ArticleCell reports. Medicine2024
Comprehensive proteogenomic characterization of rare kidney tumors.
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Article in Cell reports. Medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41citing papers in PubMed
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Who cites it
41 citing papers in PubMed.
- mTORC1 activation induces B7-H3-dependent metabolic reprogramming in renal cell carcinoma (RCC).Oncogene · 2026Article
- From fusion partner to clinical practice: A treatment-oriented framework for transcription factor E3 (Cancer pathogenesis and therapy · 2026Review
- Fusion-driven oncogenic programs shape the immune landscape in translocation renal cell carcinoma.Nature communications · 2026Article
- UDP-Glucose-6-Dehydrogenase Mediated O-GlcNAcylation of Tight Junction Protein 1 Suppresses Metastasis in Renal Cell Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Absolute quantitative proteomics guides patient-stratified drug repurposing in clear cell and papillary renal cell carcinoma.bioRxiv : the preprint server for biology · 2026Article
- Attenuation of EGFR-Mediated Cellular Signaling by Sialidase-Mediated Desialylation.Research square · 2026Article
- Spatial control of Keratin 8 phosphorylation by Aurora B facilitates cytokinesis in cancer cells of epithelial origin.The FEBS journal · 2026Article
- Tedizolid Targets AQP9-JAK/STAT Axis to Suppress Metastatic Progression in Clear Cell Renal Cell Carcinoma: Mechanism and Therapeutic Implications.International journal of molecular sciences · 2026Article
- Global impact of germline structural variation on the cancer proteome.Nature communications · 2026Article
- STAG2 loss amplifies EWS-FLI1-driven microsatellite enhancer activity promoting Ewing sarcoma aggressiveness.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Proteogenomics: decoding cancer in multiple dimensions.MedScience · 2026Review
- Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.Nature communications · 2026Article
- [Research Progress on the Role and Mechanisms of PYCR1 in Tumorigenesis and Progression].Zhongguo fei ai za zhi = Chinese journal of lung cancer · 2026Review
- Cell-free DNA epigenomic profiling enables noninvasive detection and monitoring of translocation renal cell carcinoma.The Journal of clinical investigation · 2026Article
- A data-driven pan-cancer proteogenomic analysis reveals the characteristics of human cancer protein expression.iScience · 2026Article
- Panorama: a database for the oncogenic evaluation of somatic mutations in pan-cancer.Database : the journal of biological databases and curation · 2026Article
- A cross-tissue transcriptome-wide association study identifies novel candidate genes associated with brain glymphatic system function.Molecular brain · 2025Article
- New Method Enhanced Extraction of Protein Signatures of Renal Cell Carcinoma from Proteomics Data.Journal of proteome research · 2025Article
- Divergent Clonal Evolution and Early Dissemination Promote Genetic Heterogeneity of Metastases in Castration-Resistant Prostate Cancer.Cancer research · 2025Article
- The proteogenomic landscape of the human kidney and implications for cardio-kidney-metabolic health.Nature medicine · 2025 · on this mapArticle
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Authors and funding
54 authors.
Ginny Xiaohe LiDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Lijun ChenDepartment of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
Yi HsiaoDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Rahul MannanDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
Yuping ZhangDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Jie LuoDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Francesca PetraliaDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Hanbyul ChoDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Noshad HosseiniDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Felipe da Veiga LeprevostDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Anna CalinawanDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Yize LiDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
Shankara AnandBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
Aniket DagarDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Yifat GeffenBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA.
Chandan Kumar-SinhaDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Seema ChughDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Anne LeDepartment of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
Sean PonceDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA.
Shenghao GuoDepartment of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA.
Cissy ZhangDepartment of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
Michael SchnaubeltDepartment of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
Nataly Naser Al DeenDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
Feng ChenDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA.
Wagma CaravanDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
Andrew HoustonDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
Alex HopkinsDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Chelsea J NewtonVan Andel Research Institute, Grand Rapids, MI 49503, USA.
Xiaoming WangDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Daniel A PolaskyDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Sarah HaynesDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Fengchao YuDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Xiaojun JingDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Siqi ChenDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
Ana I RoblesOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.
Mehdi MesriOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.
Mathangi ThiagarajanFrederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Eunkyung AnOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.
Gad A GetzBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
W Marston LinehanUrologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Galen HostetterVan Andel Research Institute, Grand Rapids, MI 49503, USA.
Scott D JewellVan Andel Research Institute, Grand Rapids, MI 49503, USA.
Daniel W ChanDepartment of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
Pei WangDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Gilbert S OmennDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA.
Rohit MehraDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Christopher J RickettsUrologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Li DingDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA.
Arul M ChinnaiyanDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA.
Marcin P CieslikDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Saravana M DhanasekaranDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: saravana@umich.edu.
Hui ZhangDepartment of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Electronic address: huizhang@jhu.edu.
Alexey I NesvizhskiiDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: nesvi@med.umich.edu.
Clinical Proteomic Tumor Analysis Consortium
Funding
Molecular Therapeutics of Kidney Cancer: VHL Gene and Fumarate Hydratase GeneZIABC011038 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI LINEHAN, WILLIAM MARSTON · 2009 to 2025
$29.8MStrategic Vision & Impact on Environmental HealthP30ES017885 · NIEHS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Dana Dolinoy · 2011 to 2026
$21.3MMolecular Therapeutics of Kidney Cancer: MET Gene and BHD GeneZIABC011043 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI LINEHAN, WILLIAM MARSTON · 2009 to 2025
$20.9MClinical Studies of the Molecular Genetic Basis of Kidney CancerZIABC011028 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI LINEHAN, WILLIAM MARSTON · 2009 to 2025
$17.9MClinical Nursing and Data Management CoreZIDBC011089 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI LINEHAN, WILLIAM MARSTON · 2009 to 2025
$17.4MProteogenomic Studies aimed at understanding ovarian tumor responses to agents targeting the DNA damage response and translating this knowledge into clinical benefitU01CA214114 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI BIRRER, MICHAEL, PAULOVICH, AMANDA G · 2017 to 2021
$8.4MMICROSCALED PROTEOGENOMICS FOR CANCER CLINICAL TRIALSU01CA214125 · NCI · BAYLOR COLLEGE OF MEDICINE · PI ANURAG, MEENAKSHI, CARR, STEVEN A · 2017 to 2021
$7.0MProteogenomic Translational Research Center for Clinical ProteomicU01CA214116 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI DRUKER, BRIAN J, RODLAND, KARIN D · 2017 to 2021
$6.8MCenter for Advanced Multi-Omic Characterization of CancerU24CA271012 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI Tao Liu · 2022 to 2026
$6.6MProteogenomic Characterization of Tumor Tissues and Preclinical Models with High PrecisionU24CA271079 · NCI · JOHNS HOPKINS UNIVERSITY · PI DANIEL Wanyui CHAN, Hui Zhang · 2022 to 2026
$6.6MCenter of Excellence for High Throughput Proteogenomic CharacterizationU24CA210986 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, GILLETTE, MICHAEL A · 2016 to 2020
$6.4MCOMPUTATIONAL TOOLS FOR MASS SPECTROMETRY-BASED INTERACTOME DATAR01GM094231 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Alexey I Nesvizhskii · 2010 to 2026
$5.4MNCI NIH HHS U01 CA214114NCI NIH HHS U01 CA214116NCI NIH HHS U01 CA214125NCI NIH HHS U24 CA210954NCI NIH HHS U24 CA210955NCI NIH HHS U24 CA210967NCI NIH HHS U24 CA210972NCI NIH HHS U24 CA210979NCI NIH HHS U24 CA210985NCI NIH HHS U24 CA210986NCI NIH HHS U24 CA210993NCI NIH HHS U24 CA271037NCI NIH HHS U24 CA271075NCI NIH HHS U24 CA271079NCI NIH HHS U24 CA271114NIEHS NIH HHS P30 ES017885NIGMS NIH HHS R01 GM094231
Abstract
Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.
Indexed as
Biomarkers, TumorCarcinoma, Renal CellKidney NeoplasmsProteogenomicsFemaleGene Expression Regulation, NeoplasticHumansMaleMiddle AgedTranscriptomeBiomarkers, Tumorcell-of-originCPTACdifferential diagnosis biomarkersglycoproteomicsmetabolomicsnon-clear cell renal cell carcinomaphosphoproteomicsprognostic markerproteogenomicsweighted genome instability index
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