ArticleCell2020
Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.
Open access · bronzeAbstract read
In one paragraph
Article in Cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 342 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
342citing papers in PubMed, 1 pooled it
33.5field-weighted citation impact, top 1% of its field
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
342 citing papers in PubMed, 1 synthesis or guideline pooled it, 532 citations in OpenAlex.
- A bibliometric and text-mining analysis of lipidomics and metabolomics in human disease.Frontiers in physiology · 2026Pooled it
- Precision neoadjuvant treatment with AI-assisted subtyping in HR+/HER2-breast cancer: A randomized, phase 2 trial FASCINATE-N.Cell reports. Medicine · 2026Trial
- Multi-omics graph attention network reveals neuro-immune-tumor pathways in breast cancer liver depression syndrome.Frontiers in immunology · 2026Trial
- Proteogenomic analysis of the CALGB 40601 (Alliance) HER2+ breast cancer neoadjuvant trial reveals resistance biomarkers.Cell reports. Medicine · 2025Trial
- Pathway and Kinase Analysis in Proteomics and Phosphoproteomics with rROMA.Methods in molecular biology (Clifton, N.J.) · 2027Article
- AKT Phosphorylation of FOXK2 at Ser398 Impacts Breast Cancer Cell Growth and Viability.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Identification of novel paracrine therapeutic targets in peritoneal metastases through integrative proteotranscriptomic analysis of ascites.Molecular cancer · 2026Article
- From Machine Learning-Enhanced Proteomics to a Validated Diagnostic Model: A Pipeline for Breast Cancer Biomarker Discovery via Independent and Transcriptomic Corroboration.Bioengineering (Basel, Switzerland) · 2026Article
- Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response.Nature communications · 2026Article
- Article
- Scalable phosphotyrosine enrichment with SH2 superbinder enables deep profiling of EGF responses.The EMBO journal · 2026Article
- A pre-trained large generative model for translating single-cell transcriptomes to proteomes.Nature biomedical engineering · 2026Article
- Article
- PRSS1 promotes gastric cancer invasion and metastasis by induction of the epithelial-mesenchymal transition and activation of the MAPK/ERK pathway.Translational cancer research · 2026Article
- Pan-cancer proteogenomic interrogation of the ubiquitin-proteasome system.Cell death and differentiation · 2026Article
- Bimodality in pan-cancer proteomics reveals new opportunities for biomarker discovery.Genome biology · 2026Article
- Article
- SIRT2 antagonizes MOF function during mitotic entry.Science advances · 2026Article
- SEC14L2 couples chaperone-mediated autophagy to microtubule stability by targeting Stathmin 1.Nature communications · 2026Article
- B.R.E.A.S.T. Breast canceR Enhanced AI-Supported Therapy: A New Interpretable Proteomics-Driven Machine Learning Framework for Therapy Response Prediction in Breast Cancer.International journal of molecular sciences · 2026Article
282 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
47 authors at 10 institutions in 3 countries.
Karsten KrugBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Eric J JaehnigLester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Shankha SatpathyBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Lili BlumenbergInstitute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA.
Alla KarpovaDepartment of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Meenakshi AnuragLester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
George MilesLester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Philipp MertinsBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Max Delbrück Center for Molecular Medicine in the Helmholtz Society and Berlin Institute of Health, Berlin, Germany.
Yifat GeffenBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Lauren C TangBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
David I HeimanBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Song CaoDepartment of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Yosef E MaruvkaBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Jonathan T LeiLester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Chen HuangLester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Ramani B KothadiaBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Antonio ColapricoDivision of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
Chet BirgerBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Jarey WangVerna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA.
Yongchao DouLester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Bo WenLester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Zhiao ShiLester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Yuxing LiaoLester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Maciej WiznerowiczPoznan University of Medical Sciences, Poznań 61-701, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland.
Matthew A WyczalkowskiDepartment of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Xi Steven ChenDivision of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
Jacob J KennedyClinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Amanda G PaulovichClinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, 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.
Tara HiltkeOffice 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.
Mehdi MesriOffice 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.
Henry RodriguezOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA.
Thomas F WestbrookVerna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA.
Li DingDepartment of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Gad GetzBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02114, USA.
Karl R ClauserBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
David FenyöDepartment of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Kelly V RugglesInstitute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA.
Bing ZhangLester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
D R ManiBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA. Electronic address: manidr@broadinstitute.org.
Steven A CarrBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA. Electronic address: scarr@broad.mit.edu.
Matthew J EllisLester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: mjellis@bcm.edu.
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. Electronic address: gillette@broadinstitute.org.
Clinical Proteomic Tumor Analysis Consortium
Baylor College of Medicine · USBroad Institute · USNational Cancer Institute · USWashington University in St. Louis · USFred Hutch Cancer Center · USUniversity of Miami · USInstitute for Systems Biology · USNew York University · USLeidos (United States) · USPoznan University of Medical Sciences · PL
Funding
Proteo-genomic Discovery, Prioritization and Verification of Cancer BiomarkersU24CA160034 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, PAULOVICH, AMANDA G · 2011 to 2016
$16.2MMICROSCALED 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
$6.4MPNNL 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
$4.9MIntegrated high throughput proteogenomic data analysis center for CPTACU24CA210979 · NCI · BROAD INSTITUTE, INC. · PI BIRGER, CHET, GETZ, GAD A · 2016 to 2020
$4.4MProteogenomic 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 CA160034NCI NIH HHS U24 CA210954NCI NIH HHS U24 CA210955NCI NIH HHS U24 CA210972NCI NIH HHS U24 CA210979NCI NIH HHS U24 CA210986
Abstract
The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Here this "proteogenomics" approach was applied to 122 treatment-naive primary breast cancers accrued to preserve post-translational modifications, including protein phosphorylation and acetylation. Proteogenomics challenged standard breast cancer diagnoses, provided detailed analysis of the ERBB2 amplicon, defined tumor subsets that could benefit from immune checkpoint therapy, and allowed more accurate assessment of Rb status for prediction of CDK4/6 inhibitor responsiveness. Phosphoproteomics profiles uncovered novel associations between tumor suppressor loss and targetable kinases. Acetylproteome analysis highlighted acetylation on key nuclear proteins involved in the DNA damage response and revealed cross-talk between cytoplasmic and mitochondrial acetylation and metabolism. Our results underscore the potential of proteogenomics for clinical investigation of breast cancer through more accurate annotation of targetable pathways and biological features of this remarkably heterogeneous malignancy.
Indexed as
Molecular Targeted TherapyProteogenomicsAdultAgedAged, 80 and overAPOBEC DeaminasesBreast NeoplasmsCarcinogenesisCohort StudiesDNA DamageDNA RepairErb-b2 Receptor Tyrosine KinasesFemaleHumansImmunotherapyMetabolomicsAPOBEC DeaminasesERBB2 protein, humanErb-b2 Receptor Tyrosine KinasesProtein Kinase InhibitorsProtein KinasesRetinoblastoma Proteinacetylationbreast cancerCDK 4/6 inhibitorsCPTACgenomicsimmune checkpoint therapymass spectrometryphosphoproteomicsproteogenomicsproteomics
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY-NC-ND
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.