Comprehensive proteogenomic characterization of rare kidney tumors.

CPTAC cell-of-origin differential diagnosis biomarkers glycoproteomics metabolomics non-clear cell renal cell carcinoma phosphoproteomics prognostic marker proteogenomics weighted genome instability index

Journal

Cell reports. Medicine
ISSN: 2666-3791
Titre abrégé: Cell Rep Med
Pays: United States
ID NLM: 101766894

Informations de publication

Date de publication:
26 Apr 2024
Historique:
received: 20 03 2023
revised: 29 09 2023
accepted: 10 04 2024
medline: 5 5 2024
pubmed: 5 5 2024
entrez: 4 5 2024
Statut: aheadofprint

Résumé

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.

Identifiants

DOI: 10.1016/j.xcrm.2024.101547 PMID: 38703764
pubmed: 38703764
pii: S2666-3791(24)00239-8
doi: 10.1016/j.xcrm.2024.101547
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

101547

Investigateurs

Alexander J Lazar (AJ)
Amanda G Paulovich (AG)
Andrzej Antczak (A)
Anthony Green (A)
Avi Ma'ayan (A)
Barb Pruetz (B)
Bing Zhang (B)
Boris Reva (B)
Brian J Druker (BJ)
Charles A Goldthwaite (CA)
Chet Birger (C)
D R Mani (DR)
David Chesla (D)
David Fenyö (D)
Eric E Schadt (EE)
George Wilson (G)
Iga Kołodziejczak (I)
Ivy John (I)
Jason Hafron (J)
Josh Vo (J)
Kakhaber Zaalishvili (K)
Karen A Ketchum (KA)
Karin D Rodland (KD)
Kristen Nyce (K)
Maciej Wiznerowicz (M)
Marcin J Domagalski (MJ)
Meenakshi Anurag (M)
Melissa Borucki (M)
Michael A Gillette (MA)
Michael J Birrer (MJ)
Nathan J Edwards (NJ)
Negin Vatanian (N)
Pamela VanderKolk (P)
Peter B McGarvey (PB)
Rajiv Dhir (R)
Ratna R Thangudu (RR)
Reese Crispen (R)
Richard D Smith (RD)
Samuel H Payne (SH)
Sandra Cottingham (S)
Shuang Cai (S)
Steven A Carr (SA)
Tao Liu (T)
Toan Le (T)
Weiping Ma (W)
Xu Zhang (X)
Yin Lu (Y)
Yvonne Shutack (Y)
Zhen Zhang (Z)

Informations de copyright

Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests A.I.N., F.Y., and D.A.P. receive royalties from the University of Michigan for the sale of MSFragger software licences to commercial entities. All licence transactions are managed by the University of Michigan Innovation Partnerships office and all proceeds are subject to university technology transfer policy. Related to this work a provisional patent has been filed by University of Michigan, where A.M.C., A.I.N., S.M.D., R. Mannan, R. Mehra, Y.Z., S.C., A.D., X.W., G.X.L., and Y.H. are named as inventors.

Auteurs

Ginny Xiaohe Li (GX)

Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.

Lijun Chen (L)

Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.

Yi Hsiao (Y)

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

Rahul Mannan (R)

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.

Yuping Zhang (Y)

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.

Jie Luo (J)

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.

Francesca Petralia (F)

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

Hanbyul Cho (H)

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.

Noshad Hosseini (N)

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.

Felipe da Veiga Leprevost (FDV)

Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.

Anna Calinawan (A)

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

Yize Li (Y)

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.

Shankara Anand (S)

Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.

Aniket Dagar (A)

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.

Yifat Geffen (Y)

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.

Chandan Kumar-Sinha (C)

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.

Seema Chugh (S)

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.

Anne Le (A)

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.

Sean Ponce (S)

Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA.

Shenghao Guo (S)

Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA.

Cissy Zhang (C)

Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.

Michael Schnaubelt (M)

Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.

Nataly Naser Al Deen (NN)

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.

Feng Chen (F)

Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA.

Wagma Caravan (W)

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.

Andrew Houston (A)

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.

Alex Hopkins (A)

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.

Chelsea J Newton (CJ)

Van Andel Research Institute, Grand Rapids, MI 49503, USA.

Xiaoming Wang (X)

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.

Daniel A Polasky (DA)

Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.

Sarah Haynes (S)

Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.

Fengchao Yu (F)

Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.

Xiaojun Jing (X)

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.

Siqi Chen (S)

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.

Ana I Robles (AI)

Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.

Mehdi Mesri (M)

Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.

Mathangi Thiagarajan (M)

Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.

Eunkyung An (E)

Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.

Gad A Getz (GA)

Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.

W Marston Linehan (WM)

Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Galen Hostetter (G)

Van Andel Research Institute, Grand Rapids, MI 49503, USA.

Scott D Jewell (SD)

Van Andel Research Institute, Grand Rapids, MI 49503, USA.

Daniel W Chan (DW)

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.

Pei Wang (P)

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

Gilbert S Omenn (GS)

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.

Rohit Mehra (R)

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.

Christopher J Ricketts (CJ)

Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Li Ding (L)

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.

Arul M Chinnaiyan (AM)

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.

Marcin P Cieslik (MP)

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.

Saravana M Dhanasekaran (SM)

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.

Hui Zhang (H)

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.

Alexey I Nesvizhskii (AI)

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.

Classifications MeSH