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Comprehensive proteogenomic characterization of rare kidney tumors

  1. Author:
    Li, Ginny Xiaohe
    Chen, Lijun
    Hsiao, Yi
    Mannan, Rahul
    Zhang, Yuping
    Luo, Jie
    Petralia, Francesca
    Cho, Hanbyul
    Hosseini, Noshad
    Leprevost, Felipe da Veiga
    Calinawan, Anna
    Li, Yize
    Anand, Shankara
    Dagar, Aniket
    Geffen, Yifat
    Kumar-Sinha, Chandan
    Chugh, Seema
    Le, Anne
    Ponce, Sean
    Guo, Shenghao
    Zhang, Cissy
    Schnaubelt, Michael
    Al Deen, Nataly Naser
    Chen, Feng
    Caravan, Wagma
    Houston, Andrew
    Hopkins, Alex
    Newton, Chelsea J
    Wang, Xiaoming
    Polasky, Daniel A
    Haynes, Sarah
    Yu, Fengchao
    Jing, Xiaojun
    Chen, Siqi
    Robles, Ana I
    Mesri, Mehdi
    Thiagarajan,Mathangi
    An, Eunkyung
    Getz, Gad A
    Linehan, W Marston
    Hostetter, Galen
    Jewell, Scott D
    Chan, Daniel W
    Wang, Pei
    Omenn, Gilbert S
    Mehra, Rohit
    Ricketts, Christopher J
    Ding, Li
    Chinnaiyan, Arul M
    Cieslik, Marcin P
    Dhanasekaran, Saravana M
    Zhang, Hui
    Nesvizhskii, Alexey I

  2. Author Address

    Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA., Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA., Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA., Department 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., Department 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., Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, 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., Department 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., Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Broad 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., Department 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 Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA., Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA., Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA., Van Andel Research Institute, Grand Rapids, MI 49503, USA., Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA., Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA., Department 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., 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; Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA., Department 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., Department 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., Department 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., Department 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., Department 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., Department 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.,
    1. Year: 2024
    2. Date: May 21
    3. Epub Date: 2024 04 26
  2. Journal: Cell Reports. Medicine
    1. 5
    2. 5
    3. Pages: 101547
  4. Type of Article: Article
  5. Article Number: 101547
  1. 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. Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.

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External Sources

  1. View Full Text
  2. DOI: 10.1016/j.xcrm.2024.101547
  3. PMID: 38703764
  4. PMCID: PMC11148773
  5. View record in Web of Science®
  6. WOS: 001265285700010
  7. PII : S2666-3791(24)00239-8

Library Notes

  1. Fiscal Year: FY2023-2024
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