU24CA210972 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI DING, LI, FENYO, DAVID · 2016 to 2020
$3.3MTranslational Breast Cancer Research Training ProgramT32CA203690 · NCI · BAYLOR COLLEGE OF MEDICINE · PI FUQUA, SUZANNE AW, RIMAWI, MOTHAFFAR FAHED · 2018 to 2022
$1.0MNCI NIH HHS T32 CA203690NCI 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 CA210993NIEHS NIH HHS P30 ES010126
Abstract
We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs HNSCC-associated proteins and phosphosites, prioritizes copy number drivers, and highlights an oncogenic role for RNA processing genes. Proteomic investigation of mutual exclusivity between FAT1 truncating mutations and 11q13.3 amplifications reveals dysregulated actin dynamics as a common functional consequence. Phosphoproteomics characterizes two modes of EGFR activation, suggesting a new strategy to stratify HNSCCs based on EGFR ligand abundance for effective treatment with inhibitory EGFR monoclonal antibodies. Widespread deletion of immune modulatory genes accounts for low immune infiltration in immune-cold tumors, whereas concordant upregulation of multiple immune checkpoint proteins may underlie resistance to anti-programmed cell death protein 1 monotherapy in immune-hot tumors. Multi-omic analysis identifies three molecular subtypes with high potential for treatment with CDK inhibitors, anti-EGFR antibody therapy, and immunotherapy, respectively. Altogether, proteogenomics provides a systematic framework to inform HNSCC biology and treatment.
Indexed as
AdultAgedAged, 80 and overAntineoplastic Agents, ImmunologicalErbB ReceptorsFemaleHumansImmunotherapyMaleMiddle AgedPapillomavirus InfectionsProteogenomicsProteomicsSquamous Cell Carcinoma of Head and NeckYoung AdultAntineoplastic Agents, ImmunologicalErbB ReceptorsCDK inhibitorcombination immune checkpoint blockadeCPTACEGFR mAbHNSCCimmune evasionimmunotherapypredictive biomarkerproteogenomicsproteomics
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