Evidence map›Paper›PMID 34358469›Full record

ArticleCell2021

A proteogenomic portrait of lung squamous cell carcinoma.

Shankha Satpathy, Karsten Krug, Pierre M Jean Beltran, Sara R Savage, Francesca Petralia, Chandan Kumar-Sinha, Yongchao Dou, Boris Reva, M Harry Kane, Shayan C Avanessian and 65 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 243 papers.

0numbers the graph read from it
0cells of the map it votes in
243citing papers in PubMed
21.7field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

243 citing papers in PubMed, 370 citations in OpenAlex.

  1. Article
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  6. Prognostic Significance ofMedicina (Kaunas, Lithuania) · 2026
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183 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

75 authors at 17 institutions in 1 country.

Shankha SatpathyBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA. Electronic address: shankha@broadinstitute.org.
Karsten KrugBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Pierre M Jean BeltranBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Sara R SavageLester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Francesca PetraliaDepartment of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Chandan Kumar-SinhaDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Yongchao DouLester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Boris RevaDepartment of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
M Harry KaneBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Shayan C AvanessianBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Suhas V VasaikarDepartment of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Azra KrekDepartment of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Jonathan T LeiLester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Eric J JaehnigLester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Tatiana OmelchenkoMemorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Yifat GeffenBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Erik J BergstromBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Vasileios StathiasSylvester Comprehensive Cancer Center and Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
Karen E ChristiansonBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
David I HeimanBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Marcin P CieslikDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Song CaoSiteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Xiaoyu SongDepartment of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Jiayi JiDepartment of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Wenke LiuInstitute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Kai LiLester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Bo WenLester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Yize LiSiteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Zeynep H GümüşDepartment of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Myvizhi Esai SelvanDepartment of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Rama SoundararajanDepartment of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Tanvi H VisalDepartment of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Maria G 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.
Özgün BaburComputer Science Department, University of Massachusetts Boston, Boston, MA 02125, USA.
Pankaj VatsDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Shankara AnandBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Tobias SchrainkInstitute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA.
MacIntosh CornwellInstitute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA.
Fernanda Martins RodriguesSiteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Houxiang ZhuSiteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Chia-Kuei MoSiteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Yuping ZhangDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Felipe da Veiga LeprevostDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Chen HuangLester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Arul M ChinnaiyanDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Matthew A WyczalkowskiSiteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Gilbert S OmennDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Chelsea J NewtonVan Andel Research Institute, Grand Rapids, MI 49503, USA.
Stephan SchurerSylvester Comprehensive Cancer Center and Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
Kelly V RugglesInstitute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA.
David FenyöInstitute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Scott D JewellVan Andel Research Institute, Grand Rapids, MI 49503, USA.
Mathangi ThiagarajanLeidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Mehdi MesriOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA.
Henry RodriguezOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA.
Sendurai A ManiDepartment of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Namrata D UdeshiBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Gad GetzBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
James SuhLeidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Qing Kay LiSidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD 21224, USA.
Galen HostetterVan Andel Research Institute, Grand Rapids, MI 49503, USA.
Paul K PaikMemorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Saravana M DhanasekaranDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Ramaswamy GovindanSiteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Li DingSiteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Ana I RoblesOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA.
Karl R ClauserBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, 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.
Pei WangDepartment of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Steven A CarrBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA. Electronic address: scarr@broad.mit.edu.
Bing ZhangLester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: bing.zhang@bcm.edu.
D R ManiBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA. Electronic address: manidr@broadinstitute.org.
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 02115, USA. Electronic address: gillette@broadinstitute.org.
Clinical Proteomic Tumor Analysis Consortium
Baylor College of Medicine · USBroad Institute · USUniversity of Michigan–Ann Arbor · USWashington University in St. Louis · USIcahn School of Medicine at Mount Sinai · USInstitute for Systems Biology · USMassachusetts Institute of Technology · USThe University of Texas MD Anderson Cancer Center · USNational Cancer Institute · USVan Andel Institute · USMemorial Sloan Kettering Cancer Center · USUniversity of Miami · USFrederick National Laboratory for Cancer Research · USJohns Hopkins University · USLeidos (United States) · USSidney Kimmel Comprehensive Cancer Center · USUniversity of Massachusetts Boston · US

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Hongbiao Carl Lekaye · 1985 to 2026
$347.4M
UNC-CH CENTER FOR ENVIRONMENTAL HEALTH &SUSCEPTIBILITYP30ES010126 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Stephanie Engel · 2001 to 2026
$36.3M
Tumor Biology Research ProgramP30CA240139 · NCI · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI George S. Grills · 2019 to 2026
$24.1M
Data Coordination and Integration Center for LINCS-BD2KU54HL127624 · NHLBI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MA'AYAN, AVI, SCHURER, STEPHAN C · 2014 to 2019
$23.5M
Proteogenomic 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
$8.4M
MICROSCALED PROTEOGENOMICS FOR CANCER CLINICAL TRIALSU01CA214125 · NCI · BAYLOR COLLEGE OF MEDICINE · PI ANURAG, MEENAKSHI, CARR, STEVEN A · 2017 to 2021
$7.0M
Proteogenomic Translational Research Center for Clinical ProteomicU01CA214116 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI DRUKER, BRIAN J, RODLAND, KARIN D · 2017 to 2021
$6.8M
Center of Excellence for High Throughput Proteogenomic CharacterizationU24CA210986 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, GILLETTE, MICHAEL A · 2016 to 2020
$6.4M
The 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
$5.3M
PNNL Proteome Characterization CenterU24CA210955 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI LIU, TAO, SMITH, RICHARD D · 2016 to 2020
$5.3M
iPGDAC, An Integrative Proteogenomic Data Analysis Center for CPTACU24CA210954 · NCI · BAYLOR COLLEGE OF MEDICINE · PI ZHANG, BING · 2016 to 2020
$4.9M
Systems 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
$4.6M
NCI NIH HHS P30 CA008748NCI NIH HHS P30 CA240139NCI NIH HHS T32 CA203690NCI 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 CA271037NCRR NIH HHS K26 RR026099NHLBI NIH HHS F32 HL154711NHLBI NIH HHS U54 HL127624NIEHS NIH HHS P30 ES010126NIH HHS K26 OD010945NINDS NIH HHS R01 NS095894
6 · The paper itself

Abstract

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC.

Indexed as

ProteogenomicsAcetylationAdultAgedAged, 80 and overCarcinoma, Squamous CellCluster AnalysisCyclin-Dependent Kinase 4Cyclin-Dependent Kinase 6Epithelial-Mesenchymal TransitionFemaleGene Expression Regulation, NeoplasticHumansLung NeoplasmsMaleMiddle AgedCyclin-Dependent Kinase 4Cyclin-Dependent Kinase 6Neoplasm ProteinsReceptors, Platelet-Derived Growth FactorReceptor Tyrosine Kinase-like Orphan ReceptorsROR2 protein, humanacetylationCPTACgenomicslung cancerphosphorylationproteinproteogenomicsproteomicssquamousubiquitylation

Identifiers

PMID34358469
PMCPMC8475722
OpenAlexW3188077199

What OpenQuestion holds

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Read underepoch 390

Registered trials

None linked

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.