1
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Powles T, Albiges L, Bex A, Comperat E, Grünwald V, Kanesvaran R, Kitamura H, McKay R, Porta C, Procopio G, Schmidinger M, Suarez C, Teoh J, de Velasco G, Young M, Gillessen S. Renal cell carcinoma: ESMO Clinical Practice Guideline for diagnosis, treatment and follow-up. Ann Oncol 2024; 35:692-706. [PMID: 38788900 DOI: 10.1016/j.annonc.2024.05.537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Affiliation(s)
- T Powles
- Barts Cancer Institute, Department of Medical Oncology, Queen Mary University of London and Royal Free London NHS Foundation Trust, London, UK
| | - L Albiges
- Université Paris Saclay, Institut Gustave Roussy, Villejuif, France
| | - A Bex
- Specialist Centre for Kidney Cancer, Royal Free London NHS Foundation Trust, London; Division of Surgery and Interventional Science, University College London, London, UK; Department of Urology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - E Comperat
- Department of Pathology, Medical University of Vienna, General Hospital of Vienna, Vienna, Austria
| | - V Grünwald
- Interdisciplinary Genitourinary Oncology, West German Cancer Center Clinic for Internal Medicine and Clinic for Urology, University Hospital Essen, Essen, Germany
| | - R Kanesvaran
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - H Kitamura
- Department of Urology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - R McKay
- Department of Medicine and Urology, University of California San Diego, La Jolla, USA
| | - C Porta
- Interdisciplinary Department of Medicine, University of Bari 'A. Moro', Bari; Division of Medical Oncology, A.O.U. Consorziale Policlinico di Bari, Bari
| | - G Procopio
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - M Schmidinger
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | - C Suarez
- Medical Oncology, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - J Teoh
- S. H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - G de Velasco
- Instituto de Investigación i+12 and Departamento de Oncología Médica, Hospital University 12 de Octubre, Madrid, Spain
| | - M Young
- Barts Cancer Institute, Department of Medical Oncology, Queen Mary University of London and Royal Free London NHS Foundation Trust, London, UK; Barts Cancer Institute, Department of Experimental Cancer Medicine, Queen Mary University of London, London, UK
| | - S Gillessen
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), Bellinzona; Università della Svizzera Italiana, Lugano, Switzerland
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2
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Yu A, Yesilkanal AE, Thakur A, Wang F, Yang Y, Phillips W, Wu X, Muir A, He X, Spitz F, Yang L. HYENA detects oncogenes activated by distal enhancers in cancer. Nucleic Acids Res 2024:gkae646. [PMID: 39051548 DOI: 10.1093/nar/gkae646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/07/2024] [Accepted: 07/11/2024] [Indexed: 07/27/2024] Open
Abstract
Somatic structural variations (SVs) in cancer can shuffle DNA content in the genome, relocate regulatory elements, and alter genome organization. Enhancer hijacking occurs when SVs relocate distal enhancers to activate proto-oncogenes. However, most enhancer hijacking studies have only focused on protein-coding genes. Here, we develop a computational algorithm 'HYENA' to identify candidate oncogenes (both protein-coding and non-coding) activated by enhancer hijacking based on tumor whole-genome and transcriptome sequencing data. HYENA detects genes whose elevated expression is associated with somatic SVs by using a rank-based regression model. We systematically analyze 1146 tumors across 25 types of adult tumors and identify a total of 108 candidate oncogenes including many non-coding genes. A long non-coding RNA TOB1-AS1 is activated by various types of SVs in 10% of pancreatic cancers through altered 3-dimensional genome structure. We find that high expression of TOB1-AS1 can promote cell invasion and metastasis. Our study highlights the contribution of genetic alterations in non-coding regions to tumorigenesis and tumor progression.
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Affiliation(s)
- Anqi Yu
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Ali E Yesilkanal
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Ashish Thakur
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Fan Wang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Yang Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - William Phillips
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Xiaoyang Wu
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - Alexander Muir
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Francois Spitz
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
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3
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Sicinska E, Kola VSR, Kerfoot JA, Taddei ML, Al-Ibraheemi A, Hsieh YH, Church AJ, Landesman-Bollag E, Landesman Y, Hemming ML. ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs. Cancer Res 2024; 84:2247-2264. [PMID: 38657118 PMCID: PMC11250573 DOI: 10.1158/0008-5472.can-23-2115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 02/09/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Alveolar soft part sarcoma (ASPS) is a rare mesenchymal malignancy driven by the ASPSCR1::TFE3 fusion. A better understanding of the mechanisms by which this oncogenic transcriptional regulator drives cancer growth is needed to help identify potential therapeutic targets. In this study, we characterized the transcriptional and chromatin landscapes of ASPS tumors and preclinical models, identifying the essential role of ASPSCR1::TFE3 in tumor cell viability by regulating core transcriptional programs involved in cell proliferation, angiogenesis, and mitochondrial biology. ASPSCR1::TFE3 directly interacted with key epigenetic regulators at enhancers and promoters to support ASPS-associated transcription. Among the effector programs driven by ASPSCR1::TFE3, cell proliferation was driven by high levels of cyclin D1 expression. Disruption of cyclin D1/CDK4 signaling led to a loss of ASPS proliferative capacity, and combined inhibition of CDK4/6 and angiogenesis halted tumor growth in xenografts. These results define the ASPS oncogenic program, reveal mechanisms by which ASPSCR1::TFE3 controls tumor biology, and identify a strategy for therapeutically targeting tumor cell-intrinsic vulnerabilities. Significance: The ASPSCR1::TFE3 fusion propels the growth of alveolar soft part sarcoma by activating transcriptional programs that regulate proliferation, angiogenesis, mitochondrial biogenesis, and differentiation and can be therapeutically targeted to improve treatment.
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MESH Headings
- Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism
- Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics
- Sarcoma, Alveolar Soft Part/genetics
- Sarcoma, Alveolar Soft Part/pathology
- Sarcoma, Alveolar Soft Part/metabolism
- Humans
- Animals
- Mice
- Cell Proliferation/genetics
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Gene Expression Regulation, Neoplastic
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Cell Line, Tumor
- Xenograft Model Antitumor Assays
- Cyclin-Dependent Kinase 4/genetics
- Cyclin-Dependent Kinase 4/metabolism
- Cyclin-Dependent Kinase 4/antagonists & inhibitors
- Female
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/pathology
- Neovascularization, Pathologic/metabolism
- Intracellular Signaling Peptides and Proteins
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Affiliation(s)
- Ewa Sicinska
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Vijaya S R Kola
- Division of Hematology and Oncology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Joseph A Kerfoot
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Madeleine L Taddei
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alyaa Al-Ibraheemi
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yi-Hsuan Hsieh
- Division of Hematology and Oncology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Alanna J Church
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Esther Landesman-Bollag
- Department of Medicine, Section of Hematology and Oncology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts
| | - Yosef Landesman
- Cure Alveolar Soft Part Sarcoma International, Brookline, Massachusetts
| | - Matthew L Hemming
- Division of Hematology and Oncology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts
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4
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Webster BR, Ricketts CJ, Vocke CD, Gamble D, Crooks DR, Yang Y, Friedman L, Toubaji A, Msaouel P, Hernandez JM, Linehan WM, Ball MW. Molecular Characterization of Metastatic Oncocytoma With Exceptional Response to Treatment: A Case Report. JCO Precis Oncol 2024; 8:e2400188. [PMID: 39038244 DOI: 10.1200/po.24.00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/15/2024] [Accepted: 06/12/2024] [Indexed: 07/24/2024] Open
Abstract
Comprehensive molecular characterization and effective therapy in a rare case of metastatic renal oncocytoma.
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Affiliation(s)
- Bradley R Webster
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Cathy D Vocke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Dionna Gamble
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ye Yang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Lindsay Friedman
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Antoun Toubaji
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jonathan M Hernandez
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Mark W Ball
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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5
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Sirohi D. Histologic and molecular landscape of genitourinary tumors and clinical implications. Urol Oncol 2024; 42:191-192. [PMID: 38670817 DOI: 10.1016/j.urolonc.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024]
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6
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Li L, Hossain SM, Eccles MR. The Role of the PAX Genes in Renal Cell Carcinoma. Int J Mol Sci 2024; 25:6730. [PMID: 38928435 PMCID: PMC11203709 DOI: 10.3390/ijms25126730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Renal cell carcinoma (RCC) is a significant oncological challenge due to its heterogeneous nature and limited treatment options. The PAX developmental gene family encodes nine highly conserved transcription factors that play crucial roles in embryonic development and organogenesis, which have been implicated in the occurrence and development of RCC. This review explores the molecular landscape of RCC, with a specific focus on the role of the PAX gene family in RCC tumorigenesis and disease progression. Of the various RCC subtypes, clear cell renal cell carcinoma (ccRCC) is the most prevalent, characterized by the loss of the von Hippel-Lindau (VHL) tumor suppressor gene. Here, we review the published literature on the expression patterns and functional implications of PAX genes, particularly PAX2 and PAX8, in the three most common RCC subtypes, including ccRCC, papillary RCC (PRCC), and chromophobe RCC (ChRCC). Further, we review the interactions and potential biological mechanisms involving PAX genes and VHL loss in driving the pathogenesis of RCC, including the key signaling pathways mediated by VHL in ccRCC and associated mechanisms implicating PAX. Lastly, concurrent with our update regarding PAX gene research in RCC, we review and comment on the targeting of PAX towards the development of novel RCC therapies.
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Affiliation(s)
- Lei Li
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (L.L.); (S.M.H.)
| | - Sultana Mehbuba Hossain
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (L.L.); (S.M.H.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
| | - Michael R. Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (L.L.); (S.M.H.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
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7
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Papanikolaou D, Sokolakis I, Moysidis K, Pyrgidis N, Bobos M, Meditskou S, Hatzimouratidis K. Grading Challenges and Prognostic Insights in Chromophobe Renal Cell Carcinoma: A Retrospective Study of 72 Patients. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:996. [PMID: 38929613 PMCID: PMC11205766 DOI: 10.3390/medicina60060996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Chromophobe RCC (ChRCC) carries the best prognosis among all RCC subtypes, yet it lacks a proper grading system. Various systems have been suggested in the past, causing much controversy, and Avulova et al. recently proposed a promising four-tier grading system that takes into consideration tumor necrosis. Dysregulation of the mammalian target of the rapamycin (mTOR) pathway plays a key role in ChRCC pathogenesis, highlighting its molecular complexity. The present retrospective study aimed to evaluate the prognostic factors associated with a more aggressive ChRCC phenotype. Materials and Methods: Seventy-two patients diagnosed with ChRCC between 2004 and 2017 were included in our study. Pathology reports and tissue blocks were reviewed, and immunohistochemistry (IHC) was performed in order to assess the expressions of CYLD (tumor-suppressor gene) and mTOR, among other markers. Univariate analysis was performed, and OS was assessed using the Kaplan-Meier method. Results: In our study, 74% of patients were male, with a mean age of 60 years, and the mean tumor size was 63 mm (±44). The majority (54%) were followed for more than 10 years at intervals ranging between 44 and 222 months. The risk of death was significantly higher for patients that were classified as Grade 4 in the Avulova system (HR: 5.83; 95% CI, 1.37-24.7; p: = 0.017). As far as the IHC is concerned, mTOR expression was associated with an HR of 8.57 (95% CI, 1.91-38.5; p = 0.005), and CYLD expression was associated with an HR of 17.3 (95% CI, 1.57-192; p = 0.02). Conclusions: In our study, the Avulova grading system seems to be positively correlated with OS in patients diagnosed with ChRCC. Furthermore, an elevated mTOR expression also shows a negative correlation with OS, whereas an elevated CYLD expression does not seem to exert a protective role. However, because only a small proportion (4.2%) of our patients died due to ChRCC, despite the long follow-up period, the results must be interpreted with caution. Further research is needed to validate our findings.
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Affiliation(s)
- Dimitrios Papanikolaou
- Second Department of Urology, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Ioannis Sokolakis
- Second Department of Urology, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Kyriakos Moysidis
- Second Department of Urology, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Nikolaos Pyrgidis
- Department of Urology, University Hospital, LMU Munich, 80539 Munich, Germany
| | - Mattheos Bobos
- Department of Biomedical Sciences, School of Health Sciences, International Hellenic University, 570 01 Thessaloniki, Greece
| | - Soultana Meditskou
- Laboratory of Histology and Embryology, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
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8
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Xie AX, Tansey W, Reznik E. UnitedMet harnesses RNA-metabolite covariation to impute metabolite levels in clinical samples. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.24.24307903. [PMID: 38826234 PMCID: PMC11142294 DOI: 10.1101/2024.05.24.24307903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Comprehensively studying metabolism requires the measurement of metabolite levels. However, in contrast to the broad availability of gene expression data, metabolites are rarely measured in large molecularly-defined cohorts of tissue samples. To address this basic barrier to metabolic discovery, we propose a Bayesian framework ("UnitedMet") which leverages the empirical strength of RNA-metabolite covariation to impute otherwise unmeasured metabolite levels from widely available transcriptomic data. We demonstrate that UnitedMet is equally capable of imputing whole pool sizes as well as the outcomes of isotope tracing experiments. We apply UnitedMet to investigate the metabolic impact of driver mutations in kidney cancer, identifying a novel association between BAP1 and a highly oxidative tumor phenotype. We similarly apply UnitedMet to determine that advanced kidney cancers upregulate oxidative phosphorylation relative to early-stage disease, that oxidative metabolism in kidney cancer is associated with inferior outcomes to combination therapy, and that kidney cancer metastases themselves demonstrate elevated oxidative phosphorylation relative to primary tumors. UnitedMet therefore enables the assessment of metabolic phenotypes in contexts where metabolite measurements were not taken or are otherwise infeasible, opening new avenues for the generation and evaluation of metabolite-centered hypotheses. UnitedMet is open source and publicly available (https://github.com/reznik-lab/UnitedMet).
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Affiliation(s)
- Amy X. Xie
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, NY NY 10065
- Biochemistry, Structural Biology, Cell Biology, Developmental Biology and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY
| | - Wesley Tansey
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, NY NY 10065
| | - Ed Reznik
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, NY NY 10065
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9
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Baraban EG, Elias R, Lin MT, Ged Y, Zhu J, Pallavajjala A, Singla N, Lotan TL, Argani P, Eshleman JR, Epstein JI. High-Grade, Nonsarcomatoid Chromophobe Renal Cell Carcinoma: A Series of 22 Cases With Novel Molecular Features on a Subset. Mod Pathol 2024; 37:100472. [PMID: 38492778 DOI: 10.1016/j.modpat.2024.100472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/15/2024] [Accepted: 03/07/2024] [Indexed: 03/18/2024]
Abstract
Chromophobe renal cell carcinoma (ChRCC) is the third most common subtype of renal cell carcinoma and typically exhibits indolent behavior, though a rare subset can exhibit high-grade morphologic features and is associated with a poor prognosis. Although there are limited data on the molecular characteristics of metastatic and sarcomatoid ChRCC, the molecular features of high-grade, nonsarcomatoid ChRCC remain unexplored. Herein, we characterize 22 cases of ChRCC with high-grade, nonsarcomatoid components. High-grade ChRCC frequently demonstrated advanced stage at diagnosis (64% ≥pT3a or N1), with regions of extrarenal extension, nodal metastases, and vascular invasion consisting solely of high-grade ChRCC morphologically. We performed spatially guided panel-based DNA sequencing on 11 cases comparing high-grade and low-grade regions (n = 22 samples). We identified recurring somatic alterations emblematic of ChRCC, including deletions of chromosomes 1, 2, 6, 10, 13, 17, and 21 in 91% (10/11) of cases and recurring mutations in TP53 (81.8%, n = 9/11) and PTEN (36.4%, n = 4/11). Notably, although PTEN and TP53 alterations were found in both high-grade and low-grade regions, private mutations were identified in 3 cases, indicating convergent evolution. Finally, we identified recurring RB1 mutations in 27% (n = 3) of high-grade regions leading to selective protein loss by immunohistochemistry not observed in adjacent low-grade regions. This finding was confirmed in The Cancer Genome Atlas cohort where 2 of 66 cases contained RB1 mutations and demonstrated unequivocal high-grade, nonsarcomatoid morphology. We also detected multiple chromosomal gains confined to the high-grade regions, consistent with imbalanced chromosome duplication. These findings broaden our understanding of the molecular pathogenesis of ChRCC and suggest that subclonal RB1 mutations can drive the evolution to high-grade, nonsarcomatoid ChRCC.
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Affiliation(s)
- Ezra G Baraban
- Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland.
| | - Roy Elias
- Department of Oncology, Johns Hopkins Hospital, Baltimore, Maryland
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland
| | - Yasser Ged
- Department of Oncology, Johns Hopkins Hospital, Baltimore, Maryland
| | - Jing Zhu
- Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland
| | | | - Nirmish Singla
- Department of Urology, Johns Hopkins Hospital, Baltimore, Maryland
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland
| | - Pedram Argani
- Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland
| | - James R Eshleman
- Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland
| | - Jonathan I Epstein
- Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland; Department of Oncology, Johns Hopkins Hospital, Baltimore, Maryland; Department of Urology, Johns Hopkins Hospital, Baltimore, Maryland
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10
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Alghamdi M, Chen JF, Jungbluth A, Koutzaki S, Palmer MB, Al-Ahmadie HA, Fine SW, Gopalan A, Sarungbam J, Sirintrapun SJ, Tickoo SK, Reuter VE, Chen YB. L1 Cell Adhesion Molecule (L1CAM) Expression and Molecular Alterations Distinguish Low-Grade Oncocytic Tumor From Eosinophilic Chromophobe Renal Cell Carcinoma. Mod Pathol 2024; 37:100467. [PMID: 38460672 PMCID: PMC11102321 DOI: 10.1016/j.modpat.2024.100467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/06/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
Renal low-grade oncocytic tumor (LOT) is a recently recognized renal cell neoplasm designated within the "other oncocytic tumors" category in the 2022 World Health Organization classification system. Although the clinicopathologic, immunohistochemical, and molecular features reported for LOT have been largely consistent, the data are relatively limited. The morphologic overlap between LOT and other low-grade oncocytic neoplasms, particularly eosinophilic chromophobe renal cell carcinoma (E-chRCC), remains a controversial area in renal tumor classification. To address this uncertainty, we characterized and compared large cohorts of LOT (n = 67) and E-chRCC (n = 69) and revealed notable differences between the 2 entities. Clinically, LOT predominantly affected women, whereas E-chRCC showed a male predilection. Histologically, although almost all LOTs were dominated by a small-nested pattern, E-chRCC mainly showed solid and tubular architectures. Molecular analysis revealed that 87% of LOT cases harbored mutations in the tuberous sclerosis complex (TSC)-mTOR complex 1 (mTORC1) pathway, most frequently in MTOR and RHEB genes; a subset of LOT cases had chromosomal 7 and 19q gains. In contrast, E-chRCC lacked mTORC1 mutations, and 60% of cases displayed chromosomal losses characteristic of chRCC. We also explored the cell of origin for LOT and identified L1 cell adhesion molecule (L1CAM), a collecting duct and connecting tubule principal cell marker, as a highly sensitive and specific ancillary test for differentiating LOT from E-chRCC. This distinctive L1CAM immunohistochemical labeling suggests the principal cells as the cell of origin for LOT, unlike the intercalated cell origin of E-chRCC and oncocytoma. The ultrastructural analysis of LOT showed normal-appearing mitochondria and intracytoplasmic lumina with microvilli, different from what has been described for chRCC. Our study further supports LOT as a unique entity with a benign clinical course. Based on the likely cell of origin and its clinicopathologic characteristics, we propose that changing the nomenclature of LOT to "Oncocytic Principal Cell Adenoma of the Kidney" may be a better way to define and describe this entity.
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Affiliation(s)
- Mohammed Alghamdi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Jie-Fu Chen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Achim Jungbluth
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sirma Koutzaki
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Matthew B Palmer
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Hikmat A Al-Ahmadie
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samson W Fine
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anuradha Gopalan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Judy Sarungbam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - S Joseph Sirintrapun
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Satish K Tickoo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Victor E Reuter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ying-Bei Chen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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11
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Barata P, Gulati S, Elliott A, Hammers HJ, Burgess E, Gartrell BA, Darabi S, Bilen MA, Basu A, Geynisman DM, Dawson NA, Zibelman MR, Zhang T, Wei S, Ryan CJ, Heath EI, Poorman KA, Nabhan C, McKay RR. Renal cell carcinoma histologic subtypes exhibit distinct transcriptional profiles. J Clin Invest 2024; 134:e178915. [PMID: 38652565 PMCID: PMC11142736 DOI: 10.1172/jci178915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Molecular profiling of clear cell renal cell carcinoma (ccRCC) tumors of patients in a clinical trial has identified distinct transcriptomic signatures with predictive value, yet data in non-clear cell variants (nccRCC) are lacking. We examined the transcriptional profiles of RCC tumors representing key molecular pathways, from a multi-institutional, real-world patient cohort, including ccRCC and centrally reviewed nccRCC samples. ccRCC had increased angiogenesis signature scores compared with the heterogeneous group of nccRCC tumors, while cell cycle, fatty acid oxidation/AMPK signaling, and fatty acid synthesis/pentose phosphate signature scores were increased in one or more nccRCC subtypes. Among both ccRCC and nccRCC tumors, T effector scores statistically correlated with increased immune cell infiltration and were more commonly associated with immunotherapy-related markers (PD-L1+/TMBhi/MSIhi). In conclusion, this study provides evidence of differential gene transcriptional profiles among ccRCC versus nccRCC tumors, providing insights for optimizing personalized and histology-specific therapeutic strategies for patients with advanced RCC.
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Affiliation(s)
- Pedro Barata
- Tulane Medical School, New Orleans, Louisiana, USA
- University Hospitals Seidman Cancer Center, Cleveland, Ohio, USA
| | | | | | - Hans J. Hammers
- Kidney Cancer Program, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Earle Burgess
- Levine Cancer Institute Atrium Health, Charlotte, North Carolina, USA
| | - Benjamin A. Gartrell
- Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York, USA
| | - Sourat Darabi
- Hoag Memorial Presbyterian Hospital, Newport Beach, California, USA
| | - Mehmet A. Bilen
- Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Arnab Basu
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Nancy A. Dawson
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | | | - Tian Zhang
- Kidney Cancer Program, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Shuanzeng Wei
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | | | - Elisabeth I. Heath
- Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, USA
| | | | | | - Rana R. McKay
- Moores Cancer Center, UCSD, San Diego, California, USA
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12
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Kapur P, Zhong H, Le D, Mukhopadhyay R, Miyata J, Carrillo D, Rakheja D, Rajaram S, Durinck S, Modrusan Z, Brugarolas J. Molecular underpinnings of dedifferentiation and aggressiveness in chromophobe renal cell carcinoma. JCI Insight 2024; 9:e176743. [PMID: 38775158 PMCID: PMC11141915 DOI: 10.1172/jci.insight.176743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 04/10/2024] [Indexed: 06/02/2024] Open
Abstract
Sarcomatoid dedifferentiation is common to multiple renal cell carcinoma (RCC) subtypes, including chromophobe RCC (ChRCC), and is associated with increased aggressiveness, resistance to targeted therapies, and heightened sensitivity to immunotherapy. To study ChRCC dedifferentiation, we performed multiregion integrated paired pathological and genomic analyses. Interestingly, ChRCC dedifferentiates not only into sarcomatoid but also into anaplastic and glandular subtypes, which are similarly associated with increased aggressiveness and metastases. Dedifferentiated ChRCC shows loss of epithelial markers, convergent gene expression, and whole genome duplication from a hypodiploid state characteristic of classic ChRCC. We identified an intermediate state with atypia and increased mitosis but preserved epithelial markers. Our data suggest that dedifferentiation is initiated by hemizygous mutation of TP53, which can be observed in differentiated areas, as well as mutation of PTEN. Notably, these mutations become homozygous with duplication of preexisting monosomes (i.e., chromosomes 17 and 10), which characterizes the transition to dedifferentiated ChRCC. Serving as potential biomarkers, dedifferentiated areas become accentuated by mTORC1 activation (phospho-S6) and p53 stabilization. Notably, dedifferentiated ChRCC share gene enrichment and pathway activation features with other sarcomatoid RCC, suggesting convergent evolutionary trajectories. This study expands our understanding of aggressive ChRCC, provides insight into molecular mechanisms of tumor progression, and informs pathologic classification and diagnostics.
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Affiliation(s)
- Payal Kapur
- Department of Pathology and
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, Dallas, Texas, USA
| | - Hua Zhong
- Department of Pathology and
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Daniel Le
- Molecular Biology Department, Genentech Inc., South San Francisco, California, USA
| | | | - Jeffrey Miyata
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, Dallas, Texas, USA
- Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Deyssy Carrillo
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, Dallas, Texas, USA
- Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Satwik Rajaram
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Steffen Durinck
- Molecular Biology Department, Genentech Inc., South San Francisco, California, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech Inc., South San Francisco, California, USA
| | - James Brugarolas
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, Dallas, Texas, USA
- Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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13
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Yu A, Yesilkanal AE, Thakur A, Wang F, Yang Y, Phillips W, Wu X, Muir A, He X, Spitz F, Yang L. HYENA detects oncogenes activated by distal enhancers in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.09.523321. [PMID: 38076958 PMCID: PMC10705271 DOI: 10.1101/2023.01.09.523321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Somatic structural variations (SVs) in cancer can shuffle DNA content in the genome, relocate regulatory elements, and alter genome organization. Enhancer hijacking occurs when SVs relocate distal enhancers to activate proto-oncogenes. However, most enhancer hijacking studies have only focused on protein-coding genes. Here, we develop a computational algorithm "HYENA" to identify candidate oncogenes (both protein-coding and non-coding) activated by enhancer hijacking based on tumor whole-genome and transcriptome sequencing data. HYENA detects genes whose elevated expression is associated with somatic SVs by using a rank-based regression model. We systematically analyze 1,146 tumors across 25 types of adult tumors and identify a total of 108 candidate oncogenes including many non-coding genes. A long non-coding RNA TOB1-AS1 is activated by various types of SVs in 10% of pancreatic cancers through altered 3-dimensional genome structure. We find that high expression of TOB1-AS1 can promote cell invasion and metastasis. Our study highlights the contribution of genetic alterations in non-coding regions to tumorigenesis and tumor progression.
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Affiliation(s)
- Anqi Yu
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
| | - Ali E. Yesilkanal
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
| | - Ashish Thakur
- Department of Human Genetics, University of Chicago, Chicago IL, USA
| | - Fan Wang
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
| | - Yang Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
| | - William Phillips
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
| | - Xiaoyang Wu
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - Alexander Muir
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago IL, USA
| | - Francois Spitz
- Department of Human Genetics, University of Chicago, Chicago IL, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
- Department of Human Genetics, University of Chicago, Chicago IL, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
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14
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Zhang T, Sang J, Hoang PH, Zhao W, Rosenbaum J, Johnson KE, Klimczak LJ, McElderry J, Klein A, Wirth C, Bergstrom EN, Díaz-Gay M, Vangara R, Colon-Matos F, Hutchinson A, Lawrence SM, Cole N, Zhu B, Przytycka TM, Shi J, Caporaso NE, Homer R, Pesatori AC, Consonni D, Imielinski M, Chanock SJ, Wedge DC, Gordenin DA, Alexandrov LB, Harris RS, Landi MT. APOBEC shapes tumor evolution and age at onset of lung cancer in smokers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587805. [PMID: 38617360 PMCID: PMC11014539 DOI: 10.1101/2024.04.02.587805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues1,2. Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B)3-6. However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations, whereas HAS for A3A-like mutagenesis and TP53 mutations. Unlike APOBEC3A, APOBEC3B expression is strongly associated with an upregulation of the base excision repair pathway. Hypermutation by unrepaired A3A and tobacco smoking mutagenesis combined with TP53-induced genomic instability can trigger senescence7, apoptosis8, and cell regeneration9, as indicated by high expression of pulmonary healing signaling pathway, stemness markers and distal cell-of-origin in HAS. The expected association of tobacco smoking variables (e.g., time to first cigarette) with genomic/epigenomic changes are not observed in HAS, a plausible consequence of frequent cell senescence or apoptosis. HAS have more neoantigens, slower clonal expansion, and older age at onset compared to LAS, particularly in heavy smokers, consistent with high proportions of newly generated, unmutated cells and frequent immuno-editing. These findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development, with important clinical implications.
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Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - John McElderry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alyssa Klein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher Wirth
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Frank Colon-Matos
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M. Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Angela C. Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Dario Consonni
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C. Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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15
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Hashemi Gheinani A, Kim J, You S, Adam RM. Bioinformatics in urology - molecular characterization of pathophysiology and response to treatment. Nat Rev Urol 2024; 21:214-242. [PMID: 37604982 DOI: 10.1038/s41585-023-00805-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2023] [Indexed: 08/23/2023]
Abstract
The application of bioinformatics has revolutionized the practice of medicine in the past 20 years. From early studies that uncovered subtypes of cancer to broad efforts spearheaded by the Cancer Genome Atlas initiative, the use of bioinformatics strategies to analyse high-dimensional data has provided unprecedented insights into the molecular basis of disease. In addition to the identification of disease subtypes - which enables risk stratification - informatics analysis has facilitated the identification of novel risk factors and drivers of disease, biomarkers of progression and treatment response, as well as possibilities for drug repurposing or repositioning; moreover, bioinformatics has guided research towards precision and personalized medicine. Implementation of specific computational approaches such as artificial intelligence, machine learning and molecular subtyping has yet to become widespread in urology clinical practice for reasons of cost, disruption of clinical workflow and need for prospective validation of informatics approaches in independent patient cohorts. Solving these challenges might accelerate routine integration of bioinformatics into clinical settings.
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Affiliation(s)
- Ali Hashemi Gheinani
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Urology, Inselspital, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Jina Kim
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sungyong You
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rosalyn M Adam
- Department of Urology, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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16
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Coffey NJ, Simon MC. Metabolic alterations in hereditary and sporadic renal cell carcinoma. Nat Rev Nephrol 2024; 20:233-250. [PMID: 38253811 PMCID: PMC11165401 DOI: 10.1038/s41581-023-00800-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2023] [Indexed: 01/24/2024]
Abstract
Kidney cancer is the seventh leading cause of cancer in the world, and its incidence is on the rise. Renal cell carcinoma (RCC) is the most common form and is a heterogeneous disease comprising three major subtypes that vary in their histology, clinical course and driver mutations. These subtypes include clear cell RCC, papillary RCC and chromophobe RCC. Molecular analyses of hereditary and sporadic forms of RCC have revealed that this complex and deadly disease is characterized by metabolic pathway alterations in cancer cells that lead to deregulated oxygen and nutrient sensing, as well as impaired tricarboxylic acid cycle activity. These metabolic changes facilitate tumour growth and survival. Specifically, studies of the metabolic features of RCC have led to the discovery of oncometabolites - fumarate and succinate - that can promote tumorigenesis, moonlighting functions of enzymes, and substrate auxotrophy owing to the disruption of pathways that enable the production of arginine and cholesterol. These metabolic alterations within RCC can be exploited to identify new therapeutic targets and interventions, in combination with novel approaches that minimize the systemic toxicity of metabolic inhibitors and reduce the risk of drug resistance owing to metabolic plasticity.
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Affiliation(s)
- Nathan J Coffey
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
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17
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Bories C, Lejour T, Adolphe F, Kermasson L, Couvé S, Tanguy L, Luszczewska G, Watzky M, Poillerat V, Garnier P, Groisman R, Ferlicot S, Richard S, Saparbaev M, Revy P, Gad S, Renaud F. DCLRE1B/Apollo germline mutations associated with renal cell carcinoma impair telomere protection. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167107. [PMID: 38430974 DOI: 10.1016/j.bbadis.2024.167107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 02/14/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
Hereditary renal cell carcinoma (RCC) is caused by germline mutations in a subset of genes, including VHL, MET, FLCN, and FH. However, many familial RCC cases do not harbor mutations in the known predisposition genes. Using Whole Exome Sequencing, we identified two germline missense variants in the DCLRE1B/Apollo gene (ApolloN246I and ApolloY273H) in two unrelated families with several RCC cases. Apollo encodes an exonuclease involved in DNA Damage Response and Repair (DDRR) and telomere integrity. We characterized these two functions in the human renal epithelial cell line HKC8. The decrease or inhibition of Apollo expression sensitizes these cells to DNA interstrand crosslink damage (ICLs). HKC8 Apollo-/- cells appear defective in the DDRR and present an accumulation of telomere damage. Wild-type and mutated Apollo forms could interact with TRF2, a shelterin protein involved in telomere protection. However, only ApolloWT can rescue the telomere damage in HKC8 Apollo-/- cells. Our results strongly suggest that ApolloN246I and ApolloY273H are loss-of-function mutants that cause impaired telomere integrity and could lead to genomic instability. Altogether, our results suggest that mutations in Apollo could induce renal oncogenesis.
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Affiliation(s)
- Charlie Bories
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Thomas Lejour
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Florine Adolphe
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Laëtitia Kermasson
- Laboratory of Genome Dynamics in the Immune System, Laboratoire labellisé Ligue Nationale contre le Cancer, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Sophie Couvé
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Laura Tanguy
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Gabriela Luszczewska
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Manon Watzky
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Victoria Poillerat
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Pauline Garnier
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Regina Groisman
- UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Sophie Ferlicot
- UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France; Département de Pathologie, AP-HP, Université Paris-Saclay, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Stéphane Richard
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France; Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR labellisé par l'INCa, Hôpital de Bicêtre, AP-HP, et Service d'Urologie, Le Kremlin-Bicêtre, France
| | - Murat Saparbaev
- UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Patrick Revy
- Laboratory of Genome Dynamics in the Immune System, Laboratoire labellisé Ligue Nationale contre le Cancer, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Sophie Gad
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Flore Renaud
- EPHE, PSL Université, Paris, France; UMR 9019 CNRS, Gustave Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, Villejuif 94800, France.
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18
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Siegmund SE, Al-Obaidy KI, Tsai HK, Idrees MT, Akgul M, Acosta AM, Hirsch MS. Concordance of MTOR Pathway Mutations and the Diagnosis of Renal Low-Grade Oncocytic Tumor (LOT). Int J Surg Pathol 2024; 32:316-330. [PMID: 37357748 DOI: 10.1177/10668969231178032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
The differential diagnosis for oncocytic renal tumors spans the spectrum from benign entities to more aggressive renal cell carcinomas (RCC). Recent work has characterized a provisional renal oncocytic neoplasm, namely the low-grade oncocytic tumor (LOT), which demonstrates overlapping morphologic features with oncocytoma and chromophobe RCC, but also has a unique immunoprofile (ie, diffusely positive for KRT7, negative for KIT) and a high rate (80% to 100%) of mTOR pathway gene alterations. Given the diagnostic overlap among oncocytic tumors, we looked for concordance between mTOR pathway mutations and LOT. Thirty low-grade renal oncocytic neoplasms underwent histologic review and immunohistochemistry for KRT7 and KIT. Tumors were classified as "determinate" (eg, LOT) for tumors with solid, nested or vaguely tubular growth and diffuse KRT7 staining and negative KIT, or "indeterminate" if the morphology and/or immunostains did not fully support a definitive LOT diagnosis. Next-generation sequencing was performed without any knowledge of the diagnoses, and identified mTOR pathway mutations in 80% (12/15) of the determinate tumors, compared with 7% (1/15) in the indeterminate group. One determinate tumor was reclassified as papillary RCC (MTOR mutation negative) and 6 indeterminate tumors were confirmed to be oncocytoma (N = 4), clear cell RCC or papillary RCC with reverse polarity, respectively. Overall, integration of morphology, immunohistochemistry, and molecular data enabled a final definitive diagnosis for 70% of tumors (21 of the total 30), with a high concordance (93%) for LOT specifically in the determinate group; the remaining 9 tumors (30%) were classified as renal oncocytic neoplasm, not otherwise specified.
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Affiliation(s)
- Stephanie E Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Khaleel I Al-Obaidy
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, MA, USA
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mahmut Akgul
- Department of Pathology, Albany Medical Center, Albany, NY, USA
| | - Andres M Acosta
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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19
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Chen F, Zhang Y, Sedlazeck FJ, Creighton CJ. Germline structural variation globally impacts the cancer transcriptome including disease-relevant genes. Cell Rep Med 2024; 5:101446. [PMID: 38442712 PMCID: PMC10983041 DOI: 10.1016/j.xcrm.2024.101446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/01/2024] [Accepted: 02/06/2024] [Indexed: 03/07/2024]
Abstract
Germline variation and somatic alterations contribute to the molecular profile of cancers. We combine RNA with whole genome sequencing across 1,218 cancer patients to determine the extent germline structural variants (SVs) impact expression of nearby genes. For hundreds of genes, recurrent and common germline SV breakpoints within 100 kb associate with increased or decreased expression in tumors spanning various tissues of origin. A significant fraction of germline SV expression associations involves duplication of intergenic enhancers or 3' UTR disruption. Genes altered by both somatic and germline SVs include ATRX and CEBPA. Genes essential in cancer cell lines include BARD1 and IRS2. Genes with both expression and germline SV breakpoint patterns associated with patient survival include GCLM. Our results capture a class of phenotypic variation at work in the disease setting, including genes with cancer roles. Specific germline SVs represent potential cancer risk variants for genetic testing, including those involving genes with targeting implications.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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20
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Qiu J, Deng R, Zhao Z, Tian P, Zhou J. The long-term outcomes of local tumor destruction versus partial nephrectomy for cT1a non-clear cell renal cell carcinoma and development of prognostic nomograms. J Cancer Res Clin Oncol 2024; 150:122. [PMID: 38472549 PMCID: PMC10933168 DOI: 10.1007/s00432-023-05571-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/25/2023] [Indexed: 03/14/2024]
Abstract
PURPOSE There is a lack of authoritative opinions on local tumor destruction (LTD) for clinical T1a (cT1a) non-clear cell renal cell carcinoma (nccRCC). We aim to compare the outcomes of cT1a nccRCC after partial nephrectomy (PN) or LTD and explore prognostic factors. METHODS Patients diagnosed with cT1a nccRCC receiving LTD or PN between 2000 and 2020 were identified from the Surveillance, Epidemiology, and End Results (SEER) database. A 1:1 propensity score matching (PSM) was performed for patients receiving LTD and PN. Kaplan-Meier survival analysis, Cox regression analysis, competing risk regression models, and subgroup analysis were used to compare outcomes and identify prognostic factors. Prognostic nomograms were established and evaluated based on the multivariate models. RESULTS A total of 3664 cT1a nccRCC patients were included. The LTD group had poorer overall survival (OS) and similar cancer-specific survival (CSS) compared with the PN group before and after PSM (p < 0.05), while the other-cause mortality rate of the LTD group was higher than that of the PN group. Age, marital status, household income, prior tumor history, interval between diagnosis and treatment, treatments, and tumor size were identified as independent predictive factors for OS. Age, tumor size, prior tumor history, and histological type were identified as independent predictive factors for CSS. Then the nomograms predicting OS and CSS were constructed based on these prognostic factors, which showed excellent performance in risk stratification and accuracy. CONCLUSION LTD could achieve comparable cancer-control effects as PN among cT1a nccRCC patients. The OS and CSS nomograms worked effectively for prognosis assessment.
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Affiliation(s)
- Jianhui Qiu
- Department of Urology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, People's Republic of China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
| | - Ruiyi Deng
- Department of Urology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, People's Republic of China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
| | - Zihou Zhao
- Department of Urology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, People's Republic of China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
| | - Peidong Tian
- Department of Urology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, People's Republic of China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
| | - Jingcheng Zhou
- Department of Urology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing, 100034, People's Republic of China.
- Institute of Urology, Peking University, Beijing, China.
- National Urological Cancer Center, Beijing, China.
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21
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Chen RJ, Ding T, Lu MY, Williamson DFK, Jaume G, Song AH, Chen B, Zhang A, Shao D, Shaban M, Williams M, Oldenburg L, Weishaupt LL, Wang JJ, Vaidya A, Le LP, Gerber G, Sahai S, Williams W, Mahmood F. Towards a general-purpose foundation model for computational pathology. Nat Med 2024; 30:850-862. [PMID: 38504018 DOI: 10.1038/s41591-024-02857-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/05/2024] [Indexed: 03/21/2024]
Abstract
Quantitative evaluation of tissue images is crucial for computational pathology (CPath) tasks, requiring the objective characterization of histopathological entities from whole-slide images (WSIs). The high resolution of WSIs and the variability of morphological features present significant challenges, complicating the large-scale annotation of data for high-performance applications. To address this challenge, current efforts have proposed the use of pretrained image encoders through transfer learning from natural image datasets or self-supervised learning on publicly available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using more than 100 million images from over 100,000 diagnostic H&E-stained WSIs (>77 TB of data) across 20 major tissue types. The model was evaluated on 34 representative CPath tasks of varying diagnostic difficulty. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient artificial intelligence models that can generalize and transfer to a wide range of diagnostically challenging tasks and clinical workflows in anatomic pathology.
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Affiliation(s)
- Richard J Chen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tong Ding
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Ming Y Lu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Drew F K Williamson
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Guillaume Jaume
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew H Song
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bowen Chen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew Zhang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA, USA
| | - Daniel Shao
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA, USA
| | - Muhammad Shaban
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mane Williams
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lukas Oldenburg
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Luca L Weishaupt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA, USA
| | - Judy J Wang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anurag Vaidya
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA, USA
| | - Long Phi Le
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA, USA
| | - Georg Gerber
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sharifa Sahai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Systems Biology, Harvard University, Cambridge, MA, USA
| | - Walt Williams
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Faisal Mahmood
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Data Science Initiative, Harvard University, Cambridge, MA, USA.
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22
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Barman P, Ferdoush J, Kaja A, Chakraborty P, Uprety B, Bhaumik R, Bhaumik R, Bhaumik SR. Ubiquitin-proteasome system regulation of a key gene regulatory factor, Paf1C. Gene 2024; 894:148004. [PMID: 37977317 DOI: 10.1016/j.gene.2023.148004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Paf1 (Polymerase-associated factor 1) complex (Paf1C) is evolutionarily conserved from yeast to humans, and facilitates transcription elongation as well as co-transcriptional histone covalent modifications and mRNA 3'-end processing. Thus, Paf1C is a key player in regulation of eukaryotic gene expression. Paf1C consists of Paf1, Cdc73, Ctr9, Leo1 and Rtf1 in both yeast and humans, but it has an additional component, Ski8, in humans. The abundances of these components regulate the assembly of Paf1C and/or its functions, thus implying the mechanisms involved in regulating the abundances of the Paf1C components in altered gene expression and hence cellular pathologies. Towards finding the mechanisms associated with the abundances of the Paf1C components, we analyzed here whether the Paf1C components are regulated via targeted ubiquitylation and 26S proteasomal degradation. We find that the Paf1C components except Paf1 do not undergo the 26S proteasomal degradation in both yeast and humans. Paf1 is found to be regulated by the ubiquitin-proteasome system (UPS) in yeast and humans. Alteration of such regulation changes Paf1's abundance, leading to aberrant gene expression. Intriguingly, while the Rtf1 component of Paf1C does not undergo the 26S proteasomal degradation, it is found to be ubiquitylated, suggesting that Rtf1 ubiquitylation could be engaged in Paf1C assembly and/or functions. Collectively, our results reveal distinct UPS regulation of the Paf1C components, Paf1 and Rtf1, in a proteolysis-dependent and -independent manners, respectively, with functional implications.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Jannatul Ferdoush
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Amala Kaja
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Pritam Chakraborty
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Bhawana Uprety
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Rhea Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Risa Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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23
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Zhang H, Cong X, Chen C, Liu Z. Sintilimab combined with axitinib in the treatment of advanced chromophobe renal cell carcinoma: a case report. Front Oncol 2024; 14:1325999. [PMID: 38371628 PMCID: PMC10869506 DOI: 10.3389/fonc.2024.1325999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024] Open
Abstract
Chromophobe renal cell carcinoma (ChRCC) is a rare pathological type of renal cell carcinoma (RCC). Related systematic studies involving large numbers of patients are lacking, and more importantly, there is currently no international consensus on post-line treatment guidelines for ChRCC. The rapid development of systemic treatment with molecular targeted therapies and immune checkpoint inhibitors has brought effective approaches for patients with clear cell renal cell carcinoma (ccRCC), while progress in the treatment of ChRCC is still limited. In this case report, the patient was initially diagnosed at the early stage; 4 years post-surgery, she developed lung metastases and the disease progressed once again after being treated with sunitinib monotherapy for 3 years. However, after combining the immunotherapy sintilimab with the targeted therapy axitinib as second-line treatment, imageological examination showed lesions in the lungs that gradually decreased, and the bone metastases remained stable. To date, the patient has been continuously treated for over 2 years and is still undergoing regular treatment and follow-up. This case is the first to report the long-term survival of metastatic disease by using this treatment regimen and to propose a potential therapeutic option for patients with metastatic ChRCC. Since only one case was observed in this report, further study is needed.
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Affiliation(s)
| | | | | | - Ziling Liu
- Cancer Center, The First Hospital of Jilin University, Changchun, China
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24
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Zhang X, Bolck HA, Rupp NJ, Moch H. Genomic alterations and diagnosis of renal cancer. Virchows Arch 2024; 484:323-337. [PMID: 37999735 PMCID: PMC10948545 DOI: 10.1007/s00428-023-03700-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/24/2023] [Accepted: 11/04/2023] [Indexed: 11/25/2023]
Abstract
The application of molecular profiling has made substantial impact on the classification of urogenital tumors. Therefore, the 2022 World Health Organization incorporated the concept of molecularly defined renal tumor entities into its classification, including succinate dehydrogenase-deficient renal cell carcinoma (RCC), FH-deficient RCC, TFE3-rearranged RCC, TFEB-altered RCC, ALK-rearranged RCC, ELOC-mutated RCC, and renal medullary RCC, which are characterized by SMARCB1-deficiency. This review aims to provide an overview of the most important molecular alterations in renal cancer, with a specific focus on the diagnostic value of characteristic genomic aberrations, their chromosomal localization, and associations with renal tumor subtypes. It may not yet be the time to completely shift to a molecular RCC classification, but undoubtedly, the application of molecular profiling will enhance the accuracy of renal cancer diagnosis, and ultimately guide personalized treatment strategies for patients.
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Affiliation(s)
- Xingming Zhang
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstr. 12, 8091, Zurich, Switzerland
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Hella A Bolck
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstr. 12, 8091, Zurich, Switzerland
| | - Niels J Rupp
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstr. 12, 8091, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstr. 12, 8091, Zurich, Switzerland.
- Faculty of Medicine, University of Zurich, Zurich, Switzerland.
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25
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Collins K, Acosta AM, Siegmund SE, Cheng L, Hirsch MS, Idrees MT. Genetic Profiling Uncovers Genome-Wide Loss of Heterozygosity and Provides Insight into Mechanisms of Sarcomatoid Transformation in Chromophobe Renal Cell Carcinoma. Mod Pathol 2024; 37:100396. [PMID: 38043790 DOI: 10.1016/j.modpat.2023.100396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/07/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
Sarcomatoid transformation occurs in ∼8% of chromophobe renal cell carcinoma (chRCC) and is associated with aggressive clinical behavior. In recent years, several studies have identified genomic, transcriptomic, and epigenomic correlates of aggressive behavior in chRCC; however, the molecular mechanisms associated with sarcomatoid transformation remain incompletely understood. In this study, we analyzed paired conventional and sarcomatoid histologic components of individual chRCC to elucidate the genomic alterations that underlie sarcomatoid transformation in this tumor type. Massively parallel sequencing was performed on paired (conventional and sarcomatoid) components from 8 chRCCs. All cases harbored TP53 variants (87.5% showing TP53 variants in both components and 12.5% only in the sarcomatoid component). Intratumor comparisons revealed that TP53 variants were concordant in 71% and discordant in 29% of cases. Additional recurrent single-nucleotide variants were found in RB1 (37.5% of cases) and PTEN (25% of cases), with the remaining single-nucleotide variants detected in these tumors (PBRM1, NF1, and ASXL1) being nonrecurrent. Copy number variant analysis showed the characteristic pattern of chromosomal losses associated with chRCC (1, 2, 6, 10, 13, 17, and 21) in the conventional histologic components only. Interestingly, the sarcomatoid components of these tumors demonstrated widespread loss of heterozygosity but lacked the above chromosomal losses, likely as a consequence of whole-genome duplication/imbalanced chromosomal duplication events. Overall, the findings suggest that TP53 variants followed by whole-genome duplication/imbalanced chromosomal duplication events underlie sarcomatoid transformation in chRCC.
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Affiliation(s)
- Katrina Collins
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Andres M Acosta
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Stephanie E Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Liang Cheng
- Department of Pathology, Warren Alpert Medical School of Brown University, Lifespan Academic Medical Center, Providence, Rhode Island
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
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26
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Guo X, Xiao Z, Xu H, Ren K, Li X, Wu YK, Liu Y, Zhou L, Wang L, Liu H, Dong L, Dong H, Yang X. Clinicopathological, Immunohistochemical, and Molecular Characteristics of Pigmented Microcystic Chromophobe Renal Cell Carcinoma with Favorable Prognosis. Int J Surg Pathol 2024:10668969231217632. [PMID: 38173283 DOI: 10.1177/10668969231217632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background. Pigmented microcystic chromophobe renal cell carcinoma (RCC) is a subtype of chromophobe RCC. Its distinct histopathologic features are microcystic and microtubular pattern, pigmentation, and microcalcifications. Pigmented microcystic chromophobe RCC has ultrastructure, immunophenotypic structure, and molecular results similar to chromophobe RCC. Methods. We report five tumors of pigmented microcystic chromophobe RCC. Morphological observation and immunohistochemical examination were performed, and clinical and molecular features were analyzed. Results. Microscopically, all five tumors showed brown pigmentation, microcystic, and tubular cystic structures, one tumor presented microscopic calcifications. All tumors were positive for EMA, AE1/AE3, PAX8, KRT7, KIT (CD117), claudin 7, KRT8, and E-cadherin, and three tumors expressed P504S. All tumors were negative for vimentin, CA9, KRT20, TFE3, TFEB, Melan-A, HMB45, FH, SDHB, and GATA3. Ki-67 index varied from less than 1% to 2%. In three tumors, next-generation sequencing of the 688 gene was performed, the results found gene variants with potential clinical significance such as JMJD1C, MYCL, TP53, PI3KCA, KRAS, APC, GLI1, LRRK2, and gene variants with unclear clinical significance such as NTRK1 and RAD50; All patients remained alive over a follow-up period of 8-46 months without tumor recurrence and sarcomatoid transformation. Conclusions. Pigmented microcystic chromophobe RCC has a relatively benign biological behavior, and distant metastases and sarcomatoid transformation are rare. This overview of five additional tumors of pigmented microcystic chromophobe RCC offers further insight into this special subtype of chromophobe RCC.
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Affiliation(s)
- Xingmei Guo
- Department of Pathology, Wuxi No.2 People's Hospital, Wuxi, China
| | - Zhini Xiao
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Haimin Xu
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Kai Ren
- Central Pharmacy, Wuxi 9th People's Hospital Affiliated to Soochow University, Wuxi, China
| | - Xiangyun Li
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yuan Kai Wu
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yang Liu
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Luting Zhou
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lei Wang
- Department of Pathology, Wuxi No.2 People's Hospital, Wuxi, China
| | - Hengan Liu
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lei Dong
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hui Dong
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China
| | - Xiaoqun Yang
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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27
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Tian S, Wang R, Wang Y, Chen R, Lin T, Xiao X, Liu X, Ideozu JE, Geng H, Wang Y, Yue D. p32 regulates glycometabolism and TCA cycle to inhibit ccRCC progression via copper-induced DLAT lipoylation oligomerization. Int J Biol Sci 2024; 20:516-536. [PMID: 38169635 PMCID: PMC10758103 DOI: 10.7150/ijbs.84399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
A key player in mitochondrial respiration, p32, often referred to as C1QBP, is mostly found in the mitochondrial matrix. Previously, we showed that p32 interacts with DLAT in the mitochondria. Here, we found that p32 expression was reduced in ccRCC and suppressed progression and metastasis in ccRCC animal models. We observed that increasing p32 expression led to an increase in oxidative phosphorylation by interacting with DLAT, thus, regulating the activation of the pyruvate dehydrogenase complex (PDHc). Mechanistically, reduced p32 expression, in concert with DLAT, suppresses PDHc activity and the TCA cycle. Furthermore, our research discovered that p32 has a direct binding affinity for copper, facilitating the copper-induced oligomerization of lipo-DLAT specifically in ccRCC cells. This finding reveals an innovative function of the p32/DLAT/copper complex in regulating glycometabolism and the TCA cycle in ccRCC. Importantly, our research provides important new understandings of the underlying molecular processes causing the abnormal mitochondrial metabolism linked to this cancer.
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Affiliation(s)
- Shaoping Tian
- Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin 300203, China
| | - Rui Wang
- Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin 300203, China
| | - Yiting Wang
- Department of Clinical Laboratory, Tianjin Children's Hospital/Tianjin University Children's Hospital, Tianjin 300134, China
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Tianyu Lin
- Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin 300203, China
| | - Xuesong Xiao
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Xinyu Liu
- Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin 300203, China
| | - Justin Eze Ideozu
- Genomic Medicine, Genomic Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Hua Geng
- Department of Pediatrics, University of Illinois at Chicago, Chicago, IL, USA
| | - Yong Wang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Dan Yue
- Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin 300203, China
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Pei X, Yan X, Ding C. Proteogenomic Workflow for Characterization of Microphthalmia Transcription Factor (MiT) Family Translocation Renal Cell Carcinoma. Methods Mol Biol 2024; 2823:109-127. [PMID: 39052217 DOI: 10.1007/978-1-0716-3922-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Microphthalmia transcription factor (MiT) family translocation renal cell carcinoma (tRCC) is a rare, aggressive, and heterogeneous subtype of kidney cancer, which is not well characterized. Since genetic alterations are always associated with carcinogenesis, and proteins are the major executors of biological features, multi-omics studies can reveal the systematic tRCC biological process comprehensively. Here, we describe the proteogenomic workflow for characterization of tRCC in detail to provide the knowledge foundation for integrated proteogenomic analysis of tRCC and other malignant tumors in the future.
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Affiliation(s)
- Xiaoru Pei
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute , Fudan University, Shanghai, China
| | - Xin Yan
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Science, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan, China
| | - Chen Ding
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute , Fudan University, Shanghai, China.
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29
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Alchoueiry M, Cornejo K, Henske EP. Kidney cancer: Links between hereditary syndromes and sporadic tumorigenesis. Semin Diagn Pathol 2024; 41:1-7. [PMID: 38008653 DOI: 10.1053/j.semdp.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/06/2023] [Indexed: 11/28/2023]
Abstract
Multiple hereditary syndromes predispose to kidney cancer, including Von Hippel-Lindau syndrome, BAP1-Tumor Predisposition Syndrome, Hereditary Papillary Renal Cell Carcinoma, Tuberous Sclerosis Complex, Birt-Hogg-Dubé syndrome, Hereditary Paraganglioma-Pheochromocytoma Syndrome, Fumarate Hydratase Tumor Predisposition Syndrome, and Cowden syndrome. In some cases, mutations in the genes that cause hereditary kidney cancer are tightly linked to similar histologic features in sporadic RCC. For example, clear cell RCC occurs in the hereditary syndrome VHL, and sporadic ccRCC usually has inactivation of the VHL gene. In contrast, mutations in FLCN, the causative gene for Birt-Hogg-Dube syndrome, are rarely found in sporadic RCC. Here, we focus on the genes and pathways that link hereditary and sporadic RCC.
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Affiliation(s)
- Michel Alchoueiry
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kristine Cornejo
- Pathology Department, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth P Henske
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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30
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Fukagawa A, Hama N, Totoki Y, Nakamura H, Arai Y, Saito-Adachi M, Maeshima A, Matsui Y, Yachida S, Ushiku T, Shibata T. Genomic and epigenomic integrative subtypes of renal cell carcinoma in a Japanese cohort. Nat Commun 2023; 14:8383. [PMID: 38104198 PMCID: PMC10725467 DOI: 10.1038/s41467-023-44159-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
Renal cell carcinoma (RCC) comprises several histological types characterised by different genomic and epigenomic aberrations; however, the molecular pathogenesis of each type still requires further exploration. We perform whole-genome sequencing of 128 Japanese RCC cases of different histology to elucidate the significant somatic alterations and mutagenesis processes. We also perform transcriptomic and epigenomic sequencing to identify distinguishing features, including assay for transposase-accessible chromatin sequencing (ATAC-seq) and methyl sequencing. Genomic analysis reveals that the mutational signature differs among the histological types, suggesting that different carcinogenic factors drive each histology. From the ATAC-seq results, master transcription factors are identified for each histology. Furthermore, clear cell RCC is classified into three epi-subtypes, one of which expresses highly immune checkpoint molecules with frequent loss of chromosome 14q. These genomic and epigenomic features may lead to the development of effective therapeutic strategies for RCC.
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Affiliation(s)
- Akihiko Fukagawa
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Mihoko Saito-Adachi
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akiko Maeshima
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshiyuki Matsui
- Department of Urology, National Cancer Center Hospital, Tokyo, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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31
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Kanazashi Y, Maejima K, Johnson TA, Sasagawa S, Jikuya R, Hasumi H, Matsumoto N, Maekawa S, Obara W, Nakagawa H. Mitochondrial DNA Variants at Low-Level Heteroplasmy and Decreased Copy Numbers in Chronic Kidney Disease (CKD) Tissues with Kidney Cancer. Int J Mol Sci 2023; 24:17212. [PMID: 38139039 PMCID: PMC10743237 DOI: 10.3390/ijms242417212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
The human mitochondrial genome (mtDNA) is a circular DNA molecule with a length of 16.6 kb, which contains a total of 37 genes. Somatic mtDNA mutations accumulate with age and environmental exposure, and some types of mtDNA variants may play a role in carcinogenesis. Recent studies observed mtDNA variants not only in kidney tumors but also in adjacent kidney tissues, and mtDNA dysfunction results in kidney injury, including chronic kidney disease (CKD). To investigate whether a relationship exists between heteroplasmic mtDNA variants and kidney function, we performed ultra-deep sequencing (30,000×) based on long-range PCR of DNA from 77 non-tumor kidney tissues of kidney cancer patients with CKD (stages G1 to G5). In total, this analysis detected 697 single-nucleotide variants (SNVs) and 504 indels as heteroplasmic (0.5% ≤ variant allele frequency (VAF) < 95%), and the total number of detected SNVs/indels did not differ between CKD stages. However, the number of deleterious low-level heteroplasmic variants (pathogenic missense, nonsense, frameshift and tRNA) significantly increased with CKD progression (p < 0.01). In addition, mtDNA copy numbers (mtDNA-CNs) decreased with CKD progression (p < 0.001). This study demonstrates that mtDNA damage, which affects mitochondrial genes, may be involved in reductions in mitochondrial mass and associated with CKD progression and kidney dysfunction.
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Affiliation(s)
- Yuki Kanazashi
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
- Department of Human Genetics, Yokohama City University, Yokohama 236-0004, Japan;
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
| | - Todd A. Johnson
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
| | - Ryosuke Jikuya
- Department of Urology, Yokohama City University, Yokohama 236-0004, Japan; (R.J.); (H.H.)
| | - Hisashi Hasumi
- Department of Urology, Yokohama City University, Yokohama 236-0004, Japan; (R.J.); (H.H.)
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University, Yokohama 236-0004, Japan;
| | - Shigekatsu Maekawa
- Department of Urology, Iwate Medical University, Iwate 028-3694, Japan; (S.M.); (W.O.)
| | - Wataru Obara
- Department of Urology, Iwate Medical University, Iwate 028-3694, Japan; (S.M.); (W.O.)
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
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32
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Su X, Lu X, Bazai SK, Dainese L, Verschuur A, Dumont B, Mouawad R, Xu L, Cheng W, Yan F, Irtan S, Lindner V, Paillard C, Le Bouc Y, Coulomb A, Malouf GG. Delineating the interplay between oncogenic pathways and immunity in anaplastic Wilms tumors. Nat Commun 2023; 14:7884. [PMID: 38036539 PMCID: PMC10689851 DOI: 10.1038/s41467-023-43290-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023] Open
Abstract
Wilms tumors are highly curable in up to 90% of cases with a combination of surgery and radio-chemotherapy, but treatment-resistant types such as diffuse anaplastic Wilms tumors pose significant therapeutic challenges. Our multi-omics profiling unveils a distinct desert-like diffuse anaplastic Wilms tumor subtype marked by immune/stromal cell depletion, TP53 alterations, and cGAS-STING pathway downregulation, accounting for one-third of all diffuse anaplastic cases. This subtype, also characterized by reduced CD8 and CD3 infiltration and active oncogenic pathways involving histone deacetylase and DNA repair, correlates with poor clinical outcomes. These oncogenic pathways are found to be conserved in anaplastic Wilms tumor cell models. We identify histone deacetylase and/or WEE1 inhibitors as potential therapeutic vulnerabilities in these tumors, which might also restore tumor immunogenicity and potentially enhance the effects of immunotherapy. These insights offer a foundation for predicting outcomes and personalizing treatment strategies for aggressive pediatric Wilms tumors, tailored to individual immunological landscapes.
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Affiliation(s)
- Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaofan Lu
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, Illkirch, France
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Sehrish Khan Bazai
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, Illkirch, France
| | - Linda Dainese
- Department of Pathology, Hôpital Armand Trousseau, Assistance-Publique Hôpitaux de Paris, Sorbonne Université, Paris, France
- UF Tumorothèque HUEP, Hôpital Armand Trousseau, Assistance-Publique Hôpitaux de Paris, Sorbonne Université, Paris, France
- Centre de Recherche Saint-Antoine (CRSA), INSERM, Sorbonne Université, UMR_S .938, Paris, France
| | - Arnauld Verschuur
- Department of Pediatric Oncology, Hôpital d'Enfants de La Timone, F-13005, Marseille, France
| | - Benoit Dumont
- Centre Léon Bérard, Institut d'Hématologie et d'Oncologie Pédiatrique (IHOPe), Lyon, France
| | - Roger Mouawad
- Department of Medical Oncology, Groupe Hospitalier Pitié-Salpêtrière, Assistance-Publique Hôpitaux de Paris, Paris, France
| | - Li Xu
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Wenxuan Cheng
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Fangrong Yan
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Sabine Irtan
- Department of Pediaric Surgery, AP-HP, Hôpital Armand Trousseau, Sorbonne Université, Paris, France
| | | | - Catherine Paillard
- Department of Pediatric Onco-hematology, CHRU Strasbourg, Strasbourg Université, Strasbourg, France
| | - Yves Le Bouc
- Centre de Recherche Saint-Antoine (CRSA), INSERM, Sorbonne Université, UMR_S .938, Paris, France
| | - Aurore Coulomb
- Department of Pathology, Hôpital Armand Trousseau, Assistance-Publique Hôpitaux de Paris, Sorbonne Université, Paris, France.
- UF Tumorothèque HUEP, Hôpital Armand Trousseau, Assistance-Publique Hôpitaux de Paris, Sorbonne Université, Paris, France.
- Centre de Recherche Saint-Antoine (CRSA), INSERM, Sorbonne Université, UMR_S .938, Paris, France.
| | - Gabriel G Malouf
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, Illkirch, France.
- Department of Medical Oncology, Institut de Cancérologie de Strasbourg, Strasbourg University, Strasbourg, France.
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33
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Liu Y, Wu G. The utilization of single-cell sequencing technology in investigating the immune microenvironment of ccRCC. Front Immunol 2023; 14:1276658. [PMID: 38090562 PMCID: PMC10715415 DOI: 10.3389/fimmu.2023.1276658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
The growth and advancement of ccRCC are strongly associated with the presence of immune infiltration and the tumor microenvironment, comprising tumor cells, immune cells, stromal cells, vascular cells, myeloid-derived cells, and extracellular matrix (ECM). Nevertheless, as a result of the diverse and constantly evolving characteristics of the tumor microenvironment, prior advanced sequencing methods have frequently disregarded specific less prevalent cellular traits at varying intervals, thereby concealing their significance. The advancement and widespread use of single-cell sequencing technology enable us to comprehend the source of individual tumor cells and the characteristics of a greater number of individual cells. This, in turn, minimizes the impact of intercellular heterogeneity and temporal heterogeneity of the same cell on experimental outcomes. This review examines the attributes of the tumor microenvironment in ccRCC and provides an overview of the progress made in single-cell sequencing technology and its particular uses in the current focus of immune infiltration in ccRCC.
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Affiliation(s)
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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34
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Wu HF, Liu H, Zhang ZW, Chen JM. CENPE and LDHA were potential prognostic biomarkers of chromophobe renal cell carcinoma. Eur J Med Res 2023; 28:481. [PMID: 37925501 PMCID: PMC10625266 DOI: 10.1186/s40001-023-01449-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/15/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Most sarcomatoid differentiated renal cell carcinoma was differentiated from Chromophobe renal cell carcinoma (KICH) and related to a bad prognosis. Thus, finding biomarkers is important for the therapy of KICH. METHODS The UCSC was used for determining the expression of mRNA and miRNA and clinical data in KICH and normal samples. KEGG and GO were used for predicting potential function of differently expressed genes (DEGs). Optimal prognostic markers were determined by Lasso regression. Kaplan-Meier survival, ROC, and cox regression were used for assessing prognosis value. GSEA was used for predicting potential function of markers. The relations between markers and immune cell infiltration were determined by Pearson method. The upstream miRNA of markers was predicted in TargetScan and DIANA. RESULTS The 6162 upregulated and 13,903 downregulated DEGs were identified in KICH. Further CENPE and LDHA were screened out as optimal prognostic risk signatures. CENPE was highly expressed while LDHA was lowly expressed in KICH samples, and the high expressions of 2 genes contributed to bad prognosis. The functions of CENPE and LDHA were mainly enriched in proliferation related pathways such as cell cycle and DNA replication. In addition, the correlation of 2 genes with immune infiltrates in KICH was also observed. Finally, we found that has-miR-577 was the common upstream of 2 genes and the binding sites can be predicted. CONCLUSION CENPE and LDHA were identified as the important prognostic biomarkers in KICH, and they might be involved in the proliferation of cancer cell.
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Affiliation(s)
- Hui-Feng Wu
- Department of Urology, The Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Shangcheng District, Hangzhou, 310009, Zhejiang, China
| | - Hao Liu
- Department of Urology, The Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Shangcheng District, Hangzhou, 310009, Zhejiang, China.
| | - Zhe-Wei Zhang
- Department of Urology, The Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Shangcheng District, Hangzhou, 310009, Zhejiang, China
| | - Ji-Min Chen
- Department of Urology, The Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Shangcheng District, Hangzhou, 310009, Zhejiang, China
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35
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Pavithran M S, Lukose J, Barik BK, Periasami A, Kartha VB, Chawla A, Chidangil S. Laser induced fluorescence spectroscopy analysis of kidney tissues: A pilot study for the identification of renal cell carcinoma. JOURNAL OF BIOPHOTONICS 2023; 16:e202300021. [PMID: 37589180 DOI: 10.1002/jbio.202300021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/31/2023] [Accepted: 08/15/2023] [Indexed: 08/18/2023]
Abstract
The 325 nm-excited autofluorescence spectra from cancerous and normal renal tissues were collected ex vivo biopsy tissue samples, through an optical fiber probe-based system. Noticeable changes in intensity/wavelength were observed in the fluorescence emissions from endogenous fluorophores such as collagen, Nicotinamide adenine dinucleotide (NADH), Vitamin A (retinol), and flavin adenine dinucleotide, in pathological conditions with respect to the normal state. The energy metabolism involved in clear cell renal cell carcinoma (ccRCC) and chromophobe renal cell carcinoma (chRCC) are reflected in the fluorescence emission band at 445 nm due to bound NADH attributed to enhanced oxidative phosphorylation in chRCC and emission at 465 nm contributed by free NADH showing higher glycolytic action in ccRCC. The principal component analysis and one-way ANOVA effectively discriminate ccRCC from chRCC. It is shown that laser induced fluorescence technique with 325 nm excitation can be a suitable technique for optical pathology and in vivo surgical boundary demarcation in renal cell carcinoma.
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Affiliation(s)
- Sanoop Pavithran M
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, India
| | - Jijo Lukose
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, India
| | - Bijay Kumar Barik
- Department of Biochemistry, Cell Biology and Genetics, College Medicine, American University of Antigua, Cell Biology and Genetics, American University of Antigua, College of Medicine, St. John's, Antigua and Barbuda
| | - Ammasi Periasami
- W.M. Keck Center for Cellular Imaging (KCCI), Biology, University of Virginia, Charlottesville, Virginia, USA
| | - V B Kartha
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, India
| | - Arun Chawla
- Department of Urology, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Santhosh Chidangil
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, India
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36
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Ricci C, Ambrosi F, Franceschini T, Giunchi F, Grillini A, Franchini E, Grillini M, Schiavina R, Massari F, Mollica V, Tateo V, Bianchi FM, Bianchi L, Droghetti M, Maloberti T, Tallini G, Colecchia M, Acosta AM, Lobo J, Trpkov K, Fiorentino M, de Biase D. Evaluation of an institutional series of low-grade oncocytic tumor (LOT) of the kidney and review of the mutational landscape of LOT. Virchows Arch 2023; 483:687-698. [PMID: 37845471 PMCID: PMC10673759 DOI: 10.1007/s00428-023-03673-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/24/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023]
Abstract
The 2022 WHO classification of urinary and male genital tumors introduced several novel kidney entities exhibiting eosinophilic/oncocytic features with specific mutational backgrounds. Thus, molecular techniques, such as next-generation sequencing (NGS), became more commonly used for their evaluation. We studied 12 low-grade oncocytic tumors (LOT) of the kidney (from 11 patients), identified in a cohort of 210 eosinophilic/oncocytic renal tumors, diagnosed in our institution between October 2019 and May 2023, which represented 5.7% (12/210) of all eosinophilic/oncocytic renal tumors during this period. We reviewed their clinicopathologic, histologic, and immunohistochemical features, as well as their mutational profiles. We also reviewed the literature on NGS-derived data of LOT, by selecting papers in which LOT diagnosis was rendered according to the criteria proposed initially. Median age was 65 years (mean: 63.5; range 43-79) and median tumor size was 2.0 cm (mean: 2.2; range: 0.9-3.1). All tumors were positive for PAX8, CK7, and GATA3, and negative or focally positive for CD117/KIT. We found the following gene mutations: MTOR ((6/11), 54.5%)), TSC1 ((2/11), 18.2%)), and 1 had both NOTCH1 and NOTCH4 ((1/11), 9.1%)). Wild-type status was found in 2/11 (18.2%) patients and one tumor was not analyzable. A review of 8 previous studies that included 79 LOTs revealed frequent mutations in the genes that regulate the mammalian target of rapamycin (mTOR) pathway: MTOR (32/79 (40.5%)), TSC1 (21/79 (26.6%)), and TSC2 (9/79 (11.4%)). Other mutated genes included PIK3CA, NF2, and PTEN, not typically known to affect the mTOR pathway, but potentially acting as upstream and downstream effectors. Our study shows that LOT is increasingly diagnosed in routine practice when applying the appropriate diagnostic criteria. We also confirm that the mTOR pathway is strongly implicated in the pathogenesis of this tumor mainly through MTOR, TCS1, and TSC2 mutations, but other genes could also be involved in the pathway activation, especially in LOTs without "canonical" mutations.
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Affiliation(s)
- Costantino Ricci
- Pathology Unit, Maggiore Hospital-AUSL Bologna, Bologna, Italy.
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, Italy.
| | - Francesca Ambrosi
- Pathology Unit, Maggiore Hospital-AUSL Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | | | - Francesca Giunchi
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | | | | | - Marco Grillini
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Riccardo Schiavina
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
- Division of Urology, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Francesco Massari
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Veronica Mollica
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Valentina Tateo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | | | - Lorenzo Bianchi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
- Division of Urology, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Matteo Droghetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
- Division of Urology, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Thais Maloberti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Maurizio Colecchia
- Department of Pathology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andres Martin Acosta
- Department of Pathology, Indiana University School of Medicine, Indianapolis, USA
| | - João Lobo
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), Porto, Portugal
- Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (P.CCC), Research Center of IPO Porto (GEBC CI-IPOP)/RISE@CI-IPOP (Health Research Network), Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Kiril Trpkov
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary and Alberta Precision Laboratories, Calgary, Canada
| | - Michelangelo Fiorentino
- Pathology Unit, Maggiore Hospital-AUSL Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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37
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DA Silva Prade J, DE Souza RS, DA Silva D'Αvila CM, DA Silva TC, Livinalli IC, Bertoncelli ACZ, Saccol FK, DE Oliveira Mendes T, Wenning LG, DA Rosa Salles T, Rhoden CRB, Cadona FC. An Overview of Renal Cell Carcinoma Hallmarks, Drug Resistance, and Adjuvant Therapies. CANCER DIAGNOSIS & PROGNOSIS 2023; 3:616-634. [PMID: 37927802 PMCID: PMC10619564 DOI: 10.21873/cdp.10264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023]
Abstract
Renal neoplasms are highlighted as one of the 10 most common types of cancer. Renal cell carcinoma (RCC) is the most common type of renal cancer, considered the seventh most common type of cancer in the Western world. The most frequently altered genes described as altered are VHL, PBRM1, SETD2, KDM5C, PTEN, BAP1, mTOR, TP53, TCEB1 (ELOC), SMARCA4, ARID1A, and PIK3CA. RCC therapies can be classified in three groups: monoclonal antibodies, tyrosine kinase inhibitors, and mTOR inhibitors. Besides, there are targeted agents to treat RCC. However, frequently patients present side effects and resistance. Even though many multidrug resistance mechanisms already have been reported to RCC, studies focused on revealing new biomarkers as well as more effective antitumor therapies with no or low side effects are very important. Some studies reported that natural products, such as honey, epigallocatechin-3-gallate (EGCG), curcumin, resveratrol, and englerin A showed antitumor activity against RCC. Moreover, nanoscience is another strategy to improve RCC treatment and reduce the side effects due to the improvement in pharmacokinetics and reduction of toxicities of chemotherapies. Taking this into account, we conducted a systemic review of recent research findings on RCC hallmarks, drug resistance, and adjuvant therapies. In conclusion, a range of studies reported that RCC is characterized by high incidence and increased mortality rates because of the development of resistance to standard therapies. Given the importance of improving RCC treatment and reducing adverse effects, nanoscience and natural products can be included in therapeutic strategies.
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Affiliation(s)
- Josiele DA Silva Prade
- Post-graduate Program in Health and Life Sciences, Franciscan University, Santa Maria, RS, Brazil
| | | | | | | | | | | | | | | | | | - Theodoro DA Rosa Salles
- Laboratory of Nanostructured Magnetic Materials - LaMMaN, Franciscan University, Santa Maria, RS, Brazil
- Graduate Program in Nanosciences, Franciscan University, Santa Maria, RS, Brazil
| | - Cristiano Rodrigo Bohn Rhoden
- Laboratory of Nanostructured Magnetic Materials - LaMMaN, Franciscan University, Santa Maria, RS, Brazil
- Graduate Program in Nanosciences, Franciscan University, Santa Maria, RS, Brazil
| | - Francine Carla Cadona
- Post-graduate Program in Health and Life Sciences, Franciscan University, Santa Maria, RS, Brazil
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38
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Matar S, El Ahmar N, Laimon YN, Ghandour F, Signoretti S. The Role of the Pathologist in Renal Cell Carcinoma Management. Hematol Oncol Clin North Am 2023; 37:849-862. [PMID: 37258353 DOI: 10.1016/j.hoc.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent advances in our understanding of the molecular alterations underlying different types of renal cell carcinoma (RCC), as well as the implementation of immune checkpoint inhibitors in the treatment of patients with advanced disease, have significantly expanded the role of pathologists in the management of RCC patients and in the identification of predictive biomarkers that can guide patient treatment. In this chapter, we examine pathologists' evolving role in patient care and the development of precision medicine strategies for RCC.
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Affiliation(s)
- Sayed Matar
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Nourhan El Ahmar
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Yasmin Nabil Laimon
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Fatme Ghandour
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Merkin Building, 415 Main Street, Cambridge, MA 02142, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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Semenescu LE, Kamel A, Ciubotaru V, Baez-Rodriguez SM, Furtos M, Costachi A, Dricu A, Tătăranu LG. An Overview of Systemic Targeted Therapy in Renal Cell Carcinoma, with a Focus on Metastatic Renal Cell Carcinoma and Brain Metastases. Curr Issues Mol Biol 2023; 45:7680-7704. [PMID: 37754269 PMCID: PMC10528141 DOI: 10.3390/cimb45090485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 09/28/2023] Open
Abstract
The most commonly diagnosed malignancy of the urinary system is represented by renal cell carcinoma. Various subvariants of RCC were described, with a clear-cell type prevailing in about 85% of all RCC tumors. Patients with metastases from renal cell carcinoma did not have many effective therapies until the end of the 1980s, as long as hormonal therapy and chemotherapy were the only options available. The outcomes were unsatisfactory due to the poor effectiveness of the available therapeutic options, but then interferon-alpha and interleukin-2 showed treatment effectiveness, providing benefits but only for less than half of the patients. However, it was not until 2004 that targeted therapies emerged, prolonging the survival rate. Currently, new technologies and strategies are being developed to improve the actual efficacy of available treatments and their prognostic aspects. This article summarizes the mechanisms of action, importance, benefits, adverse events of special interest, and efficacy of immunotherapy in metastatic renal cell carcinoma, with a focus on brain metastases.
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Affiliation(s)
- Liliana Eleonora Semenescu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, Str. Petru Rares nr. 2-4, 710204 Craiova, Romania; (L.E.S.); (A.C.)
| | - Amira Kamel
- Neurosurgical Department, Clinical Emergency Hospital “Bagdasar-Arseni”, Soseaua Berceni 12, 041915 Bucharest, Romania; (A.K.); (V.C.); (S.M.B.-R.); (L.G.T.)
| | - Vasile Ciubotaru
- Neurosurgical Department, Clinical Emergency Hospital “Bagdasar-Arseni”, Soseaua Berceni 12, 041915 Bucharest, Romania; (A.K.); (V.C.); (S.M.B.-R.); (L.G.T.)
| | - Silvia Mara Baez-Rodriguez
- Neurosurgical Department, Clinical Emergency Hospital “Bagdasar-Arseni”, Soseaua Berceni 12, 041915 Bucharest, Romania; (A.K.); (V.C.); (S.M.B.-R.); (L.G.T.)
| | - Mircea Furtos
- Neurosurgical Department, University Emergency Hospital of Bucharest, 050098 Bucharest, Romania;
| | - Alexandra Costachi
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, Str. Petru Rares nr. 2-4, 710204 Craiova, Romania; (L.E.S.); (A.C.)
| | - Anica Dricu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, Str. Petru Rares nr. 2-4, 710204 Craiova, Romania; (L.E.S.); (A.C.)
| | - Ligia Gabriela Tătăranu
- Neurosurgical Department, Clinical Emergency Hospital “Bagdasar-Arseni”, Soseaua Berceni 12, 041915 Bucharest, Romania; (A.K.); (V.C.); (S.M.B.-R.); (L.G.T.)
- Department of Neurosurgery, Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 020022 Bucharest, Romania
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Chen F, Zhang Y, Chandrashekar DS, Varambally S, Creighton CJ. Global impact of somatic structural variation on the cancer proteome. Nat Commun 2023; 14:5637. [PMID: 37704602 PMCID: PMC10499989 DOI: 10.1038/s41467-023-41374-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/01/2023] [Indexed: 09/15/2023] Open
Abstract
Both proteome and transcriptome data can help assess the relevance of non-coding somatic mutations in cancer. Here, we combine mass spectrometry-based proteomics data with whole genome sequencing data across 1307 human tumors spanning various tissues to determine the extent somatic structural variant (SV) breakpoint patterns impact protein expression of nearby genes. We find that about 25% of the hundreds of genes with SV-associated cis-regulatory alterations at the mRNA level are similarly associated at the protein level. SVs associated with enhancer hijacking, retrotransposon translocation, altered DNA methylation, or fusion transcripts are implicated in protein over-expression. SVs combined with altered protein levels considerably extend the numbers of patients with tumors somatically altered for critical pathways. We catalog both SV breakpoint patterns involving patient survival and genes with nearby SV breakpoints associated with increased cell dependency in cancer cell lines. Pan-cancer proteogenomics identifies targetable non-coding alterations, by virtue of the associated deregulated genes.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Darshan S Chandrashekar
- Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- Genomic Diagnostics and Bioinformatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Sooryanarayana Varambally
- Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- The Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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Liang WW, Lu RJH, Jayasinghe RG, Foltz SM, Porta-Pardo E, Geffen Y, Wendl MC, Lazcano R, Kolodziejczak I, Song Y, Govindan A, Demicco EG, Li X, Li Y, Sethuraman S, Payne SH, Fenyö D, Rodriguez H, Wiznerowicz M, Shen H, Mani DR, Rodland KD, Lazar AJ, Robles AI, Ding L. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin. Cancer Cell 2023; 41:1567-1585.e7. [PMID: 37582362 DOI: 10.1016/j.ccell.2023.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/30/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
DNA methylation plays a critical role in establishing and maintaining cellular identity. However, it is frequently dysregulated during tumor development and is closely intertwined with other genetic alterations. Here, we leveraged multi-omic profiling of 687 tumors and matched non-involved adjacent tissues from the kidney, brain, pancreas, lung, head and neck, and endometrium to identify aberrant methylation associated with RNA and protein abundance changes and build a Pan-Cancer catalog. We uncovered lineage-specific epigenetic drivers including hypomethylated FGFR2 in endometrial cancer. We showed that hypermethylated STAT5A is associated with pervasive regulon downregulation and immune cell depletion, suggesting that epigenetic regulation of STAT5A expression constitutes a molecular switch for immunosuppression in squamous tumors. We further demonstrated that methylation subtype-enrichment information can explain cell-of-origin, intra-tumor heterogeneity, and tumor phenotypes. Overall, we identified cis-acting DNA methylation events that drive transcriptional and translational changes, shedding light on the tumor's epigenetic landscape and the role of its cell-of-origin.
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Affiliation(s)
- Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rita Jui-Hsien Lu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Reyka G Jayasinghe
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Steven M Foltz
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Eduard Porta-Pardo
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Yifat Geffen
- 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
| | - Michael C Wendl
- 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; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rossana Lazcano
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Iga Kolodziejczak
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Yizhe Song
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Akshay Govindan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Elizabeth G Demicco
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Xiang Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Sunantha Sethuraman
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Heliodor Swiecicki Clinical Hospital in Poznań, Ul. Przybyszewskiego 49, 60-355 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA.
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Shelton SD, House S, Ramesh V, Chen Z, Wei T, Wang X, Llamas CB, Venigalla SSK, Menezes CJ, Zhao Z, Gill JG, DeBerardinis RJ, Morrison SJ, Tasdogan A, Mishra P. Pathogenic mitochondrial DNA mutations inhibit melanoma metastasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555986. [PMID: 37732192 PMCID: PMC10508716 DOI: 10.1101/2023.09.01.555986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations are frequently observed in cancer, but their contribution to tumor progression is controversial. To evaluate the impact of mtDNA variants on tumor growth and metastasis, we created human melanoma cytoplasmic hybrid (cybrid) cell lines transplanted with wildtype mtDNA or pathogenic mtDNA encoding variants that partially or completely inhibit oxidative phosphorylation. Homoplasmic pathogenic mtDNA cybrids reliably established tumors despite dysfunctional oxidative phosphorylation. However, pathogenic mtDNA variants disrupted spontaneous metastasis of subcutaneous tumors and decreased the abundance of circulating melanoma cells in the blood. Pathogenic mtDNA did not induce anoikis or inhibit organ colonization of melanoma cells following intravenous injections. Instead, migration and invasion were reduced, indicating that limited circulation entry functions as a metastatic bottleneck amidst mtDNA dysfunction. Furthermore, analysis of selective pressure exerted on the mitochondrial genomes of heteroplasmic cybrid lines revealed a suppression of pathogenic mtDNA allelic frequency during melanoma growth. Collectively, these findings demonstrate that functional mtDNA is favored during melanoma growth and enables metastatic entry into the blood.
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Affiliation(s)
- Spencer D. Shelton
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
| | - Sara House
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
| | - Vijayashree Ramesh
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
| | - Zhenkang Chen
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
| | - Tao Wei
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
| | - Xun Wang
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
| | - Claire B. Llamas
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
| | - Siva Sai Krishna Venigalla
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
| | - Cameron J. Menezes
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
| | - Zhiyu Zhao
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
| | - Jennifer G. Gill
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Ralph J. DeBerardinis
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Sean J. Morrison
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Alpaslan Tasdogan
- Department of Dermatology, University Hospital Essen & German Cancer Consortium, Partner Site, Essen, Germany
| | - Prashant Mishra
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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43
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Mannan R, Wang X, Bawa PS, Zhang Y, Skala SL, Chinnaiyan AK, Dagar A, Wang L, Zelenka-Wang SB, McMurry LM, Daniel N, Cao X, Sangoi AR, Gupta S, Vaishampayan UN, Hafez KS, Morgan TM, Spratt DE, Tretiakova MS, Argani P, Chinnaiyan AM, Dhanasekaran SM, Mehra R. Characterization of Intercalated Cell Markers KIT and LINC01187 in Chromophobe Renal Cell Carcinoma and Other Renal Neoplasms. Int J Surg Pathol 2023; 31:1027-1040. [PMID: 36250542 DOI: 10.1177/10668969221125793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Introduction. Chromophobe renal cell carcinoma (chromophobe RCC) is the third major subcategory of renal tumors after clear cell RCC and papillary RCC, accounting for approximately 5% of all RCC subtypes. Other oncocytic neoplasms seen commonly in surgical pathology practice include the eosinophilic variant of chromophobe RCC, renal oncocytoma, and low-grade oncocytic unclassified RCC. Methods. In our recent next-generation sequencing based study, we nominated a lineage-specific novel biomarker LINC01187 (long intergenic non-protein coding RNA 1187) which was found to be enriched in chromophobe RCC. Like KIT (cluster of differentiation 117; CD117), a clinically utilized chromophobe RCC related biomarker, LINC01187 is expressed in intercalated cells of the nephron. In this follow-up study, we performed KIT immunohistochemistry and LINC01187 RNA in situ hybridization (RNA-ISH) on a cohort of chromophobe RCC and other renal neoplasms, characterized the expression patterns, and quantified the expression signals of the two biomarkers in both primary and metastatic settings. Results. LINC01187, in comparison to KIT, exhibits stronger and more uniform expression within tumors while maintaining temporal and spatial consistency. LINC01187 also is devoid of intra-tumoral heterogeneous expression pattern, a phenomenon commonly noted with KIT. Conclusions. LINC01187 expression can augment the currently utilized KIT assay and help facilitate easy microscopic analyses in routine surgical pathology practice.
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Affiliation(s)
- Rahul Mannan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Xiaoming Wang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Pushpinder S Bawa
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Stephanie L Skala
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Aniket Dagar
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Lisha Wang
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Sylvia B Zelenka-Wang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Lisa M McMurry
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Nikita Daniel
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Xuhong Cao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, Ann Arbor, MI, USA
| | - Ankur R Sangoi
- Department of Pathology, El Camino Hospital, Mountain View, CA, USA
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ulka N Vaishampayan
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Department of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Khaled S Hafez
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Maria S Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Pedram Argani
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
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Venkatesh N, Martini A, McQuade JL, Msaouel P, Hahn AW. Obesity and renal cell carcinoma: Biological mechanisms and perspectives. Semin Cancer Biol 2023; 94:21-33. [PMID: 37286114 PMCID: PMC10526958 DOI: 10.1016/j.semcancer.2023.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
Obesity, defined by body mass index (BMI), is an established risk factor for specific renal cell carcinoma (RCC) subtypes such as clear cell RCC, the most common RCC histology. Many studies have identified an association between obesity and improved survival after diagnosis of RCC, a potential "obesity paradox." Clinically, there is uncertainty whether improved outcomes observed after diagnosis are driven by stage, type of treatment received, or artifacts of longitudinal changes in weight and body composition. The biological mechanisms underlying obesity's influence on RCC are not fully established, but multiomic and mechanistic studies suggest an impact on tumor metabolism, particularly fatty acid metabolism, angiogenesis, and peritumoral inflammation, which are known to be key biological hallmarks of clear cell RCC. Conversely, high-intensity exercise associated with increased muscle mass may be a risk factor for renal medullary carcinoma, a rare RCC subtype that predominantly occurs in individuals with sickle hemoglobinopathies. Herein, we highlight methodologic challenges associated with studying the influence of obesity on RCC and review the clinical evidence and potential underlying mechanisms associating RCC with BMI and body composition.
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Affiliation(s)
- Neha Venkatesh
- Department of Internal Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Alberto Martini
- Department of Urology, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer L McQuade
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
| | - Andrew W Hahn
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Kozman D, Kao CS, Nguyen JK, Smith SC, Kehr EL, Tretiakova M, Przybycin CG, Williamson SR, Argani P, Eng C, Campbell SC, McKenney JK, Alaghehbandan R. Renal Neoplasia Occurring in Patients With PTEN Hamartoma Tumor Syndrome : Clinicopathologic Study of 12 Renal Cell Carcinomas From 9 Patients and Association With Intrarenal "Lipomas". Am J Surg Pathol 2023; 47:1001-1010. [PMID: 37357918 DOI: 10.1097/pas.0000000000002079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
The aim of this study was to assess the histopathologic spectrum of renal tumors in patients with PTEN hamartoma tumor syndrome (PHTS), with a specific focus on potential features predictive of the underlying syndrome. A multi-institutional study was conducted to obtain clinical and pathologic data on renal tumors arising in patients with PHTS, either diagnosed by germline mutational analysis or clinical criteria for Cowden syndrome. Histologic sections of the renal tumors were re-reviewed for classification. Twelve renal epithelial tumors from 9 patients were identified (4 males and 5 females, with a mean age of 41.8 y), 7 of whom carried germline PTEN mutations. All 12 renal epithelial tumors were renal cell carcinomas (RCCs): 5 were chromophobe RCCs, 4 papillary RCCs, and 3 RCC not otherwise specified. Pathologic stage distribution was: 7 (59%) pT1a, 2 (17%) pT1b, 1 (8%) pT2a, 1 (8%) pT2b, and 1 (8%) pT3a. World Health Organization/International Society of Urological Pathology (WHO/ISUP) histologic grade was applicable in 7 (54%) nonchromophobe tumors: 4 (57%) G2, 2 (29%) G3, and 1 (14%) G4. An unexpected histologic finding was the presence of 2 patients with incidental microscopic collections of intrarenal adipocytes that had no features of angiomyolipoma (and were negative with 2 sensitive PEComa markers: cathepsin-K and GPNMB); both were classified as lipoma/"lipomatous hamartomas." The average follow-up interval was 67.8 months (13 to 172 mo): 5 patients had no evidence of disease, 2 were lost to follow-up, 1 died of other (non-PHTS) causes (ie, prostate cancer), and 1 was alive with metastatic RCC to the lung (RCC not otherwise specified with rhabdoid differentiation). All tumors showed loss of nuclear PTEN staining by immunohistochemistry. Fumarate hydratase was retained and 2SC was negative in all papillary RCCs. CK7 was moderate-strong/diffuse positive in 4 of 5 chromophobe RCCs and in 3 of 4 papillary RCCs. Renal epithelial tumors associated with PHTS represent a heterogeneous group of RCCs, but classic chromophobe and papillary RCC are most common. The majority have a favorable clinical behavior as would be predicted by subtype. In contrast to other hereditary renal neoplasia syndromes, morphologic features of the RCCs do not allow identification of PHTS-associated neoplasia with any degree of specificity in the absence of clinical setting and/or prior history, but the presence of microscopic "lipomas" within the kidney may provide a clue in rare cases. Therefore, clinical suspicion and genetic counseling with germline testing remain necessary for identifying PHTS-associated RCC.
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Affiliation(s)
- Diana Kozman
- Robert J. Tomsich Pathology and Laboratory Medicine Institute
| | - Chia-Sui Kao
- Department of Pathology, Stanford Medical Center, Stanford, CA
| | - Jane K Nguyen
- Robert J. Tomsich Pathology and Laboratory Medicine Institute
| | - Steven C Smith
- Departments of Departments of Pathology, Urology, and Massey Cancer Center, VCU School of Medicine
- Richmond VA Medical Center, Richmond, VA
| | | | - Maria Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | | | | | - Pedram Argani
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Steven C Campbell
- Section of Urologic Oncology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH
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46
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Bimbatti D, Pierantoni F, Lai E, Ballestrin M, Cavasin N, Erbetta E, De Toni C, Basso U, Maruzzo M. Advanced Non-Clear Cell Renal Cell Carcinoma Treatments and Survival: A Real-World Single-Centre Experience. Cancers (Basel) 2023; 15:4353. [PMID: 37686629 PMCID: PMC10487077 DOI: 10.3390/cancers15174353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Non-clear cell renal cell carcinoma (nccRCC) is a heterogeneous group of cancer. Treatment recommendations are extrapolated from ccRCC and lack solid evidence. Here, we review advanced nccRCC patients treated at our institute. PATIENTS AND METHODS We collected retrospective data on all advanced nccRCC pts treated at the Istituto Oncologico Veneto from January 2008. We compared overall response rate (ORR), progression free survival (PFS) and overall survival (OS) according to histological subtypes and type of systemic treatments. Kaplan-Meier method, log-rank test and Cox regression were used to estimate and compare PFS and OS. RESULTS Of 1370 RCC patients, 289 had a diagnosis of nccRCC and 121 were eligible for the analysis. Fifty-three pts showed papillary histology (pRCC), 15 chromophobe; 37 unclassified RCC (NOS-RCC), 16 other histologies. Pts with chromophobe and other hystologies showed poorer survival rates compared to pRCC and NOS-RCC (mOS 10.7 vs. 20.7 vs. 30.7, p = 0.34). Pts treated with combination regimens achieved a better OS (30.7 vs. 13.7, p = 0.10), PFS (12.7 vs. 6.4, p = 0.10) and ORR (42.4% vs. 13.9%, p = 0.002) than those treated with monotherapy. IMDC and Meet-URO score retained their prognostic value. CONCLUSION Our retrospective real-life cohort of advanced nccRCC patients shows that immunotherapy-based combinations could improve ORR, PFS and OS compared to TKI monotherapy. Prospective trials for nccRCC patients utilizing novel therapies are ongoing and their results eagerly awaited.
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Affiliation(s)
- Davide Bimbatti
- Oncology 1 Unit, Istituto Oncologico Veneto, IOV-IRCCS, 35128 Padova, Italy; (D.B.); (E.L.); (N.C.); (E.E.); (C.D.T.); (U.B.)
| | - Francesco Pierantoni
- Oncology 3 Unit, Istituto Oncologico Veneto, IOV-IRCCS, 35128 Padova, Italy; (F.P.); (M.B.)
- Department of Surgery, Oncology and Gastroenterology, University of Padua, 35128 Padova, Italy
| | - Eleonora Lai
- Oncology 1 Unit, Istituto Oncologico Veneto, IOV-IRCCS, 35128 Padova, Italy; (D.B.); (E.L.); (N.C.); (E.E.); (C.D.T.); (U.B.)
- Department of Surgery, Oncology and Gastroenterology, University of Padua, 35128 Padova, Italy
| | - Melissa Ballestrin
- Oncology 3 Unit, Istituto Oncologico Veneto, IOV-IRCCS, 35128 Padova, Italy; (F.P.); (M.B.)
| | - Nicolò Cavasin
- Oncology 1 Unit, Istituto Oncologico Veneto, IOV-IRCCS, 35128 Padova, Italy; (D.B.); (E.L.); (N.C.); (E.E.); (C.D.T.); (U.B.)
- Department of Surgery, Oncology and Gastroenterology, University of Padua, 35128 Padova, Italy
| | - Elisa Erbetta
- Oncology 1 Unit, Istituto Oncologico Veneto, IOV-IRCCS, 35128 Padova, Italy; (D.B.); (E.L.); (N.C.); (E.E.); (C.D.T.); (U.B.)
- Department of Surgery, Oncology and Gastroenterology, University of Padua, 35128 Padova, Italy
| | - Chiara De Toni
- Oncology 1 Unit, Istituto Oncologico Veneto, IOV-IRCCS, 35128 Padova, Italy; (D.B.); (E.L.); (N.C.); (E.E.); (C.D.T.); (U.B.)
| | - Umberto Basso
- Oncology 1 Unit, Istituto Oncologico Veneto, IOV-IRCCS, 35128 Padova, Italy; (D.B.); (E.L.); (N.C.); (E.E.); (C.D.T.); (U.B.)
| | - Marco Maruzzo
- Oncology 1 Unit, Istituto Oncologico Veneto, IOV-IRCCS, 35128 Padova, Italy; (D.B.); (E.L.); (N.C.); (E.E.); (C.D.T.); (U.B.)
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Henske EP, Cheng L, Hakimi AA, Choueiri TK, Braun DA. Chromophobe renal cell carcinoma. Cancer Cell 2023; 41:1383-1388. [PMID: 37541245 DOI: 10.1016/j.ccell.2023.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 08/06/2023]
Abstract
Chromophobe renal cell carcinoma (ChRCC) is the second most common variant histology (non-clear cell) RCC. ChRCC is distinct from clear cell RCC (ccRCC) in terms of genetics, genomics, metabolism, cell of origin, and response to targeted and immune therapies. The pathogenesis of ChRCC remains unclear, but current data suggest two potential mechanisms: mTORC1 hyperactivation through PTEN pathway mutations and mitochondrial dysfunction leading to oxidative stress. There are no specific approved treatments for ChRCC, although some responses to tyrosine kinase and mTOR inhibitors have been observed. Response to immunotherapy is generally limited. Targetable pathways involving innate lymphoid cells/IL-15 and cysteine homeostasis/ferroptosis have recently been identified.
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Affiliation(s)
| | - Liang Cheng
- Brown University Warren Alpert Medical School and the Legorreta Cancer Center, Brown University, Providence, RI, USA
| | - A Ari Hakimi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Toni K Choueiri
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - David A Braun
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
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48
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Kapur P, Brugarolas J, Trpkov K. Recent Advances in Renal Tumors with TSC/mTOR Pathway Abnormalities in Patients with Tuberous Sclerosis Complex and in the Sporadic Setting. Cancers (Basel) 2023; 15:4043. [PMID: 37627070 PMCID: PMC10452688 DOI: 10.3390/cancers15164043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
A spectrum of renal tumors associated with frequent TSC/mTOR (tuberous sclerosis complex/mechanistic target of rapamycin) pathway gene alterations (in both the germline and sporadic settings) have recently been described. These include renal cell carcinoma with fibromyomatous stroma (RCC FMS), eosinophilic solid and cystic renal cell carcinoma (ESC RCC), eosinophilic vacuolated tumor (EVT), and low-grade oncocytic tumor (LOT). Most of these entities have characteristic morphologic and immunohistochemical features that enable their recognition without the need for molecular studies. In this report, we summarize recent advances and discuss their evolving complexity.
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Affiliation(s)
- Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kiril Trpkov
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2L 2K5, Canada
- Alberta Precision Labs, Rockyview General Hospital, 7007 14 St., Calgary, AB T2V 1P9, Canada
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49
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Gopal RK, Vantaku VR, Panda A, Reimer B, Rath S, To TL, Fisch AS, Cetinbas M, Livneh M, Calcaterra MJ, Gigliotti BJ, Pierce KA, Clish CB, Dias-Santagata D, Sadow PM, Wirth LJ, Daniels GH, Sadreyev RI, Calvo SE, Parangi S, Mootha VK. Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma. Cancer Discov 2023; 13:1904-1921. [PMID: 37262067 PMCID: PMC10401073 DOI: 10.1158/2159-8290.cd-22-0976] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 04/05/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
Oncocytic (Hürthle cell) carcinoma of the thyroid (HCC) is genetically characterized by complex I mitochondrial DNA mutations and widespread chromosomal losses. Here, we utilize RNA sequencing and metabolomics to identify candidate molecular effectors activated by these genetic drivers. We find glutathione biosynthesis, amino acid metabolism, mitochondrial unfolded protein response, and lipid peroxide scavenging to be increased in HCC. A CRISPR-Cas9 knockout screen in a new HCC model reveals which pathways are key for fitness, and highlights loss of GPX4, a defense against lipid peroxides and ferroptosis, as a strong liability. Rescuing complex I redox activity with the yeast NADH dehydrogenase (NDI1) in HCC cells diminishes ferroptosis sensitivity, while inhibiting complex I in normal thyroid cells augments ferroptosis induction. Our work demonstrates unmitigated lipid peroxide stress to be an HCC vulnerability that is mechanistically coupled to the genetic loss of mitochondrial complex I activity. SIGNIFICANCE HCC harbors abundant mitochondria, mitochondrial DNA mutations, and chromosomal losses. Using a CRISPR-Cas9 screen inspired by transcriptomic and metabolomic profiling, we identify molecular effectors essential for cell fitness. We uncover lipid peroxide stress as a vulnerability coupled to mitochondrial complex I loss in HCC. See related article by Frank et al., p. 1884. This article is highlighted in the In This Issue feature, p. 1749.
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Affiliation(s)
- Raj K. Gopal
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Venkata R. Vantaku
- Harvard Medical School, Boston, Massachusetts
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Apekshya Panda
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Bryn Reimer
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sneha Rath
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Tsz-Leung To
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Adam S. Fisch
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Murat Cetinbas
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Maia Livneh
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | | | - Kerry A. Pierce
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Dora Dias-Santagata
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Peter M. Sadow
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Lori J. Wirth
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Gilbert H. Daniels
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Thyroid Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Ruslan I. Sadreyev
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Sarah E. Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sareh Parangi
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Vamsi K. Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
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50
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Lin Y, Yang B, Huang Y, Zhang Y, Jiang Y, Ma L, Shen YQ. Mitochondrial DNA-targeted therapy: A novel approach to combat cancer. CELL INSIGHT 2023; 2:100113. [PMID: 37554301 PMCID: PMC10404627 DOI: 10.1016/j.cellin.2023.100113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 08/10/2023]
Abstract
Mitochondrial DNA (mtDNA) encodes proteins and RNAs that are essential for mitochondrial function and cellular homeostasis, and participates in important processes of cellular bioenergetics and metabolism. Alterations in mtDNA are associated with various diseases, especially cancers, and are considered as biomarkers for some types of tumors. Moreover, mtDNA alterations have been found to affect the proliferation, progression and metastasis of cancer cells, as well as their interactions with the immune system and the tumor microenvironment (TME). The important role of mtDNA in cancer development makes it a significant target for cancer treatment. In recent years, many novel therapeutic methods targeting mtDNA have emerged. In this study, we first discussed how cancerogenesis is triggered by mtDNA mutations, including alterations in gene copy number, aberrant gene expression and epigenetic modifications. Then, we described in detail the mechanisms underlying the interactions between mtDNA and the extramitochondrial environment, which are crucial for understanding the efficacy and safety of mtDNA-targeted therapy. Next, we provided a comprehensive overview of the recent progress in cancer therapy strategies that target mtDNA. We classified them into two categories based on their mechanisms of action: indirect and direct targeting strategies. Indirect targeting strategies aimed to induce mtDNA damage and dysfunction by modulating pathways that are involved in mtDNA stability and integrity, while direct targeting strategies utilized molecules that can selectively bind to or cleave mtDNA to achieve the therapeutic efficacy. This study highlights the importance of mtDNA-targeted therapy in cancer treatment, and will provide insights for future research and development of targeted drugs and therapeutic strategies.
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Affiliation(s)
- Yumeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Bowen Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yibo Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - You Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yu Jiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Longyun Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Ying-Qiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
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