ArticleNature communications2017
Proteogenomic integration reveals therapeutic targets in breast cancer xenografts.
Erratum issuedAbstract read
In one paragraph
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 110 papers.
0numbers the graph read from it
0cells of the map it votes in
110citing papers in PubMed
–field-weighted citation impact
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.
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.
Who cites it
110 citing papers in PubMed.
- Molecular evaluation of residual disease following neoadjuvant chemotherapy in triple-negative breast cancer CALGB 40603 (Alliance).The Journal of clinical investigation · 2026Trial
- Proteomic Biomarker Discovery in Breast Cancer: Advances, Challenges, and Translational Prospects.Journal of biochemical and molecular toxicology · 2026Review
- Regulation of NAT1 activity in modern humans by a novel phosphorylation site.Science advances · 2026Article
- Multi-Tissue Omics Analysis Uncovers Translational Regulation Underlying Complex Traits in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Mutant p53 Directs PARP to Regulate Replication Stress and Drive Breast Cancer Metastasis.bioRxiv : the preprint server for biology · 2026Article
- Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.Nature communications · 2026Article
- Enrichment of Phosphorylated and Glycosylated MHC Peptides for Mass Spectrometry-Based Neoantigen Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- SIMD: Synergistic integration mutualistic platform based on single-cell and proteotranscriptomics for drug repositioning.NPJ breast cancer · 2025Article
- Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer.Cancer discovery · 2025Article
- Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures.Cancer cell · 2025Article
- B7-H3 and CSPG4 co-targeting as Pan-CAR-T cell treatment of triple-negative breast cancer.Journal for immunotherapy of cancer · 2025Article
- Advancements in proteogenomics for preclinical targeted cancer therapy research.Biophysics reports · 2025Article
- New Insights into Colorectal Cancer through the Lens of Precision Oncology and Personalized Medicine: Multi-Omics Helps Aging of Predisposed People.Current aging science · 2025Review
- Master regulators governing protein abundance across ten human cancer types.bioRxiv : the preprint server for biology · 2024Article
- Uncovering therapeutic targets for macrophage-mediated T cell suppression and PD-L1 therapy sensitization.Cell reports. Medicine · 2024Article
- Personalizing non-small cell lung cancer treatment through patient-derived xenograft models: preclinical and clinical factors for consideration.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2024Article
- Death-associated protein kinase 3 modulates migration and invasion of triple-negative breast cancer cells.PNAS nexus · 2024Article
- A novel model based on protein post-translational modifications comprising the immune landscape and prediction of colorectal cancer prognosis.Journal of gastrointestinal oncology · 2024Article
- DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples.Journal of proteome research · 2024Article
- Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models.Cancer research communications · 2024Article
50 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
45 authors.
Kuan-Lin HuangDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Shunqiang LiDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Philipp MertinsThe Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Song CaoMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Harsha P GunawardenaDepartment of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
Kelly V RugglesCenter for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA.ORCID 0000-0002-0152-0863
D R ManiThe Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Karl R ClauserThe Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Maki TaniokaLineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
Jerry UsaryLineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
Shyam M KavuriLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Ling XieDepartment of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
Christopher YoonDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Jana W QiaoThe Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
John WrobelDepartment of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
Matthew A WyczalkowskiMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.ORCID 0000-0003-4197-551X
Petra Erdmann-GilmoreDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Jacqueline E SniderDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Jeremy HoogDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Purba SinghLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Beifung NiuMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Zhanfang GuoDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Sam Qiancheng SunDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Souzan SanatiDepartment of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Emily KawalerCenter for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA.
Xuya WangCenter for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA.
Adam ScottMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Kai YeMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Michael D McLellanMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Michael C WendlMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Anna MalovannayaLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Jason M HeldDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Michael A GilletteThe Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
David FenyöCenter for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA.
Christopher R KinsingerNational Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Mehdi MesriNational Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Henry RodriguezNational Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Sherri R DaviesDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Charles M PerouLineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
Cynthia MaDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
R Reid TownsendDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.
Xian ChenDepartment of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
Steven A CarrThe Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Matthew J EllisLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Li DingDepartment of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.ORCID 0000-0003-1517-2975
Funding
Washington University Center for Cellular ImagingP30CA091842 · NCI · WASHINGTON UNIVERSITY · PI TIMOTHY J. EBERLEIN · 2001 to 2026
$128.0MTissue Procurement & PathologyP50CA058223 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI KATHERINE A. HOADLEY · 1992 to 2026
$59.3MProteo-genomic Discovery, Prioritization and Verification of Cancer BiomarkersU24CA160034 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, PAULOVICH, AMANDA G · 2011 to 2016
$16.2MCancer Proteome Center at Washington Univ, Univ of North Carolina & Boise StateU24CA160035 · NCI · WASHINGTON UNIVERSITY · PI CHEN, XIAN, ELLIS, MATTHEW J · 2011 to 2016
$11.8MA Turnkey System for High-throughput Variant Discovery and InterpretationU01HG006517 · NHGRI · WASHINGTON UNIVERSITY · PI DING, LI · 2012 to 2015
$3.0MDeep Discovery and Clinical Interpretation of Germline and Somatic Cancer DriversU24CA211006 · NCI · WASHINGTON UNIVERSITY · PI DING, LI, GOVINDAN, RAMASWAMY · 2016 to 2020
$1.8MMouse Models of Metastatic Triple-Negative Breast Cancer for Therapeutic TestingR01CA195754 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI PEROU, CHARLES M, ROSEN, JEFFREY MARK · 2015 to 2017
$1.7MCANCER SUSCEPTIBILITY VARIANT DISCOVERY IN HIGH THROUGHPUT SEQUENCING DATAR01CA180006 · NCI · WASHINGTON UNIVERSITY · PI DING, LI · 2013 to 2016
$1.1MNCI NIH HHS P30 CA091842NCI NIH HHS P50 CA058223NCI NIH HHS R01 CA180006NCI NIH HHS R01 CA195754NCI NIH HHS U24 CA160034NCI NIH HHS U24 CA160035NCI NIH HHS U24 CA211006NHGRI NIH HHS U01 HG006517
Abstract
Recent advances in mass spectrometry (MS) have enabled extensive analysis of cancer proteomes. Here, we employed quantitative proteomics to profile protein expression across 24 breast cancer patient-derived xenograft (PDX) models. Integrated proteogenomic analysis shows positive correlation between expression measurements from transcriptomic and proteomic analyses; further, gene expression-based intrinsic subtypes are largely re-capitulated using non-stromal protein markers. Proteogenomic analysis also validates a number of predicted genomic targets in multiple receptor tyrosine kinases. However, several protein/phosphoprotein events such as overexpression of AKT proteins and ARAF, BRAF, HSP90AB1 phosphosites are not readily explainable by genomic analysis, suggesting that druggable translational and/or post-translational regulatory events may be uniquely diagnosed by MS. Drug treatment experiments targeting HER2 and components of the PI3K pathway supported proteogenomic response predictions in seven xenograft models. Our study demonstrates that MS-based proteomics can identify therapeutic targets and highlights the potential of PDX drug response evaluation to annotate MS-based pathway activities.
Indexed as
Molecular Targeted TherapyProteogenomicsXenograft Model Antitumor AssaysAnimalsBreast NeoplasmsFemaleHumansMicePhosphorylationSignal TransductionTranscriptome
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
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.