ArticleCell2016
Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer.
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Article in Cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 141 papers.
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141citing papers in PubMed
20.8field-weighted citation impact, top 1% of its field
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Who cites it
141 citing papers in PubMed, 234 citations in OpenAlex.
- Citron kinase activity controls alternative splicing events that drive prostate cancer growth.Science advances · 2026Article
- The phosphoproteome of ovarian carcinoma delineates signaling signatures and potentially druggable targets across histotype stages.NPJ precision oncology · 2026Article
- Targeted proteomics for the detection of androgen receptor variants in preclinical models of castration-resistant prostate cancer.Clinical proteomics · 2026Article
- Network Pharmacology and Molecular Docking ofInternational journal of molecular sciences · 2026Article
- Proteome profiles of esophageal squamous cell carcinoma tie mitochondrial complex I to immunotherapy.EMBO molecular medicine · 2026Article
- Conserved Phosphoprotein Networks Identify Actionable Adhesion/Wnt and Metallothionein Modules in Cholangiocarcinoma.Medical sciences (Basel, Switzerland) · 2026Article
- Concordant RNA-protein evidence and human tissue metabolomics prioritize UPP1-associated nucleotide remodeling in prostate cancer.PloS one · 2026Article
- PatientProfiler: building patient-specific signaling models from proteogenomic data.Molecular systems biology · 2025Article
- Computational Approaches for Pathway-Centric Analysis of Protein Post-Translational Modifications.Proteomics · 2025Review
- Single-cell RNA profiling reveals an immunosuppressive microenvironment inTranslational lung cancer research · 2025Article
- Multi-layer stratified oncology platform utilizing transcriptomics, prostate cancer organoids, and modeling of drug response.Journal of experimental & clinical cancer research : CR · 2025Article
- Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability.bioRxiv : the preprint server for biology · 2025Article
- EZH2-TTP-mTORC1 Axis Drives Phenotypic Plasticity and Therapeutic Vulnerability in Lethal Prostate Cancer.bioRxiv : the preprint server for biology · 2025Article
- Bigpicc: a graph-based approach to identifying carcinogenic gene combinations from mutation data.BMC bioinformatics · 2025Article
- Article
- The primate-specific Nedd4-1(NE) localizes to late endosomes in response to amino acids to suppress autophagy.Nature communications · 2025Article
- PhosNetVis: A web-based tool for fast kinase-substrate enrichment analysis and interactive 2D/3D network visualizations of phosphoproteomics data.Patterns (New York, N.Y.) · 2025Article
- No transcription, no problem: Protein phosphorylation changes and the transition from oocyte to embryo.Current topics in developmental biology · 2025Review
- Transcriptomic and proteomic signatures of host NK cells delineate distinct immune states across tuberculosis infection statuses.Frontiers in immunology · 2025Article
- Article
81 more citing papers are in PubMed but not listed here.
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Authors and funding
20 authors at 7 institutions in 1 country.
Justin M DrakeDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Rutgers Cancer Institute of New Jersey and Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA. Electronic address: justin.drake@cinj.rutgers.edu.
Evan O PaullDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Nicholas A GrahamCrump Institute for Molecular Imaging, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA.
John K LeeDivision of Hematology and Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Bryan A SmithDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Bjoern TitzCrump Institute for Molecular Imaging, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Tanya StoyanovaDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, Palo Alto, CA 94304, USA.
Claire M FaltermeierMolecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Vladislav UzunangelovDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Daniel E CarlinDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Daniel Teo FlemingDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Christopher K WongDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Yulia NewtonDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Sud SudhaDepartment of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
Ajay A VashishtDepartment of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Jiaoti HuangJonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA.
James A WohlschlegelDepartment of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Thomas G GraeberCrump Institute for Molecular Imaging, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Owen N WitteDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: owenwitte@mednet.ucla.edu.
Joshua M StuartDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. Electronic address: jstuart@ucsc.edu.
University of California, Los Angeles · USUniversity of California, Santa Cruz · USCalifornia NanoSystems Institute · USHoward Hughes Medical Institute · USRutgers, The State University of New Jersey · USUniversity of Michigan · USUniversity of Southern California · US
Funding
Women's CancersP30CA016042 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI JOHN A GLASPY · 1985 to 2026
$134.5MUCLA Clinical and Translational Science InstituteUL1TR000124 · NCATS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI DUBINETT, STEVEN M. · 2012 to 2015
$57.0MUCLA SPORE IN PROSTATE CANCERP50CA092131 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI FREEMAN, MICHAEL R · 2002 to 2023
$42.6MUCLA Tumor Immunology Training ProgramT32CA009120 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Steven M. Dubinett, MICHAEL A TEITELL · 1985 to 2026
$10.3MPharmaco Response Signatures and Disease MechanismU54HG006097 · NHGRI · HARVARD MEDICAL SCHOOL · PI MITCHISON, TIMOTHY J, SORGER, PETER KARL · 2010 to 2013
$9.7MUCSC-Buck Inst. Genome Data Analysis Center for TCGA Research Network (GDAC)U24CA143858 · NCI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI BENZ, CHRISTOPHER, HAUSSLER, DAVID H · 2009 to 2016
$8.9MTARGETED COMBINATORIAL TREATMENT OF BRAF MELANOMASP01CA168585 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI RIBAS, ANTONI · 2013 to 2017
$8.4MUCLA Scholars in Oncologic Molecular lmaging (SOMI)R25CA098010 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI PHELPS, MICHAEL E · 2003 to 2013
$5.0MProteolytic Control of Iron Metabolism by the Ubiquitin Ligase FBXL5R01GM089778 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI WOHLSCHLEGEL, JAMES AKIRA · 2010 to 2023
$4.0MBIGDATA: Mid-Scale DCM: DA: ESCE: Discovering Molecular ProcessesR01CA180778 · NCI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI STUART, JOSHUA MICHAEL · 2013 to 2017
$3.5MIdentification of DNA methylation markers for risk of metastasis in localized proR01CA181242 · NCI · KAISER FOUNDATION RESEARCH INSTITUTE · PI CHAO, CHUN R. · 2015 to 2019
$3.0MNew Integrative Pathway Analysis Methods to Predict Biomedical OutcomesR01GM109031 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI STUART, JOSHUA MICHAEL · 2014 to 2018
$2.9MHHMINCATS NIH HHS UL1 TR000124NCI NIH HHS P01 CA168585NCI NIH HHS P30 CA016042NCI NIH HHS P50 CA092131NCI NIH HHS R00 CA184397NCI NIH HHS R01 CA172603NCI NIH HHS R01 CA180778NCI NIH HHS R01 CA181242NCI NIH HHS R01 CA195505NCI NIH HHS R03 CA230819NCI NIH HHS R25 CA098010NCI NIH HHS T32 CA009120NCI NIH HHS U24 CA143858NHGRI NIH HHS U54 HG006097NIGMS NIH HHS R01 GM089778NIGMS NIH HHS R01 GM109031
Abstract
We used clinical tissue from lethal metastatic castration-resistant prostate cancer (CRPC) patients obtained at rapid autopsy to evaluate diverse genomic, transcriptomic, and phosphoproteomic datasets for pathway analysis. Using Tied Diffusion through Interacting Events (TieDIE), we integrated differentially expressed master transcriptional regulators, functionally mutated genes, and differentially activated kinases in CRPC tissues to synthesize a robust signaling network consisting of druggable kinase pathways. Using MSigDB hallmark gene sets, six major signaling pathways with phosphorylation of several key residues were significantly enriched in CRPC tumors after incorporation of phosphoproteomic data. Individual autopsy profiles developed using these hallmarks revealed clinically relevant pathway information potentially suitable for patient stratification and targeted therapies in late stage prostate cancer. Here, we describe phosphorylation-based cancer hallmarks using integrated personalized signatures (pCHIPS) that shed light on the diversity of activated signaling pathways in metastatic CRPC while providing an integrative, pathway-based reference for drug prioritization in individual patients.
Indexed as
AlgorithmsHumansMalePhosphoproteinsPrecision MedicineProstatic Neoplasms, Castration-ResistantProteomeSignal TransductionTranscriptomePhosphoproteinsProteome
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