Evidence map›Paper›PMID 30268436›Full record

ArticleCell systems2018

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily.

Anil Korkut, Sobia Zaidi, Rupa S Kanchi, Shuyun Rao, Nancy R Gough, Andre Schultz, Xubin Li, Philip L Lorenzi, Ashton C Berger, Gordon Robertson and 36 more

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

Article in Cell systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers.

0numbers the graph read from it
0cells of the map it votes in
127citing papers in PubMed
7.8field-weighted citation impact, top 2% 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

127 citing papers in PubMed, 189 citations in OpenAlex.

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  8. TGF-β Pathway-Based Polygenic Risk Score Modifies the Association between Red Meat Intake and Colorectal Cancer Risk: Application of a Novel Pathway-Based PRS Method.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2026
    Article
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  14. Serum Proteomic Profile Based on the TGF-β Pathway Stratifies Risk of Hepatocellular Carcinoma.Liver international : official journal of the International Association for the Study of the Liver · 2025
    Article
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67 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

46 authors at 17 institutions in 6 countries.

Anil KorkutDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Sobia ZaidiCenter for Translational Medicine, Department of Surgery, George Washington University, Washington, DC 20037, USA.
Rupa S KanchiDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Shuyun RaoCenter for Translational Medicine, Department of Surgery, George Washington University, Washington, DC 20037, USA.
Nancy R GoughCenter for Translational Medicine, Department of Surgery, George Washington University, Washington, DC 20037, USA.
Andre SchultzDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Xubin LiDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Philip L LorenziDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Ashton C BergerCancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
Gordon RobertsonCanada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
Lawrence N KwongDepartment of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Mike DattoDepartment of Pathology, Duke School of Medicine Durham, Durham, NC 27710, USA.
Jason RoszikDepartment of Melanoma Medical Oncology and Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA.
Shiyun LingDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Visweswaran RavikumarDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Ganiraju ManyamDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Arvind RaoDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Simon ShelleyDepartment of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA.
Yuexin LiuDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Zhenlin JuDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Donna HanselDepartment of Pathology, University of California, San Diego, La Jolla, CA 92093, USA.
Guillermo de VelascoDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medical Oncology, University Hospital 12 de Octubre, Madrid 28041, Spain.
Arjun PennathurDepartment of Cardiothoracic Surgery, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.
Jesper B AndersenDepartment of Health and Medical Sciences, Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark.
Colm J O'RourkeDepartment of Health and Medical Sciences, Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark.
Kazufumi OhshiroCenter for Translational Medicine, Department of Surgery, George Washington University, Washington, DC 20037, USA.
Wilma JogunooriCenter for Translational Medicine, Department of Surgery, George Washington University, Washington, DC 20037, USA; Veterans Affairs Medical Center, Institute of Clinical Research, Washington, DC 20422, USA.
Bao-Ngoc NguyenCenter for Translational Medicine, Department of Surgery, George Washington University, Washington, DC 20037, USA.
Shulin LiDepartment of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Hatice U OsmanbeyogluMemorial Sloan Kettering Cancer Center, Computational & Systems Biology Program, New York, NY 10065, USA.
Jaffer A AjaniDepartment of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Sendurai A ManiDepartment of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Andres HousemanCollege of Public Health and Human Sciences, Oregon State University, Corvallis, OR 9733, USA.
Maciej WiznerowiczPoznań University of Medical Sciences, Poznań 61701, Poland; Greater Poland Cancer Center, Poznań 61866, Poland; International Institute for Molecular Oncology, Poznań 60203, Poland.
Jian ChenDepartment of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Shoujun GuCenter for Translational Medicine, Department of Surgery, George Washington University, Washington, DC 20037, USA.
Wencai MaDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Jiexin ZhangDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Pan TongDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Andrew D CherniackCancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
Chuxia DengCenter for Translational Medicine, Department of Surgery, George Washington University, Washington, DC 20037, USA; Faculty of Health Sciences, University of Macau, Macau, Macau SAR, China.
Linda ResarDepartments of Medicine, Division of Hematology, Oncology and Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Cancer Genome Atlas Research Network
John N WeinsteinDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030, USA.
Lopa MishraCenter for Translational Medicine, Department of Surgery, George Washington University, Washington, DC 20037, USA; Veterans Affairs Medical Center, Institute of Clinical Research, Washington, DC 20422, USA. Electronic address: lopamishra2@gmail.com.
Rehan AkbaniDepartment of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: rakbani@mdanderson.org.
The University of Texas MD Anderson Cancer Center · USBayer (United States) · USGeorge Washington University · USBC Cancer Agency · CABroad Institute · USJohns Hopkins University · USUniversity of Wisconsin–Madison · USResearch Institute Hospital 12 de Octubre · ESUniversity of California San Diego · USDuke University · USMemorial Sloan Kettering Cancer Center · USPoznan University of Medical Sciences · PLUniversity of Copenhagen · DKInternational Institute for Molecular Oncology · PLOregon State University · USUniversity of Pittsburgh Medical Center · USWashington University Medical Center · US

Funding

Large Scale Sequencing and Analysis of GenomesU54HG003067 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY, LANDER, ERIC S · 2004 to 2015
$568.6M
Large Scale Genome SequencingU54HG003079 · NHGRI · WASHINGTON UNIVERSITY · PI DUTCHER, SUSAN K · 2004 to 2016
$445.7M
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Nicholas D Socci · 1985 to 2026
$347.4M
The Human Genome Sequencing CenterU54HG003273 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2004 to 2015
$341.3M
Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Scott Kopetz · 1985 to 2026
$290.8M
Translational Research Central ServicesP30CA006973 · NCI · JOHNS HOPKINS UNIVERSITY · PI Rosalie Wollett · 1985 to 2026
$208.6M
Gene Expression Patterns in Human Tumors Identified Using Transcript SequencingU24CA143848 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAYES, DAVID N, PEROU, CHARLES M · 2009 to 2016
$20.8M
Genome Characterization Center (GCC)U24CA143867 · NCI · BROAD INSTITUTE, INC. · PI GABRIEL, STACEY, MEYERSON, MATTHEW L. · 2009 to 2016
$17.0M
The Cancer Genome Atlas Data Analysis CenterU24CA143845 · NCI · BROAD INSTITUTE, INC. · PI CHIN, LYNDA, GETZ, GAD A · 2009 to 2016
$16.0M
Harvard Genome Characterization CenterU24CA144025 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI KUCHERLAPATI, RAJU S. · 2009 to 2016
$14.0M
The USC-JHU Cancer Epigenome Characterization CenterU24CA143882 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI BAYLIN, STEPHEN B., WEISENBERGER, DANIEL JOSEPH · 2009 to 2016
$13.3M
MSKCC Center for Translational Cancer Genomic AnalysisU24CA143840 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI LADANYI, MARC, SANDER, CHRIS · 2009 to 2016
$11.5M
BLRD VA I01 BX003732NCI NIH HHS P01 CA130821NCI NIH HHS P30 CA006973NCI NIH HHS P30 CA008748NCI NIH HHS P30 CA016672NCI NIH HHS R00 CA207871NCI NIH HHS R01 CA183793NCI NIH HHS R01 CA232741NCI NIH HHS R01 CA236591NCI NIH HHS U01 CA230690NCI NIH HHS U24 CA143799NCI NIH HHS U24 CA143835NCI NIH HHS U24 CA143840NCI NIH HHS U24 CA143843NCI NIH HHS U24 CA143845NCI NIH HHS U24 CA143848NCI NIH HHS U24 CA143858NCI NIH HHS U24 CA143866NCI NIH HHS U24 CA143867NCI NIH HHS U24 CA143882NCI NIH HHS U24 CA143883NCI NIH HHS U24 CA144025NCI NIH HHS U24 CA199461NCI NIH HHS U24 CA210949NCI NIH HHS U24 CA210950NHGRI NIH HHS U54 HG003067NHGRI NIH HHS U54 HG003079NHGRI NIH HHS U54 HG003273NIAAA NIH HHS R01 AA023146NIDDK NIH HHS R01 DK102943
6 · The paper itself

Abstract

We present an integromic analysis of gene alterations that modulate transforming growth factor β (TGF-β)-Smad-mediated signaling in 9,125 tumor samples across 33 cancer types in The Cancer Genome Atlas (TCGA). Focusing on genes that encode mediators and regulators of TGF-β signaling, we found at least one genomic alteration (mutation, homozygous deletion, or amplification) in 39% of samples, with highest frequencies in gastrointestinal cancers. We identified mutation hotspots in genes that encode TGF-β ligands (BMP5), receptors (TGFBR2, AVCR2A, and BMPR2), and Smads (SMAD2 and SMAD4). Alterations in the TGF-β superfamily correlated positively with expression of metastasis-associated genes and with decreased survival. Correlation analyses showed the contributions of mutation, amplification, deletion, DNA methylation, and miRNA expression to transcriptional activity of TGF-β signaling in each cancer type. This study provides a broad molecular perspective relevant for future functional and therapeutic studies of the diverse cancer pathways mediated by the TGF-β superfamily.

Indexed as

Mutation RateSignal TransductionBone Morphogenetic Protein 5DNA MethylationHumansMicroRNAsNeoplasmsReceptor, Transforming Growth Factor-beta Type ISmad ProteinsTransforming Growth Factor betaBMP5 protein, humanBone Morphogenetic Protein 5MicroRNAsReceptor, Transforming Growth Factor-beta Type ISmad ProteinsTransforming Growth Factor betacancerDNA methylationmicroRNAmutation hotspotPan-CancerTCGATGF-βTGF-β pathwayThe Cancer Genome Atlastranscription

Identifiers

PMID30268436
PMCPMC6370347
OpenAlexW2894166779

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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.