Evidence map›Paper›PMID 31031003›Full record

ArticleCell2019

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities.

Suhas Vasaikar, Chen Huang, Xiaojing Wang, Vladislav A Petyuk, Sara R Savage, Bo Wen, Yongchao Dou, Yun Zhang, Zhiao Shi, Osama A Arshad and 23 more

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

Article in Cell, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 477 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
477citing papers in PubMed, 1 pooled it
35.3field-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

477 citing papers in PubMed, 1 synthesis or guideline pooled it, 819 citations in OpenAlex.

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417 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

33 authors at 8 institutions in 1 country.

Suhas VasaikarLester 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.
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.
Xiaojing WangLester 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.
Vladislav A PetyukBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Sara R SavageDepartment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, 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.
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.
Yun ZhangLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, 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.
Osama A ArshadBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Marina A GritsenkoBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Lisa J ZimmermanDepartment of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.
Jason E McDermottBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Therese R ClaussBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Ronald J MooreBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Rui ZhaoBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Matthew E MonroeBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Yi-Ting WangBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Matthew C ChambersDepartment of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.
Robbert J C SlebosDepartment of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.
Ken S LauDepartment of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
Qianxing MoDan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Li DingThe McDonnell Genome Institute, Washington University in St. Louis, Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108, USA.
Matthew EllisLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Mathangi ThiagarajanLeidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Christopher R KinsingerOffice 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.
Richard D SmithBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Karin D RodlandBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA. Electronic address: karin.rodland@pnnl.gov.
Daniel C LieblerDepartment of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA. Electronic address: daniel.liebler@vanderbilt.edu.
Tao LiuBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. Electronic address: tao.liu@pnnl.gov.
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; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: bing.zhang@bcm.edu.
Clinical Proteomic Tumor Analysis Consortium
Pacific Northwest National Laboratory · USBaylor College of Medicine · USVanderbilt University · USNational Cancer Institute · USFrederick National Laboratory for Cancer Research · USOregon Health & Science University · USVanderbilt University Medical Center · USWashington University in St. Louis · US

Funding

Washington University Center for Cellular ImagingP30CA091842 · NCI · WASHINGTON UNIVERSITY · PI TIMOTHY J. EBERLEIN · 2001 to 2026
$128.0M
Translational Analysis CoreP30DK058404 · NIDDK · VANDERBILT UNIVERSITY MEDICAL CENTER · PI RICHARD M. PEEK · 2002 to 2026
$29.9M
PNNL Clinical Proteome Characterization CenterU24CA160019 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI RODLAND, KARIN D, SMITH, RICHARD D · 2011 to 2016
$15.7M
Vanderbilt Proteome Characterization CenterU24CA159988 · NCI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI LIEBLER, DANIEL C · 2011 to 2016
$13.9M
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
NCI NIH HHS P30 CA091842NCI NIH HHS U24 CA159988NCI NIH HHS U24 CA160019NCI NIH HHS U24 CA210954NCI NIH HHS U24 CA210955NIDDK NIH HHS P30 DK058404
6 · The paper itself

Abstract

We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development.

Indexed as

ApoptosisBiomarkers, TumorCD8-Positive T-LymphocytesCell ProliferationColonic NeoplasmsGenomicsGlycolysisHumansMicrosatellite InstabilityMutationPhosphorylationProspective StudiesProteogenomicsProteomicsRetinoblastoma ProteinBiomarkers, TumorRetinoblastoma Proteinbiomarkerscolon cancerdrug targetsglycolysisimmune evasionproteogenomicsproteomicsRB1SOX9tumor antigen

Identifiers

PMID31031003
PMCPMC6768830
OpenAlexW2940627982

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.