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Cimadamore A, Franzese C, Di Loreto C, Blanca A, Lopez-Beltran A, Crestani A, Giannarini G, Tan PH, Carneiro BA, El-Deiry WS, Montironi R, Cheng L. Predictive and prognostic biomarkers in urological tumours. Pathology 2024; 56:228-238. [PMID: 38199927 DOI: 10.1016/j.pathol.2023.10.016] [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: 08/24/2023] [Revised: 09/29/2023] [Accepted: 10/09/2023] [Indexed: 01/12/2024]
Abstract
Advancements in cutting-edge molecular profiling techniques, such as next-generation sequencing and bioinformatic analytic tools, have allowed researchers to examine tumour biology in detail and stratify patients based on factors linked with clinical outcome and response to therapy. This manuscript highlights the most relevant prognostic and predictive biomarkers in kidney, bladder, prostate and testicular cancers with recognised impact in clinical practice. In bladder and prostate cancer, new genetic acquisitions concerning the biology of tumours have modified the therapeutic scenario and led to the approval of target directed therapies, increasing the quality of patient care. Thus, it has become of paramount importance to choose adequate molecular tests, i.e., FGFR screening for urothelial cancer and BRCA1-2 alterations for prostate cancer, to guide the treatment plan for patients. While no tissue or blood-based biomarkers are currently used in routine clinical practice for renal cell carcinoma and testicular cancers, the field is quickly expanding. In kidney tumours, gene expression signatures might be the key to identify patients who will respond better to immunotherapy or anti-angiogenic drugs. In testicular germ cell tumours, the use of microRNA has outperformed conventional serum biomarkers in the diagnosis of primary tumours, prediction of chemoresistance, follow-up monitoring, and relapse prediction.
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Affiliation(s)
- Alessia Cimadamore
- Institute of Pathological Anatomy, Department of Medicine (DAME), Udine University, Udine, Italy.
| | - Carmine Franzese
- Department of Urology, Ospedale Santa Maria Della Misericordia di Udine, Udine, Italy
| | - Carla Di Loreto
- Institute of Pathological Anatomy, Department of Medicine (DAME), Udine University, Udine, Italy
| | - Ana Blanca
- Maimonides Biomedical Research Institute of Cordoba, Department of Urology, University Hospital of Reina Sofia, UCO, Cordoba, Spain
| | | | - Alessandro Crestani
- Department of Urology, Ospedale Santa Maria Della Misericordia di Udine, Udine, Italy
| | - Gianluca Giannarini
- Department of Urology, Ospedale Santa Maria Della Misericordia di Udine, Udine, Italy
| | | | - Benedito A Carneiro
- The Legorreta Cancer Center at Brown University, Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Lifespan Academic Medical Center, Providence, RI, USA
| | - Wafik S El-Deiry
- The Legorreta Cancer Center at Brown University, Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Lifespan Academic Medical Center, Providence, RI, USA
| | - Rodolfo Montironi
- Molecular Medicine and Cell Therapy Foundation, Department of Clinical and Molecular Sciences, Polytechnic University of the Marche Region, Ancona, Italy
| | - Liang Cheng
- The Legorreta Cancer Center at Brown University, Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Lifespan Academic Medical Center, Providence, RI, USA.
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Cotta BH, Choueiri TK, Cieslik M, Ghatalia P, Mehra R, Morgan TM, Palapattu GS, Shuch B, Vaishampayan U, Van Allen E, Ari Hakimi A, Salami SS. Current Landscape of Genomic Biomarkers in Clear Cell Renal Cell Carcinoma. Eur Urol 2023; 84:166-175. [PMID: 37085424 DOI: 10.1016/j.eururo.2023.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 03/16/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
CONTEXT Dramatic gains in our understanding of the molecular biology of clear cell renal cell carcinoma (ccRCC) have created a foundation for clinical translation to improve patient care. OBJECTIVE To review and contextualize clinically impactful data surrounding genomic biomarkers in ccRCC. EVIDENCE ACQUISITION A systematic literature search was conducted focusing on genomic-based biomarkers with an emphasis on studies assessing clinical outcomes. EVIDENCE SYNTHESIS The advancement of tumor sequencing techniques has led to a rapid increase in the knowledge of the molecular underpinnings of ccRCC and with that the discovery of multiple candidate genomic biomarkers. These include somatic gene mutations such as VHL, PBRM1, SETD2, and BAP1; copy number variations; transcriptomic multigene signatures; and specific immune cell populations. Many of these biomarkers have been assessed for their association with survival and a smaller number as potential predictors of a response to systemic therapy. In this scoping review, we discuss many of these biomarkers in detail. Further studies are needed to continue to refine and validate these molecular tools for risk stratification, with the ultimate goal of improving clinical decision-making and patient outcomes. CONCLUSIONS While no tissue or blood-based biomarkers for ccRCC have been incorporated into routine clinical practice to date, the field continues to expand rapidly. There remains a critical need to develop and validate these tools in order to improve the care for patients with kidney cancer. PATIENT SUMMARY Genomic biomarkers have the potential to better predict outcome and select the most appropriate treatment for patients with kidney cancer; however, further research is needed before any of these currently developed biomarkers are adopted into clinical practice.
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Affiliation(s)
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marcin Cieslik
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Pooja Ghatalia
- Department of Hematology and Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Rohit Mehra
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Todd M Morgan
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Ganesh S Palapattu
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Brian Shuch
- Department of Urology, University of California, Los Angeles, CA, USA
| | - Ulka Vaishampayan
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Department of Internal Medicine, Michigan Medicine, Ann Arbor, MI, USA
| | - Eliezer Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - A Ari Hakimi
- Division of Urology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simpa S Salami
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA.
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3
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Andreou A, Yngvadottir B, Bassaganyas L, Clark G, Martin E, Whitworth J, Cornish AJ, Houlston RS, Rich P, Egan C, Hodgson SV, Warren AY, Snape K, Maher ER. Elongin C (ELOC/TCEB1)-associated von Hippel-Lindau disease. Hum Mol Genet 2022; 31:2728-2737. [PMID: 35323939 PMCID: PMC9402235 DOI: 10.1093/hmg/ddac066] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/02/2022] Open
Abstract
Around 95% of patients with clinical features that meet the diagnostic criteria for von Hippel-Lindau disease (VHL) have a detectable inactivating germline variant in VHL. The VHL protein (pVHL) functions as part of the E3 ubiquitin ligase complex comprising pVHL, elongin C, elongin B, cullin 2 and ring box 1 (VCB-CR complex), which plays a key role in oxygen sensing and degradation of hypoxia-inducible factors. To date, only variants in VHL have been shown to cause VHL disease. We undertook trio analysis by whole-exome sequencing in a proband with VHL disease but without a detectable VHL mutation. Molecular studies were also performed on paired DNA extracted from the proband's kidney tumour and blood and bioinformatics analysis of sporadic renal cell carcinoma (RCC) dataset was undertaken. A de novo pathogenic variant in ELOC NM_005648.4(ELOC):c.236A>G (p.Tyr79Cys) gene was identified in the proband. ELOC encodes elongin C, a key component [C] of the VCB-CR complex. The p.Tyr79Cys substitution is a mutational hotspot in sporadic VHL-competent RCC and has previously been shown to mimic the effects of pVHL deficiency on hypoxic signalling. Analysis of an RCC from the proband showed similar findings to that in somatically ELOC-mutated RCC (expression of hypoxia-responsive proteins, no somatic VHL variants and chromosome 8 loss). These findings are consistent with pathogenic ELOC variants being a novel cause for VHL disease and suggest that genetic testing for ELOC variants should be performed in individuals with suspected VHL disease with no detectable VHL variant.
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Affiliation(s)
- Avgi Andreou
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Bryndis Yngvadottir
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Laia Bassaganyas
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Graeme Clark
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK,Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Ezequiel Martin
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK,Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - James Whitworth
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | | | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Philip Rich
- Department of Neuroradiology, St. George’s University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Catherine Egan
- NIHR Biomedical Research Center at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Shirley V Hodgson
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University NHS Foundation Trust, Cambridge CB2 OQQ, UK
| | - Katie Snape
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK,St George's University of London, UK
| | - Eamonn R Maher
- To whom correspondence should be addressed at: Department of Medical Genetics, University of Cambridge, Box 238, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK. Tel: +44 01223746715; Fax: +44 01223746777;
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4
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Cao P, Yang A, Li P, Xia X, Han Y, Zhou G, Wang R, Yang F, Li Y, Zhang Y, Cui Y, Ji H, Lu L, He F, Zhou G. Genomic gain of RRS1 promotes hepatocellular carcinoma through reducing the RPL11-MDM2-p53 signaling. SCIENCE ADVANCES 2021; 7:7/35/eabf4304. [PMID: 34433556 PMCID: PMC8386927 DOI: 10.1126/sciadv.abf4304] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 07/02/2021] [Indexed: 05/20/2023]
Abstract
Hepatocellular carcinomas (HCCs) are characterized by frequent somatic genomic copy number alterations (CNAs), with most of them biologically unexplored. Here, we performed integrative analyses combining CNAs with the transcriptomic data to reveal the cis- and trans-effects of CNAs in HCC. We identified recurrent genomic gains of chromosome 8q, which exhibit strong trans-effects and are broadly associated with ribosome biogenesis activity. Furthermore, 8q gain-driven overexpression of ribosome biogenesis regulator (RRS1) promotes growth of HCC cells in vitro and in vivo. Mechanistically, RRS1 attenuates ribosomal stress through retaining RPL11 in the nucleolus, which, in turn, potentiates MDM2-mediated ubiquitination and degradation of p53. Clinically, higher RRS1 expression levels predict poor clinical outcomes for patients with HCC, especially in those with intact p53 Our findings established that the chromosome 8q oncogene RRS1 promotes HCC development through attenuating the RPL11-MDM2-p53 pathway and provided new potential targets for treatment of this malignancy.
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Affiliation(s)
- Pengbo Cao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Aiqing Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Peiyao Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xia Xia
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yuqing Han
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Guangming Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Rui Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Fei Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yuanfeng Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Ying Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Ying Cui
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning City, China
| | - Hongzan Ji
- Department of Gastroenterology and Hepatology, Jinling Hospital, Clinical School of Nanjing University, Nanjing City, China
| | - Lei Lu
- Department of Surgical Oncology, Jingdu Hospital, Nanjing City, China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China.
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China.
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, China
- Anhui Medical University, Hefei City, China
- Hebei University, Shijiazhuang City, China
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5
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Rossi T, Palleschi M, Angeli D, Tebaldi M, Martinelli G, Vannini I, Puccetti M, Limarzi F, Maltoni R, Gallerani G, Fabbri F. Case Report: Analysis of Circulating Tumor Cells in a Triple Negative Spindle-Cell Metaplastic Breast Cancer Patient. Front Med (Lausanne) 2021; 8:689895. [PMID: 34249978 PMCID: PMC8264184 DOI: 10.3389/fmed.2021.689895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/17/2021] [Indexed: 12/26/2022] Open
Abstract
Circulating tumor cells (CTCs) are a rare population of cells found in the bloodstream and represent key players in the metastatic cascade. Their analysis has proved to provide further core information concerning the tumor. Herein, we aim at investigating CTCs isolated from a 32-year-old patient diagnosed with triple negative spindle-shaped metaplastic breast cancer (MpBC), a rare tumor poorly responsive to therapies and with a dismal prognosis. The molecular analysis performed on the primary tumor failed to underline effective actionable targets to address the therapeutic strategy. Besides the presence of round-shaped CTCs, cells with a spindle shape were present as well, and through molecular analysis, we confirmed their malignant nature. This aspect was coherent with the primary tumor histology, proving that CTCs are released regardless of their morphology. Copy number aberration (CNA) profiling and variant analysis using next-generation sequencing (NGS) showed that these cells did not harbor the alterations exhibited by the primary tumor (PIK3CA G1049A mutation, MYC copy number gain). However, despite the great heterogeneity observed, the amplification of regions involved in metastasis emerged (8q24.22–8q24.23). Our findings support the investigation of CTCs to identify alterations that could have a role in the metastatic process. To the best of our knowledge, this is the first examination of CTCs in an MpBC patient.
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Affiliation(s)
- Tania Rossi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Michela Palleschi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Michela Tebaldi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Scientifico Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Ivan Vannini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | | | | | - Roberta Maltoni
- Healthcare Administration, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giulia Gallerani
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Francesco Fabbri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
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6
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Czyzyk-Krzeska MF, Landero Figueroa JA, Gulati S, Cunningham JT, Meller J, ShamsaeI B, Vemuri B, Plas DR. Molecular and Metabolic Subtypes in Sporadic and Inherited Clear Cell Renal Cell Carcinoma. Genes (Basel) 2021; 12:genes12030388. [PMID: 33803184 PMCID: PMC7999481 DOI: 10.3390/genes12030388] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 01/18/2023] Open
Abstract
The promise of personalized medicine is a therapeutic advance where tumor signatures obtained from different omics platforms, such as genomics, transcriptomics, proteomics, and metabolomics, in addition to environmental factors including metals and metalloids, are used to guide the treatments. Clear cell renal carcinoma (ccRCC), the most common type of kidney cancer, can be sporadic (frequently) or genetic (rare), both characterized by loss of the von Hippel-Lindau (VHL) gene that controls hypoxia inducible factors. Recently, several genomic subtypes were identified with different prognoses. Transcriptomics, proteomics, metabolomics and metallomic data converge on altered metabolism as the principal feature of the disease. However, in view of multiple biochemical alterations and high level of tumor heterogeneity, identification of clearly defined subtypes is necessary for further improvement of treatments. In the future, single-cell combined multi-omics approaches will be the next generation of analyses gaining deeper insights into ccRCC progression and allowing for design of specific signatures, with better prognostic/predictive clinical applications.
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Affiliation(s)
- Maria F. Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
- Department of Veterans Affairs, Cincinnati Veteran Affairs Medical Center, Cincinnati, OH 45220, USA
- Department of Pharmacology and System Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.A.L.F.); (J.M.)
- Correspondence:
| | - Julio A. Landero Figueroa
- Department of Pharmacology and System Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.A.L.F.); (J.M.)
- Agilent Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Shuchi Gulati
- Division of Hematology and Oncology, Department of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - John T. Cunningham
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
| | - Jarek Meller
- Department of Pharmacology and System Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.A.L.F.); (J.M.)
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45267, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH 45267, USA;
- Department of Electrical Engineering and Computer Science, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Behrouz ShamsaeI
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - Bhargav Vemuri
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
| | - David R. Plas
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
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7
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Fernandes FG, Silveira HCS, Júnior JNA, da Silveira RA, Zucca LE, Cárcano FM, Sanches AON, Neder L, Scapulatempo-Neto C, Serrano SV, Jonasch E, Reis RM, Evangelista AF. Somatic Copy Number Alterations and Associated Genes in Clear-Cell Renal-Cell Carcinoma in Brazilian Patients. Int J Mol Sci 2021; 22:2265. [PMID: 33668731 PMCID: PMC7956176 DOI: 10.3390/ijms22052265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 12/24/2022] Open
Abstract
Somatic copy number aberrations (CNAs) have been associated with clear-cell renal carcinoma (ccRCC) pathogenesis and are a potential source of new diagnostic, prognostic and therapeutic biomarkers. Recurrent CNAs include loss of chromosome arms 3p, 14q, 9p, and gains of 5q and 8q. Some of these regional CNAs are suspected of altering gene expression and could influence clinical outcomes. Despite many studies of CNAs in RCC, there are currently no descriptions of genomic copy number alterations in a Brazilian ccRCC cohort. This study was designed to evaluate the chromosomal profile of CNAs in Brazilian ccRCC tumors and explore clinical associations. A total of 92 ccRCC Brazilian patients that underwent nephrectomy at Barretos Cancer Hospital were analyzed for CNAs by array comparative genomic hybridization. Most patients in the cohort had early-stage localized disease. The most significant alterations were loss of 3p (87.3%), 14q (35.8%), 6q (29.3%), 9p (28.6%) and 10q (25.0%), and gains of 5q (59.7%), 7p (29.3%) and 16q (20.6%). Bioinformatics analysis revealed 19 genes mapping to CNA significant regions, including SETD2, BAP1, FLT4, PTEN, FGFR4 and NSD1. Moreover, gain of 5q34-q35.3 (FLT4 and NSD1) and loss of 6q23.2-q23.3 (MYB) and 9p21.3 (MLLT3) had gene expression levels that correlated with TCGA data and was also associated with advanced disease features, such as larger tumors, Fuhrman 3, metastasis at diagnosis and death. The loss of region 14q22.1 which encompasses the NIN gene was associated with poor overall survival. Overall, this study provides the first CNA landscape of Brazilian patients and pinpoints genomic regions and specific genes worthy of more detailed investigations. Our results highlight important genes that are associated with copy number changes involving large chromosomal regions that are potentially related to ccRCC tumorigenesis and disease biology for future clinical investigations.
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Affiliation(s)
- Flávia Gonçalves Fernandes
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
| | | | - João Neif Antonio Júnior
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
| | - Rosana Antunes da Silveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
| | - Luis Eduardo Zucca
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
| | - Flavio Mavignier Cárcano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
- Barretos School of Health Sciences Dr Paulo Prata-FACISB, Barretos 14785-002, Brazil
| | - André Octavio Nicolau Sanches
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
| | - Luciano Neder
- Department of Pathology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (L.N.); (C.S.-N.)
| | | | - Sergio Vicente Serrano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
- Barretos School of Health Sciences Dr Paulo Prata-FACISB, Barretos 14785-002, Brazil
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
- Life and Health Sci Research Institute (ICVS), Medical School, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
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8
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Prognostic and Predictive Factors in Metastatic Renal Cell Carcinoma: Current Perspective and a Look Into the Future. ACTA ACUST UNITED AC 2020; 26:365-375. [PMID: 32947304 DOI: 10.1097/ppo.0000000000000468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Metastatic renal cell carcinoma (mRCC) comprises a highly heterogeneous group of diseases with varied clinical outcomes. As a result, models to estimate prognosis were developed in an attempt to aid patient counseling, treatment selection, and clinical trial design. Contemporary prognostic models have been mostly generated based on clinical factors because of their ease of use. Recent advances in molecular techniques have allowed unprecedented molecular profiling of RCC and the discovery of genomic and proteotranscriptomic factors that may contribute to disease trajectory. With the advent of multiple systemic therapies in mRCC in recent years, predictive biomarkers have become increasingly relevant in treatment selection. In this review, we discuss the existing staging systems and prognostic models in mRCC. We also highlight various promising molecular biomarkers according to the subtypes of RCC and explore their integration into the traditional prognostic models. In addition, we discuss emerging predictive biomarkers in the era of immuno-oncology. Lastly, we explore future directions with a focus on liquid biopsies and composite biomarkers.
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9
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Denu RA, Burkard ME. Analysis of the "centrosome-ome" identifies MCPH1 deletion as a cause of centrosome amplification in human cancer. Sci Rep 2020; 10:11921. [PMID: 32681070 PMCID: PMC7368085 DOI: 10.1038/s41598-020-68629-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 06/23/2020] [Indexed: 11/09/2022] Open
Abstract
The centrosome is the microtubule organizing center of human cells and facilitates a myriad of cellular functions including organization of the mitotic spindle to ensure faithful chromosome segregation during mitosis, cell polarization and migration, and primary cilia formation. A numerical increase in centrosomes, or centrosome amplification (CA), is common in cancer and correlates with more aggressive clinical features and worse patient outcomes. However, the causes of CA in human cancer are unclear. Many previous studies have identified mechanisms of CA in cellulo, such as overexpression of PLK4, but it is unclear how often these are the primary mechanism in human disease. To identify a primary cause of CA, we analyzed The Cancer Genome Atlas (TCGA) genomic and transcriptomic data for genes encoding the 367 proteins that localize to the centrosome (the "centrosome-ome"). We identified the following candidates for primary causes of CA: gain-of-function alterations of CEP19, CEP72, CTNNB1, PTK2, NDRG1, SPATC1, TBCCD1; and loss-of-function alterations of CEP76, MCPH1, NEURL4, and NPM1. In cellulo analysis of these candidates revealed that loss of MCPH1/microcephalin caused the most robust increase in centriole number. MCPH1 deep gene deletions are seen in 5-15% of human cancers, depending on the anatomic site of the tumor. Mechanistic experiments demonstrated that loss of MCPH1 caused a CDK2-dependent increase in STIL levels at the centrosome to drive CA. We conclude that loss of MCPH1 is common in human cancer and is likely to be a cause of CA.
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Affiliation(s)
- Ryan A Denu
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 6059 WIMR, 1111 Highland Avenue, Madison, WI, 53705, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark E Burkard
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 6059 WIMR, 1111 Highland Avenue, Madison, WI, 53705, USA.
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA.
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10
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Overall tumor genomic instability: an important predictor of recurrence-free survival in patients with localized clear cell renal cell carcinoma. Cancer Biol Ther 2020; 21:424-431. [PMID: 32116106 DOI: 10.1080/15384047.2020.1721251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Measurement of a tumor's overall genomic instability has gathered recent interest over the identification of specific genomic imbalances, as it may provide a more robust measure of tumor aggressiveness. Here we demonstrate the association of tumor genomic instability in the prediction of disease recurrence in patients with clinically localized clear cell renal cell carcinoma (ccRCC). Genomic copy number analysis was performed using SNP-based microarrays on tumors from 103 ccRCC patients. The number of copy number alterations (CNAs) for each tumor was calculated, and a genomic imbalance threshold (GIT) associated with high stage and high-grade disease was determined. Cox proportional hazards regression analyzes were performed to assess the effect of GIT on recurrence-free survival adjusting for known confounders. In the cohort, copy number losses in chromosome arms 3p, 14q, 6q, 9p, and 1p and gains of 5q and 7p/q were common. CNA burden significantly increased with increasing stage (p < .001) and grade (p < .001). The median CNA burden associated with patients presenting with advanced stage (IV) and high-grade (III/IV) tumors was ≥9, defining the GIT. On regression analysis, GIT was a superior predictor of recurrence (Hazard Ratio 4.44 [CI 1.36-14.48], p = .01) independent of stage, with similar results adjusting for grade. These findings were confirmed using an alternative measure of genomic instability, weighted Genomic Integrity Index. Our data support a key role for genomic instability in ccRCC progression. More importantly, we have identified a GIT (≥ 9 CNAs) that is a superior and independent predictor of disease recurrence in high-risk ccRCC patients.
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11
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von Loga K, Woolston A, Punta M, Barber LJ, Griffiths B, Semiannikova M, Spain G, Challoner B, Fenwick K, Simon R, Marx A, Sauter G, Lise S, Matthews N, Gerlinger M. Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer. Nat Commun 2020; 11:139. [PMID: 31949146 PMCID: PMC6965135 DOI: 10.1038/s41467-019-13915-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/05/2019] [Indexed: 01/09/2023] Open
Abstract
Mismatch repair deficient (dMMR) gastro-oesophageal adenocarcinomas (GOAs) show better outcomes than their MMR-proficient counterparts and high immunotherapy sensitivity. The hypermutator-phenotype of dMMR tumours theoretically enables high evolvability but their evolution has not been investigated. Here we apply multi-region exome sequencing (MSeq) to four treatment-naive dMMR GOAs. This reveals extreme intratumour heterogeneity (ITH), exceeding ITH in other cancer types >20-fold, but also long phylogenetic trunks which may explain the exquisite immunotherapy sensitivity of dMMR tumours. Subclonal driver mutations are common and parallel evolution occurs in RAS, PIK3CA, SWI/SNF-complex genes and in immune evasion regulators. MSeq data and evolution analysis of single region-data from 64 MSI GOAs show that chromosome 8 gains are early genetic events and that the hypermutator-phenotype remains active during progression. MSeq may be necessary for biomarker development in these heterogeneous cancers. Comparison with other MSeq-analysed tumour types reveals mutation rates and their timing to determine phylogenetic tree morphologies.
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Affiliation(s)
- Katharina von Loga
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
- Biomedical Research Centre, The Royal Marsden Hospital, London, SM2 5PT, United Kingdom
| | - Andrew Woolston
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Marco Punta
- Bioinformatics Core, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, United Kingdom
| | - Louise J Barber
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Beatrice Griffiths
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Maria Semiannikova
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Georgia Spain
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Benjamin Challoner
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Andreas Marx
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Institute of Pathology, University Hospital Fuerth, 90766, Fuerth, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Stefano Lise
- Bioinformatics Core, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, United Kingdom
| | - Nik Matthews
- Tumour Profiling Unit, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Marco Gerlinger
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom.
- Gastrointestinal Cancer Unit, The Royal Marsden Hospital, London, SW3 6JJ, United Kingdom.
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12
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Xiong Y, Qi Y, Bai Q, Xia Y, Liu L, Guo J. Relevance of arm somatic copy number alterations for oncologic outcomes and tumor immune microenvironment in clear cell renal cell carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:646. [PMID: 31930047 DOI: 10.21037/atm.2019.10.54] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Prognostic value of arm somatic copy number alterations (SCNAs) in clear cell renal cell carcinoma (ccRCC) have not been systematically evaluated in a large cohort. Its association with tumor microenvironment remained unknown. Methods We retrospectively correlated arm SCNAs with OS and recurrence free survival (RFS) in a cohort of 524 ccRCC patients. The prognostic landscape of arm SCNA was depicted by bubble heatmap. Associations between arm SCNAs and tumor microenvironment were evaluated by CIBERSORT and Gene Set Enrichment Analysis (GSEA). Results We found that amplifications of 1p, 3p and loss of 4p, 4q, 5p, 5q, 11p, 11q, 11q, 13q, 19p were independent adverse risk factor for OS, while amplification of 1q and deletions of 4p, 4q, 9p, 9q associated with worse RFS. Loss of 4q were independent adverse risk factor for OS (P=0.012, HR =1.614) and RFS (P=0.001, HR =2.005). It could identify a subset of early stage ccRCC patients with high risk of death and recurrence. CXCL9, CXCL10, CXCL11 mRNA level and CD8+ T cell infiltration were downregulated in ccRCC with 4q deletion. Patients with high arm SCNA level had shorter OS (P=0.005) and RFS (P=0.001). Markers, immune cells and pathways referring to immune suppression were elevated in tumors with high arm SCNA level. Conclusions In conclusion, loss of 4q was an independent adverse risk factor for OS and RFS in ccRCC patients and contributed to cytotoxic cell exclusion via downregulation of CXCL9, CXCL10 and CXCL11. Patients with higher arm SCNAs had worse survival and a more immunosuppressive tumor microenvironment.
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Affiliation(s)
- Ying Xiong
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yu Qi
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qi Bai
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yu Xia
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Li Liu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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13
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Quddus MB, Pratt N, Nabi G. Chromosomal aberrations in renal cell carcinoma: An overview with implications for clinical practice. Urol Ann 2019; 11:6-14. [PMID: 30787564 PMCID: PMC6362797 DOI: 10.4103/ua.ua_32_18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Chromosomal instability and aberrations are known in many cancers including renal cell carcinoma. Detailed understanding of these changes has led to an improved drug discovery and continued developments in other therapeutic options. Chromosomal aberrations have a potential to be used to monitor disease including prognostication. There has been a growing experience in cytogenetic techniques and gap between clinic and laboratory has narrowed significantly in the recent past. Nevertheless, more work on validation of these techniques, establishing threshold and interobserver agreement needs to be carried out for these diagnostic/prognostic tests before utilizing them in clinics as a part of “personalized medicine” care. The review presented here is a summary of common genetic disorders in renal cancer and some of acquired genetic changes which can be used as biomarkers. The review also describes basics of commonly used genetic techniques for wider clinical community involved in the management of renal cancer.
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Affiliation(s)
- Muhammad Bilal Quddus
- Department of Urology, Academic Urology Unit, School of Medicine, Ninewells Hospital, Dundee, Scotland, UK
| | - Norman Pratt
- Department of Urology, Clinical Genetic Unit, Ninewells Hospital, NHS Tayside, Dundee, Scotland, UK
| | - Ghulam Nabi
- Department of Urology, Academic Urology Unit, School of Medicine, Ninewells Hospital, Dundee, Scotland, UK
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14
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Xiao W, Wang X, Wang T, Xing J. TRIM2 downregulation in clear cell renal cell carcinoma affects cell proliferation, migration, and invasion and predicts poor patients' survival. Cancer Manag Res 2018; 10:5951-5964. [PMID: 30538545 PMCID: PMC6255054 DOI: 10.2147/cmar.s185270] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background and aim Tripartite motif containing (TRIM) family protein has been involved in multiple pathogenesis of cancers. TRIM2 is a member of the family, and its role in clear cell renal cell carcinoma (ccRCC) remains to be unclarifid. Here, we showed the clinical value and biological role of TRIM2 in ccRCC. Methods ROC curves analyzed the clinicopathological parameters, Kaplan-Meier survival analysis determined the correlation of OS and DFS time, multivariate analysis demonstrated the prognostic indicator in overall survival and disease-free survival of ccRCC with TRIM2 expression in The Cancer Genome Atlas Kidney Clear Cell Carcinoma (TCGA-KIRC) database. Western blotting and immunohistochemistry were used to check the level of TRIM2 expression. Gain-of-function assay by exogenous overexpression of TRIM2 studied the biological role of TRIM2 in renal cell carcinoma cells. Results TRIM2 expression was associated with various clinicopathologicalfactors and lower TRIM2 expression was interrelated to a poor prognosis. The levels of TRIM2 expression were also scanty in ccRCC tissues and renal cancer cell lines than in normal control. The biological role of TRIM2 in ccRCC was identifid by bioinformatics analysis and functional analysis. Exogenous overexpression of TRIM2 with the gain-of-function assay in renal cell carcinoma cells showed that the cell proliferation, migration, and invasion were signifiantly suppressed. Conclusion These results showed that TRIM2 acted as an antitumor gene and a specifi prognostic indicator for patients with ccRCC, which indicated that positive modulation of TRIM2 might be a novel treatment strategy for ccRCC.
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Affiliation(s)
- Wen Xiao
- Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China,
| | - Xuegang Wang
- Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China,
| | - Tao Wang
- Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China,
| | - Jinchun Xing
- Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China,
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15
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Zhao K, Zhao Y, Zhu JY, Dong H, Cong WM, Yu Y, Wang H, Zhu ZZ, Xu Q. A Panel of Genes Identified as Targets for 8q24.13-24.3 Gain Contributing to Unfavorable Overall Survival in Patients with Hepatocellular Carcinoma. Curr Med Sci 2018; 38:590-596. [PMID: 30128866 DOI: 10.1007/s11596-018-1918-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/17/2018] [Indexed: 12/12/2022]
Abstract
Copy number aberrations (CNAs) in chromosome arm 8q have been associated with unfavorable clinical outcomes of several cancers and progressive tumor characteristics of hepatocellular carcinoma (HCC). This study was to identify correlation of CNAs in 8q with clinical outcomes of HCC patients, and further screen for differentially expressed genes in outcome-related CNAs. Array comparative genomic hybridization and expression arrays were performed to detect CNAs and expression levels, respectively. The correlations between CNAs in 8q and outcomes were analyzed in 66 patients, with a median follow-up time of 45.0 months (range, 2.6-108.6 months). One hundred and nine cases were further evaluated to identify differentially expressed genes in the potential outcome-related CNAs. Copy number gain in 8q was observed in 22 (33.3%) of the 66 HCC cases. The most recurrent gains (with frequencies >20%) were 8q13.3-21.3,8q21.3-23.3,8q23.3-24.13,8q24.13-24.3, and 8q24.3. Survival analysis showed that 8q24.13-24.3 gain was significantly associated with reduced overall survival (jP=0.010). Multivariate Cox analysis identified 8q24.13-24.3 gain as an independent prognostic factor for poor overall survival (HR=2.47; 95% CI=1.16-5.26; Р=0.019). Apanel of 17 genes within the 8q24.13-24.3 region, including ATAD2,SQLE,PVT1,ASAP1, and NDRG1 were significantly upregulated in HCCs with 8q24.13-24.3 gain compared to those without. These results suggest that copy number gain at 8q24.13-24.3 is an unfavorable prognostic marker for HCC patients, and the potential oncogenes ATAD2,SQLE, PVT1, ASAP1,and NDRG1 within the regional gain, may contribute coordinately to the 8q24.13-24.3 gain-related poor prognosis.
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Affiliation(s)
- Kun Zhao
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China.,Shanghai Clinical College of Anhui Medical University, Shanghai, 200072, China
| | - Yu Zhao
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Jia-Yi Zhu
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hui Dong
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, China
| | - Wen-Ming Cong
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, China
| | - Yi Yu
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Hui Wang
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Zhong-Zheng Zhu
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
| | - Qing Xu
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
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16
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Mitchell TJ, Rossi SH, Klatte T, Stewart GD. Genomics and clinical correlates of renal cell carcinoma. World J Urol 2018; 36:1899-1911. [PMID: 30099580 PMCID: PMC6280817 DOI: 10.1007/s00345-018-2429-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 07/31/2018] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Clear cell, papillary cell, and chromophobe renal cell carcinomas (RCCs) have now been well characterised thanks to large collaborative projects such as The Cancer Genome Atlas (TCGA). Not only has knowledge of the genomic landscape helped inform the development of new drugs, it also promises to fine tune prognostication. METHODS A literature review was performed summarising the current knowledge on the genetic basis of RCC. RESULTS The Von Hippel-Lindau (VHL) tumour suppressor gene undergoes bi-allelic knockout in the vast majority of clear cell RCCs. The next most prevalent aberrations include a cohort of chromatin-modifying genes with diverse roles including PBRM1, SETD2, BAP1, and KMD5C. The most common non-clear cell renal cancers have also undergone genomic profiling and are characterised by distinct genomic landscapes. Many recurrent mutations have prognostic value and show promise in aiding decisions regarding treatment stratification. Intra-tumour heterogeneity appears to hamper the clinical applicability of sparsely sampled tumours. Ways to abrogate heterogeneity will be required to optimise the genomic classification of tumours. CONCLUSION The somatic mutational landscape of the more common renal cancers is well known. Correlation with outcome needs to be more comprehensively furnished, particularly for small renal masses, rarer non-clear cell renal cancers, and for all tumours undergoing targeted therapy.
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Affiliation(s)
- Thomas J Mitchell
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK. .,Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK. .,Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK.
| | - Sabrina H Rossi
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK.,Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
| | - Tobias Klatte
- Department of Urology, Royal Bournemouth and Christchurch Hospitals NHS Foundation Trust, Bournemouth, BH7 7DW, UK
| | - Grant D Stewart
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK.,Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
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17
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[Low-grade eosinophilic unclassified renal cell carcinoma, a recently proposed entity in the spectrum of eosinophilic renal cells tumors: Report of one case and discussion]. Ann Pathol 2018; 38:395-400. [PMID: 30077423 DOI: 10.1016/j.annpat.2018.05.013] [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: 12/16/2017] [Revised: 05/01/2018] [Accepted: 05/31/2018] [Indexed: 11/22/2022]
Abstract
Low-grade eosinophilic unclassified renal cell carcinoma is a rare kidney tumor recently described, not included in the WHO classification, which is very close to oncocytoma. It is unknown to most pathologists and clinicians. From a histopathological point of view, this tumor is composed of oncocytic cells arranged in a diffuse and solid pattern, without cell nests, that makes it possible to differentiate it from oncocytoma, and expresses cytokeratin 7 (CK7) heterogeneously. We report a case with a cranial vault metastasis, and present the features to differentiate this entity from oncocytoma. Furthemore, we discuss about unclassified renal cell carcinomas with oncocytic cells.
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18
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Kluzek K, Srebniak MI, Majer W, Ida A, Milecki T, Huminska K, van der Helm RM, Silesian A, Wrzesinski TM, Wojciechowicz J, Beverloo BH, Kwias Z, Bluyssen HAR, Wesoly J. Genetic characterization of Polish ccRCC patients: somatic mutation analysis of PBRM1, BAP1 and KDMC5, genomic SNP array analysis in tumor biopsy and preliminary results of chromosome aberrations analysis in plasma cell free DNA. Oncotarget 2018; 8:28558-28574. [PMID: 28212566 PMCID: PMC5438672 DOI: 10.18632/oncotarget.15331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/10/2017] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Mutation analysis and cytogenetic testing in clear cell renal cell carcinoma (ccRCC) is not yet implemented in a routine diagnostics of ccRCC. MATERIAL AND METHODS We characterized the chromosomal alterations in 83 ccRCC tumors from Polish patients using whole genome SNP genotyping assay. Moreover, the utility of next generation sequencing of cell free DNA (cfDNA) in patients plasma as a potential tool for non-invasive cytogenetic analysis was tested. Additionally, tumor specific somatic mutations in PBRM1, BAP1 and KDM5C were determined. RESULTS We confirmed a correlation between deletions at 9p and higher tumor size, and deletion of chromosome 20 and the survival time. In Fuhrman grade 1, only aberrations of 3p and 8p deletion, gain of 5q and 13q and gains of chromosome 7 and 16 were present. The number of aberrations increased with Fuhrman grade, all chromosomes displayed cytogenetic changes in G3 and G4. ccRCC specific chromosome aberrations were observed in cfDNA, although discrepancies were found between cfDNA and tumor samples. In total 12 common and 94 rare variants were detected in PBRM1, BAP1 and KDM5C, with four potentially pathogenic variants. We observed markedly lower mutation load in PBRM1. CONCLUSIONS Cytogenetic analysis of cfDNA may allow more accurate diagnosis of tumor aberrations and therefore the correlation between the chromosome aberrations in cfDNA and clinical outcome should be studied in larger cohorts. The functional studies on in BAP1, KDM5C, PBRM1 mutations in large, independent sample set would be necessary for the assessment of their prognostic and diagnostic potential.
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Affiliation(s)
- Katarzyna Kluzek
- Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Malgorzata I Srebniak
- Department of Clinical Genetics, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Weronika Majer
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Agnieszka Ida
- Department of Urology and Urological Oncology, Poznan University of Medical Sciences, 61-285 Poznan, Poland
| | - Tomasz Milecki
- Department of Urology and Urological Oncology, Poznan University of Medical Sciences, 61-285 Poznan, Poland
| | - Kinga Huminska
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland.,Genomic Laboratory, DNA Research Center, 61-612 Poznan, Poland
| | - Robert M van der Helm
- Department of Clinical Genetics, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Adrian Silesian
- Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Tomasz M Wrzesinski
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | | | - Berna H Beverloo
- Department of Clinical Genetics, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Zbigniew Kwias
- Department of Urology and Urological Oncology, Poznan University of Medical Sciences, 61-285 Poznan, Poland
| | - Hans A R Bluyssen
- Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Joanna Wesoly
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
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19
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Mehrazin R, Dulaimi E, Uzzo RG, Devarjan K, Pei J, Smaldone MC, Kutikov A, Testa JR, Al-Saleem T. The correlation between gain of chromosome 8q and survival in patients with clear and papillary renal cell carcinoma. Ther Adv Urol 2018; 10:3-10. [PMID: 29344091 DOI: 10.1177/1756287217732660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 08/30/2017] [Indexed: 11/17/2022] Open
Abstract
Background The proto-oncogene c-MYC, located on chromosome 8q, can be upregulated through gain of 8q, causing alteration in biology of renal cell carcinoma (RCC). The aim of this study was to evaluate the prevalence of c-MYC through chromosome 8q gain and to correlate findings with cancer-specific mortality (CSM), and overall survival (OS). Methods Cytogenetic analysis by conventional or Chromosomal Genomic Microarray Analysis (CMA) was performed on 414 renal tumors. Nonclear and nonpapillary RCC were excluded. Impact of gain in chromosome 8q status on CSM, OS, and its correlation with clinicopathological variables were evaluated. CSM and OS were assessed using log-rank test and the Cox proportional hazards model. Results A total of 297 RCC tumors with cytogenetic analysis were included. Gain of 8q was detected in 18 (6.1%) tumors (9 clear cell and 9 papillary RCC), using conventional method (n = 11) or CMA (n = 7). Gain of 8q was associated with higher T stage (p < 0.001), grade (p < 0.001), nodal involvement (p = 0.005), and distant metastasis (p < 0.001). No association between gain of 8q and age (p = 0.23), sex (p = 0.46), and Charlson comorbidity index (CCI, p = 0.59) were seen. Gain of 8q was associated with an 8.38-fold [95% confidence interval (CI), 3.83-18.34, p < 0.001] and 3.31-fold (95% CI, 1.56-7.04, p = 0.001) increase in CSM and decrease in OS, respectively, at a median follow up of 56 months. Conclusion Chromosome 8q harbors the proto-oncogene c-MYC, which can be upregulated by gain of 8q. Our findings suggest that gain of 8q, can predict aggressive tumor phenotype and inferior survival in RCC.
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Affiliation(s)
- Reza Mehrazin
- Department of Urology and Oncological Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Essel Dulaimi
- Divisions of Pathology and Cancer Biology, Fox Chase Cancer Center-Temple Health System, Philadelphia, PA, USA
| | - Robert G Uzzo
- Divisions of Urologic Oncology, Fox Chase Cancer Center-Temple Health System, Philadelphia, PA, USA
| | - Karthik Devarjan
- Divisions of Biostatistics; Fox Chase Cancer Center-Temple Health System, Philadelphia, PA, USA
| | - Jianming Pei
- Divisions of Pathology and Cancer Biology, Fox Chase Cancer Center-Temple Health System, Philadelphia, PA, USA
| | - Marc C Smaldone
- Divisions of Urologic Oncology, Fox Chase Cancer Center-Temple Health System, Philadelphia, PA, USA
| | - Alexander Kutikov
- Divisions of Urologic Oncology, Fox Chase Cancer Center-Temple Health System, Philadelphia, PA, USA
| | - Joseph R Testa
- Divisions of Pathology and Cancer Biology, Fox Chase Cancer Center-Temple Health System, Philadelphia, PA, USA
| | - Tahseen Al-Saleem
- Divisions of Pathology and Cancer Biology, Fox Chase Cancer Center-Temple Health System, Philadelphia, PA, USA
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20
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Manley BJ, Zabor EC, Casuscelli J, Tennenbaum DM, Redzematovic A, Becerra MF, Benfante N, Sato Y, Morikawa T, Kume H, Fukayama M, Homma Y, Ogawa S, Arcila ME, Voss MH, Feldman DR, Coleman JA, Reuter VE, Motzer RJ, Russo P, Hsieh JJ, Hakimi AA. Integration of Recurrent Somatic Mutations with Clinical Outcomes: A Pooled Analysis of 1049 Patients with Clear Cell Renal Cell Carcinoma. Eur Urol Focus 2017; 3:421-427. [PMID: 28753773 PMCID: PMC5650556 DOI: 10.1016/j.euf.2016.06.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 06/14/2016] [Accepted: 06/24/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND Analyses of associations between clinicopathologic outcomes and recurrent somatic mutations in clear cell renal cell carcinoma (ccRCC) have been limited to individual cohorts. OBJECTIVE To define clinicopathologic associations between specific mutations and ccRCC disease characteristics. DESIGN, SETTING, AND PARTICIPANTS DNA sequencing data were pooled from three collaborative genomic cohorts (n=754) and our institutional database (n=295). All patients had clinical data and identification of somatic mutations from their primary tumors. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Analysis of gene mutations for associations with maximal tumor size (linear regression) and pathologic stage (logistic regression). Cancer-specific survival (CSS) and recurrence-free survival (RFS) were calculated using competing risks methods. Analyses were adjusted for cohort site, and results were adjusted for multiple testing (q value). Relevant genes were used in multivariable models that included confounding variables and the validated Mayo Clinic Stage, Size, Grade, and Necrosis (SSIGN) score. RESULTS AND LIMITATIONS Association with tumor size was found for mutations in BAP1 (q=0.013). No mutations were found to be associated with stage after adjusted analysis. Mutations in BAP1 (q=0.004) and TP53 (q=0.001) were associated with decreased CSS in a multivariable model; only TP53 (q=0.005) remained significant when SSIGN score was included. SETD2 mutations (q=0.047) were associated with decreased RFS in multivariable models, including models with SSIGN score. CONCLUSIONS In >1000 patients with ccRCC, pooled analysis and multivariable modeling demonstrated that three mutated genes have statistically significant associations with poor clinical outcomes. This included the more commonly mutated BAP1 and SETD2 and the less frequently mutated TP53. After adjustment for clinical confounders, mutations of TP53 and SETD2 were associated with decreased CSS and RFS, respectively. PATIENT SUMMARY Using rigorous statistical methods, this study affirmed that certain mutations in clear cell renal cell carcinoma may portend inferior survival and an increased risk of recurrence.
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Affiliation(s)
- Brandon John Manley
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily C Zabor
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jozefina Casuscelli
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel M Tennenbaum
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Almedina Redzematovic
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria F Becerra
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole Benfante
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yusuke Sato
- Department of Urology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan; Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Teppei Morikawa
- Department of Pathology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Yukio Homma
- Department of Urology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin H Voss
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Darren R Feldman
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan A Coleman
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert J Motzer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul Russo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James J Hsieh
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Ari Hakimi
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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21
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Bailey ST, Smith AM, Kardos J, Wobker SE, Wilson HL, Krishnan B, Saito R, Lee HJ, Zhang J, Eaton SC, Williams LA, Manocha U, Peters DJ, Pan X, Carroll TJ, Felsher DW, Walter V, Zhang Q, Parker JS, Yeh JJ, Moffitt RA, Leung JY, Kim WY. MYC activation cooperates with Vhl and Ink4a/Arf loss to induce clear cell renal cell carcinoma. Nat Commun 2017; 8:15770. [PMID: 28593993 PMCID: PMC5472759 DOI: 10.1038/ncomms15770] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 04/26/2017] [Indexed: 11/17/2022] Open
Abstract
Renal carcinoma is a common and aggressive malignancy whose histopathogenesis is incompletely understood and that is largely resistant to cytotoxic chemotherapy. We present two mouse models of kidney cancer that recapitulate the genomic alterations found in human papillary (pRCC) and clear cell RCC (ccRCC), the most common RCC subtypes. MYC activation results in highly penetrant pRCC tumours (MYC), while MYC activation, when combined with Vhl and Cdkn2a (Ink4a/Arf) deletion (VIM), produce kidney tumours that approximate human ccRCC. RNAseq of the mouse tumours demonstrate that MYC tumours resemble Type 2 pRCC, which are known to harbour MYC activation. Furthermore, VIM tumours more closely simulate human ccRCC. Based on their high penetrance, short latency, and histologic fidelity, these models of papillary and clear cell RCC should be significant contributions to the field of kidney cancer research. Renal cell carcinoma (RCC) is a common and aggressive malignancy. Here, the authors generate two mouse models of the most common RCC subtypes: the human papillary RCC through MYC activation and clear cell RCC through MYC activation combined with Vhl and Cdkn2a deletion.
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Affiliation(s)
- Sean T Bailey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Aleisha M Smith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jordan Kardos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Sara E Wobker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Pathology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Harper L Wilson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Bhavani Krishnan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Ryoichi Saito
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Hyo Jin Lee
- Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Jing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Pathology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Samuel C Eaton
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Lindsay A Williams
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Ujjawal Manocha
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Dorien J Peters
- Department of Pathology, Leiden University Medical Center, Leiden 2333, The Netherlands
| | - Xinchao Pan
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Thomas J Carroll
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Dean W Felsher
- Department of Medicine, Stanford University School of Medicine, Palo Alto, California 94305-5151, USA
| | - Vonn Walter
- Department of Biochemistry and Molecular Biology, Penn State Milton S. Hershey College of Medicine, 500 University Drive, Hershey, Pennsylvania 17033, USA
| | - Qing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Pathology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Richard A Moffitt
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Janet Y Leung
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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22
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Harlander S, Schönenberger D, Toussaint NC, Prummer M, Catalano A, Brandt L, Moch H, Wild PJ, Frew IJ. Combined mutation in Vhl, Trp53 and Rb1 causes clear cell renal cell carcinoma in mice. Nat Med 2017; 23:869-877. [PMID: 28553932 PMCID: PMC5509015 DOI: 10.1038/nm.4343] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 04/15/2017] [Indexed: 12/17/2022]
Abstract
Clear cell renal cell carcinomas (ccRCC) frequently exhibit inactivation of the VHL tumour suppressor gene and often harbour multiple copy number alterations in genes that regulate cell cycle progression. We show here that modelling these genetic alterations by combined renal epithelium-specific deletion of Vhl, Trp53 and Rb1 in mice caused ccRCC. These tumours arose from proximal tubule epithelial cells and shared molecular markers and mRNA expression profiles with human ccRCC. Exome sequencing revealed that mouse and human ccRCCs exhibit recurrent mutations in genes associated with the primary cilium, uncovering a mutational convergence on this organelle and implicating a subset of ccRCCs as genetic ciliopathies. Different mouse tumours responded differently to standard therapies for advanced human ccRCC, mimicking the range of clinical behaviours in the human disease. Inhibition of HIF-α transcription factors with Acriflavine as third line therapy had therapeutic effects in some tumours, providing pre-clinical evidence for further investigation of HIF-α inhibition as a ccRCC treatment. This autochthonous mouse ccRCC model represents a tool to investigate the biology of ccRCC and to identify new treatment strategies.
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Affiliation(s)
- Sabine Harlander
- Institute of Physiology, University of Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | | | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Michael Prummer
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Antonella Catalano
- Institute of Physiology, University of Zurich, Zurich, Switzerland.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,Center for Translational Cell Research, Clinic of Internal Medicine I, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laura Brandt
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Peter J Wild
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Ian J Frew
- Institute of Physiology, University of Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,Center for Translational Cell Research, Clinic of Internal Medicine I, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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23
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Clear cell renal cell carcinoma: a comparative study of histological and chromosomal characteristics between primary tumors and their corresponding metastases. Virchows Arch 2017; 471:107-115. [PMID: 28488172 DOI: 10.1007/s00428-017-2124-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/16/2017] [Accepted: 04/07/2017] [Indexed: 10/19/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) has a poor prognosis with a 50% risk of metastases. Little is known about the phenotypic and molecular profiles of metastases regarding their corresponding primary tumors. This study aimed to screen phenotypic and genotypic differences between metastases and their corresponding primary tumors. We selected four cases with available frozen material. The histological, immunohistochemical (VEGFA, CD31, SMA, Ki67, p53, PAR-3), FISH (VHL gene), next-generation sequencing (VHL and c-MET genes), multiplex ligation-dependent probe amplification, and array-(comparative genomic hybridization) CGH analyses were realized. Metastases were nodal, hepatic (synchronous), adrenal, and pulmonary (metachronous). High-grade tumor cells were significantly more frequent in metastases (p = 0.019). Metastases and high-grade zones of primary tumors shared similar characteristics compared to low-grade zones: a lower microscopic vascular density (43.5 vs 382.5 vessels/mm2; p = 0.0027), a higher expression of VEGF (73 vs 10%, p = 0.045), Ki67 (37.6 vs 8.3%; p = 0.011), and p53 (54 vs 10.6%; p = 0.081), and a cytoplasmic and membranous PAR-3 staining. Metastases exhibited more chromosomal imbalances than primary tumors in total (18.75 ± 6.8; p = 0.044) with more genomic gains (13.5 ± 7; p = 0.013). The loss of chromosome 9 and gain of Xq were found in both primary tumors and metastases but gains of loci or chromosomes 2p, 3q, 5, 8q, 12, and 20 were only found in metastases. The VHL gene status was similar in each tumor couple. Although metastases and primary tumors share common histological features, this study highlights chromosomal differences specific to metastases which could be involved in ccRCC metastatic evolution.
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24
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Schödel J, Grampp S, Maher ER, Moch H, Ratcliffe PJ, Russo P, Mole DR. Hypoxia, Hypoxia-inducible Transcription Factors, and Renal Cancer. Eur Urol 2016; 69:646-657. [PMID: 26298207 PMCID: PMC5012644 DOI: 10.1016/j.eururo.2015.08.007] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/05/2015] [Indexed: 12/18/2022]
Abstract
CONTEXT Renal cancer is a common urologic malignancy, and therapeutic options for metastatic disease are limited. Most clear cell renal cell carcinomas (ccRCC) are associated with loss of von Hippel-Lindau tumor suppressor (pVHL) function and deregulation of hypoxia pathways. OBJECTIVE This review summarizes recent evidence from genetic and biological studies showing that hypoxia and hypoxia-related pathways play critical roles in the development and progress of renal cancer. EVIDENCE ACQUISITION We used a systematic search for articles using the keywords hypoxia, HIF, renal cancer, and VHL. EVIDENCE SYNTHESIS Identification of the tumor suppressor pVHL has allowed the characterization of important ccRCC-associated pathways. pVHL targets α-subunits of hypoxia-inducible transcription factors (HIF) for proteasomal degradation. The two main HIF-α isoforms have opposing effects on RCC biology, possibly through distinct interactions with additional oncogenes. Furthermore, HIF-1α activity is commonly diminished by chromosomal deletion in ccRCCs, and increased HIF-1 activity reduces tumor burden in xenograft tumor models. Conversely, polymorphisms at the HIF-2α gene locus predispose to the development of ccRCCs, and HIF-2α promotes tumor growth. Genetic studies have revealed a prominent role for chromatin-modifying enzyme genes in ccRCC, and these may further modulate specific aspects of the HIF response. This suggests that, rather than global activation of HIF, specific components of the response are important in promoting kidney cancer. Some of these processes are already targets for current therapeutic strategies, and further dissection of this pathway might yield novel methods of treating RCC. CONCLUSIONS In contrast to many tumor types, HIF-1α and HIF-2α have opposing effects in ccRCC biology, with HIF-1α acting as a tumor suppressor and HIF-2α acting as an oncogene. The overall effect of VHL inactivation will depend on fine-tuning of the HIF response. PATIENT SUMMARY High levels of hypoxia-inducible transcription factors (HIF) are particularly important in the clear cell type of kidney cancer, in which they are no longer properly regulated by the von Hippel-Lindau protein. The two HIF-α proteins have opposing effects on tumor evolution.
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Affiliation(s)
- Johannes Schödel
- Medizinische Klinik 4 and Translational Research Center, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany.
| | - Steffen Grampp
- Medizinische Klinik 4 and Translational Research Center, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Cambridge NIHR Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Peter J Ratcliffe
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, UK
| | - Paul Russo
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, NY, NY, USA; Weill Medical College, Cornell University, Memorial Sloan Kettering Cancer Center, NY, NY, USA
| | - David R Mole
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, UK
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25
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Silva MP, Barros-Silva JD, Vieira J, Lisboa S, Torres L, Correia C, Vieira-Coimbra M, Martins AT, Jerónimo C, Henrique R, Paulo P, Teixeira MR. NCOA2 is a candidate target gene of 8q gain associated with clinically aggressive prostate cancer. Genes Chromosomes Cancer 2016; 55:365-74. [PMID: 26799514 DOI: 10.1002/gcc.22340] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/16/2015] [Accepted: 11/30/2015] [Indexed: 12/28/2022] Open
Abstract
Prostate carcinomas harboring 8q gains are associated with poor clinical outcome, but the target genes of this genomic alteration remain to be unveiled. In this study, we aimed to identify potential 8q target genes associated with clinically aggressive prostate cancer (PCa) using fluorescence in situ hybridization (FISH), genome-wide mRNA expression, and protein expression analyses. Using FISH, we first characterized the relative copy number of 8q (assessed with MYC flanking probes) of a series of 50 radical prostatectomy specimens, with available global gene expression data and typed for E26 transformation specific (ETS) rearrangements, and then compared the gene expression profile of PCa subsets with and without 8q24 gain using Significance Analysis of Microarrays. In the subset of tumors with ERG fusion genes (ERG+), five genes were identified as significantly overexpressed (false discovery rate [FDR], ≤ 5%) in tumors with relative 8q24 gain, namely VN1R1, ZNF417, CDON, IKZF2, and NCOA2. Of these, only NCOA2 is located in 8q (8q13.3), showing a statistically higher mRNA expression in the subgroup with relative 8q gain, both in the ERG+ subgroup and in the whole series (P = 0.000152 and P = 0.008, respectively). Combining all the cases with NCOA2 overexpression, either at the mRNA or at the protein level, we identified a group of tumors with NCOA2 copy-number increase, independently of ETS status and relative 8q24 gain. Furthermore, for the first time, we detected a structural rearrangement involving NCOA2 in PCa. These findings warrant further studies with larger series to evaluate if NCOA2 relative copy-number gain presents prognostic value independently of the well-established poor prognosis associated with MYC relative copy-number gain.
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Affiliation(s)
- Maria P Silva
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - João D Barros-Silva
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Joana Vieira
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Susana Lisboa
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Lurdes Torres
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Cecília Correia
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Márcia Vieira-Coimbra
- Cancer Biology and Epigenetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Ana T Martins
- Cancer Biology and Epigenetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Paula Paulo
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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26
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Recurrent amplification of MYC and TNFRSF11B in 8q24 is associated with poor survival in patients with gastric cancer. Gastric Cancer 2016; 19:116-27. [PMID: 25618371 DOI: 10.1007/s10120-015-0467-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 01/12/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gastric cancer (GC) is an aggressive malignancy whose mechanisms of development and progression are poorly understood. The identification of prognosis-related genomic loci and genes may suffer from the relatively small case numbers and a lack of systematic validation in previous studies. METHODS Array-based comparative genomic hybridization (aCGH) coupled with patient clinical information was applied to identify prognosis-related loci and genes with high-frequency recurrent gains in 129 GC patients. The candidate loci and genes were then validated using an independent cohort of 384 patients through branched DNA signal amplification analysis (QuantiGene assays). RESULTS In the 129 patients, a copy number gain of three chromosome regions-namely, 8q22 (including ESRP1 and CCNE2), 8q24 (including MYC and TNFRSF11B), and 20q11-q13 (including SRC, MMP9, and CSE1L)--conferred poor survival for patients. In addition, the correlation between the branched DNA signal amplification analysis results and the aCGH results was analyzed in 73 of these 129 patients, and MYC, TNFRSF11B, ESRP1, CSE1L, and MMP9 were found to be well correlated. Further validation using an independent cohort (n = 384) verified that only MYC and TNFRSF11B within 8q24 are related to survival. Patients with gains in both MYC and TNFRSF11B had poorer survival than those with no gains, particularly those with noncardia GC. Gains in both of these genes were also a significant independent prognostic indicator. CONCLUSIONS Our results revealed that copy number gains in MYC and TNFRSF11B located at 8q24 are associated with survival in GC, particularly noncardia GC.
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Ito T, Pei J, Dulaimi E, Menges C, Abbosh PH, Smaldone MC, Chen DYT, Greenberg RE, Kutikov A, Viterbo R, Uzzo RG, Testa JR. Genomic Copy Number Alterations in Renal Cell Carcinoma with Sarcomatoid Features. J Urol 2015; 195:852-8. [PMID: 26602888 DOI: 10.1016/j.juro.2015.10.180] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2015] [Indexed: 01/31/2023]
Abstract
PURPOSE Sarcomatoid changes in renal cell carcinoma are associated with a poor prognosis. The identification of genetic alterations that drive this aggressive phenotype could aid in the development of more effective targeted therapies. In this study we aimed to pinpoint unique copy number alterations in sarcomatoid renal cell carcinoma compared to classical renal cell carcinoma subtypes. MATERIALS AND METHODS Genomic copy number analysis was performed using single nucleotide polymorphism based microarrays on tissue extracted from the tumors of 81 patients who underwent renal mass excision, including 17 with sarcomatoid renal cell carcinoma. RESULTS Sarcomatoid renal cell carcinoma showed a significantly higher number of copy number alterations than clear cell, papillary and chromophobe renal cell carcinoma (mean 18.0 vs 5.8, 6.5 and 7.2, respectively, p <0.0001). Copy number losses of chromosome arms 9q, 15q, 18p/q and 22q, and gains of 1q and 8q occurred in a significantly higher proportion of sarcomatoid renal cell carcinomas than in the other 3 histologies. Patients with sarcomatoid renal cell carcinoma demonstrated significantly worse overall survival compared to those without that condition on Kaplan-Meier analysis (p = 0.0001). Patients with 9 or more copy number alterations also demonstrated significantly worse overall survival than those with fewer than 9 copy number alterations (p = 0.004). CONCLUSIONS Sarcomatoid changes in renal cell carcinoma are associated with a high rate of chromosomal imbalances with losses of 9q, 15q, 18p/q and 22q, and gains of 1q and 8q occurring at significantly higher frequencies in comparison to nonsarcomatoid renal cell carcinoma. Identifying candidate driver genes or tumor suppressor loci in these chromosomal regions may help identify targets for future therapies.
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Affiliation(s)
- Timothy Ito
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jianming Pei
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Essel Dulaimi
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Craig Menges
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Philip H Abbosh
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Marc C Smaldone
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - David Y T Chen
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Richard E Greenberg
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Alexander Kutikov
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Rosalia Viterbo
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Robert G Uzzo
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Joseph R Testa
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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RANK/OPG ratio of expression in primary clear-cell renal cell carcinoma is associated with bone metastasis and prognosis in patients treated with anti-VEGFR-TKIs. Br J Cancer 2015; 113:1313-22. [PMID: 26528707 PMCID: PMC4815796 DOI: 10.1038/bjc.2015.352] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/27/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022] Open
Abstract
Background: Bone metastases (BMs) are associated with poor outcome in metastatic clear-cell renal carcinoma (m-ccRCC) treated with anti-vascular endothelial growth factor tyrosine kinase inhibitors (anti-VEGFR-TKIs). We aimed to investigate whether expression in the primary tumour of genes involved in the development of BM is associated with outcome in m-ccRCC patients treated with anti-VEGFR-TKIs. Methods: Metastatic clear-cell renal cell carcinoma patients with available fresh-frozen tumour and treated with anti-VEGFR-TKIs. Quantitative real-time PCR (qRT–PCR) for receptor activator of NF-kB (RANK), RANK-ligand (RANKL), osteoprotegerin (OPG), the proto-oncogene SRC and DKK1 (Dickkopf WNT signalling pathway inhibitor-1). Time-to-event analysis by Kaplan–Meier estimates and Cox regression. Results: We included 129 m-ccRCC patients treated between 2005 and 2013. An elevated RANK/OPG ratio was associated with shorter median time to metastasis (HR 0.50 (95% CI 0.29–0.87); P=0.014), shorter time to BM (HR 0.54 (95% CI 0.31–0.97); P=0.037), shorter median overall survival (mOS) since initial diagnosis (HR 2.27 (95% CI 1.44–3.60); P=0.0001), shorter median progression-free survival (HR 0.44 (95% CI 0.28–0.71); P=0.001) and mOS (HR 0.31 (95% CI 0.19–0.52); P<0.0001) on first-line anti-VEGFR-TKIs in the metastatic setting. Higher RANK expression was associated with shorter mOS on first-line anti-VEGFR-TKIs (HR 0.46 (95% CI 0.29–0.73); P=0.001). Conclusions: RANK/OPG ratio of expression in primary ccRCC is associated with BM and prognosis in patients treated with anti-VEGFR-TKIs. Prospective validation is warranted.
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White-Al Habeeb NM, Di Meo A, Scorilas A, Rotondo F, Masui O, Seivwright A, Gabril M, Girgis AHA, Jewett MA, Yousef GM. Alpha-enolase is a potential prognostic marker in clear cell renal cell carcinoma. Clin Exp Metastasis 2015; 32:531-41. [DOI: 10.1007/s10585-015-9725-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/27/2015] [Indexed: 01/20/2023]
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Beuselinck B, Job S, Becht E, Karadimou A, Verkarre V, Couchy G, Giraldo N, Rioux-Leclercq N, Molinié V, Sibony M, Elaidi R, Teghom C, Patard JJ, Méjean A, Fridman WH, Sautès-Fridman C, de Reyniès A, Oudard S, Zucman-Rossi J. Molecular subtypes of clear cell renal cell carcinoma are associated with sunitinib response in the metastatic setting. Clin Cancer Res 2015; 21:1329-39. [PMID: 25583177 DOI: 10.1158/1078-0432.ccr-14-1128] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Selecting patients with metastatic clear-cell renal cell carcinoma (m-ccRCC) who might benefit from treatment with targeted tyrosine kinase inhibitors (TKI) is a challenge. Our aim was to identify molecular markers associated with outcome in patients with m-ccRCC treated with sunitinib. EXPERIMENTAL DESIGN We performed global transcriptome analyses on 53 primary resected ccRCC tumors from patients who developed metastatic disease and were treated with first-line sunitinib. We also determined chromosome copy-number aberrations, methylation status, and gene mutations in von Hippel-Lindau and PBRM1. Molecular data were analyzed in relation with response rate (RR), progression-free survival (PFS), and overall survival (OS). Validation was performed in 47 additional ccRCC samples treated in first-line metastatic setting with sunitinib. RESULTS Unsupervised transcriptome analysis identified 4 robust ccRCC subtypes (ccrcc1 to 4) related to previous molecular classifications that were associated with different responses to sunitinib treatment. ccrcc1/ccrcc4 tumors had a lower RR (P = 0.005) and a shorter PFS and OS than ccrcc2/ccrcc3 tumors (P = 0.001 and 0.0003, respectively). These subtypes were the only significant covariate in the multivariate Cox model for PFS and OS (P = 0.017 and 0.006, respectively). ccrcc1/ccrcc4 tumors were characterized by a stem-cell polycomb signature and CpG hypermethylation, whereas ccrcc3 tumors, sensitive to sunitinib, did not exhibit cellular response to hypoxia. Moreover, ccrcc4 tumors exhibited sarcomatoid differentiation with a strong inflammatory, Th1-oriented but suppressive immune microenvironment, with high expression of PDCD1 (PD-1) and its ligands. CONCLUSIONS ccRCC molecular subtypes are predictive of sunitinib response in metastatic patients, and could be used for personalized mRCC treatment with TKIs, demethylating or immunomodulatory drugs.
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Affiliation(s)
- Benoit Beuselinck
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Paris, France. Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. Labex Immuno-oncology, Paris, France. Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Department of Oncology, Paris, France
| | - Sylvie Job
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Etienne Becht
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. Labex Immuno-oncology, Paris, France. UMR_S1138, Centre de Recherche des Cordeliers, Paris, France
| | - Alexandra Karadimou
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Paris, France. Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. Labex Immuno-oncology, Paris, France
| | - Virginie Verkarre
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants malades, Department of Pathology, Paris, France
| | - Gabrielle Couchy
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Paris, France. Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. Labex Immuno-oncology, Paris, France
| | - Nicolas Giraldo
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. UMR_S1138, Centre de Recherche des Cordeliers, Paris, France
| | | | | | - Mathilde Sibony
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Department of Pathology, Paris, France
| | - Reza Elaidi
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Department of Oncology, Paris, France
| | - Corinne Teghom
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Department of Oncology, Paris, France
| | | | - Arnaud Méjean
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Department of Oncology, Paris, France
| | - Wolf Herman Fridman
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. Labex Immuno-oncology, Paris, France. UMR_S1138, Centre de Recherche des Cordeliers, Paris, France
| | - Catherine Sautès-Fridman
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. Labex Immuno-oncology, Paris, France. UMR_S1138, Centre de Recherche des Cordeliers, Paris, France
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Stéphane Oudard
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Department of Oncology, Paris, France
| | - Jessica Zucman-Rossi
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Paris, France. Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France. Labex Immuno-oncology, Paris, France. Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Department of Oncology, Paris, France.
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Gulati S, Martinez P, Joshi T, Birkbak NJ, Santos CR, Rowan AJ, Pickering L, Gore M, Larkin J, Szallasi Z, Bates PA, Swanton C, Gerlinger M. Systematic evaluation of the prognostic impact and intratumour heterogeneity of clear cell renal cell carcinoma biomarkers. Eur Urol 2014; 66:936-48. [PMID: 25047176 PMCID: PMC4410302 DOI: 10.1016/j.eururo.2014.06.053] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/30/2014] [Indexed: 12/23/2022]
Abstract
BACKGROUND Candidate biomarkers have been identified for clear cell renal cell carcinoma (ccRCC) patients, but most have not been validated. OBJECTIVE To validate published ccRCC prognostic biomarkers in an independent patient cohort and to assess intratumour heterogeneity (ITH) of the most promising markers to guide biomarker optimisation. DESIGN, SETTING, AND PARTICIPANTS Cancer-specific survival (CSS) for each of 28 identified genetic or transcriptomic biomarkers was assessed in 350 ccRCC patients. ITH was interrogated in a multiregion biopsy data set of 10 ccRCCs. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Biomarker association with CSS was analysed by univariate and multivariate analyses. RESULTS AND LIMITATIONS A total of 17 of 28 biomarkers (TP53 mutations; amplifications of chromosomes 8q, 12, 20q11.21q13.32, and 20 and deletions of 4p, 9p, 9p21.3p24.1, and 22q; low EDNRB and TSPAN7 expression and six gene expression signatures) were validated as predictors of poor CSS in univariate analysis. Tumour stage and the ccB expression signature were the only independent predictors in multivariate analysis. ITH of the ccB signature was identified in 8 of 10 tumours. Several genetic alterations that were significant in univariate analysis were enriched, and chromosomal instability indices were increased in samples expressing the ccB signature. The study may be underpowered to validate low-prevalence biomarkers. CONCLUSIONS The ccB signature was the only independent prognostic biomarker. Enrichment of multiple poor prognosis genetic alterations in ccB samples indicated that several events may be required to establish this aggressive phenotype, catalysed in some tumours by chromosomal instability. Multiregion assessment may improve the precision of this biomarker. PATIENT SUMMARY We evaluated the ability of published biomarkers to predict the survival of patients with clear cell kidney cancer in an independent patient cohort. Only one molecular test adds prognostic information to routine clinical assessments. This marker showed good and poor prognosis results within most individual cancers. Future biomarkers need to consider variation within tumours to improve accuracy.
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Affiliation(s)
- Sakshi Gulati
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Pierre Martinez
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Tejal Joshi
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Nicolai Juul Birkbak
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Claudio R Santos
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Andrew J Rowan
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | | | | | | | - Zoltan Szallasi
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark; Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Paul A Bates
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, UK.
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK; UCL Cancer Institute, London, UK.
| | - Marco Gerlinger
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK; Present address: Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
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Sirintrapun SJ, Geisinger KR, Cimic A, Snow A, Hagenkord J, Monzon F, Legendre BL, Ghazalpour A, Bender RP, Gatalica Z. Oncocytoma-like renal tumor with transformation toward high-grade oncocytic carcinoma: a unique case with morphologic, immunohistochemical, and genomic characterization. Medicine (Baltimore) 2014; 93:e81. [PMID: 25275525 PMCID: PMC4616290 DOI: 10.1097/md.0000000000000081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Renal oncocytoma is a benign tumor with characteristic histologic findings. We describe an oncocytoma-like renal tumor with progression to high-grade oncocytic carcinoma and metastasis. A 74-year-old man with no family history of cancer presented with hematuria. Computed tomography showed an 11 cm heterogeneous multilobulated mass in the right kidney lower pole, enlarged aortocaval lymph nodes, and multiple lung nodules. In the nephrectomy specimen, approximately one third of the renal tumor histologically showed regions classic for benign oncocytoma transitioning to regions of high-grade carcinoma without sharp demarcation. With extensive genomic investigation using single nucleotide polymorphism-based array virtual karyotyping, multiregion sequencing, and expression array analysis, we were able to show a common lineage between the benign oncocytoma and high-grade oncocytic carcinoma regions in the tumor. We were also able to show karyotypic differences underlying this progression. The benign oncocytoma showed no chromosomal aberrations, whereas the high-grade oncocytic carcinoma showed loss of the 17p region housing FLCN (folliculin [Birt-Hogg-Dubé protein]), loss of 8p, and gain of 8q. Gene expression patterns supported dysregulation and activation of phosphoinositide 3-kinase (PI3K)/v-akt murine thymoma viral oncogene homolog (Akt), mitogen-activated protein kinase (MAPK)/extracellular-signal-regulated kinase (ERK), and mechanistic target of rapamycin (serine/threonine kinase) (mTOR) pathways in the high-grade oncocytic carcinoma regions. This was partly attributable to FLCN underexpression but further accentuated by overexpression of numerous genes on 8q. In the high-grade oncocytic carcinoma region, vascular endothelial growth factor A along with metalloproteinases matrix metallopeptidase 9 and matrix metallopeptidase 12 were overexpressed, facilitating angiogenesis and invasiveness. Genetic molecular testing provided evidence for the development of an aggressive oncocytic carcinoma from an oncocytoma, leading to aggressive targeted treatment but eventual death 39 months after the diagnosis.
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Affiliation(s)
- Sahussapont J Sirintrapun
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (SJS); University of Mississippi Medical Center, Jackson, MS (KRG); Department of Pathology, Wake Forest Baptist Health, Winston-Salem, NC (AC, AS); 23andMe, Mountain View (JH); Invitae, San Francisco (FM), CA; Transgenomic (BLL); Creighton University School of Medicine (ZG), Omaha, NE; and Caris Life Sciences, Phoenix, AZ (AG, RPB, ZG)
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Dagher J, Dugay F, Rioux-Leclercq N, Verhoest G, Oger E, Bensalah K, Cabillic F, Jouan F, Kammerer-Jacquet SF, Fergelot P, Vigneau C, Arlot-Bonnemains Y, Belaud-Rotureau MA. Cytoplasmic PAR-3 protein expression is associated with adverse prognostic factors in clear cell renal cell carcinoma and independently impacts survival. Hum Pathol 2014; 45:1639-46. [DOI: 10.1016/j.humpath.2014.03.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 02/20/2014] [Accepted: 03/27/2014] [Indexed: 01/18/2023]
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Hakimi AA, Mano R, Ciriello G, Gonen M, Mikkilineni N, Sfakianos JP, Kim PH, Motzer RJ, Russo P, Reuter VE, Hsieh JJ, Ostrovnaya I. Impact of recurrent copy number alterations and cancer gene mutations on the predictive accuracy of prognostic models in clear cell renal cell carcinoma. J Urol 2014; 192:24-9. [PMID: 24518768 PMCID: PMC4146751 DOI: 10.1016/j.juro.2014.01.088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2014] [Indexed: 11/30/2022]
Abstract
PURPOSE Several recently reported recurrent genomic alterations in clear cell renal cell carcinoma are linked to pathological and clinical outcomes. We determined whether any recurrent cancer gene mutations or copy number alterations identified in the TCGA (The Cancer Genome Atlas) clear cell renal cell carcinoma data set could add to the predictive accuracy of current prognostic models. MATERIALS AND METHODS In 413 patients who underwent nephrectomy/partial nephrectomy we investigated whole exome, copy number array analyses and clinical variables. We identified 65 recurrent genomic alterations based on prevalence and combined them into 35 alterations, including 12 cancer gene mutations. Genomic markers were modeled using the elastic net algorithm with preoperative variables (tumor size plus patient age) and in the postoperative setting using the externally validated Mayo Clinic SSIGN (stage, size, grade and necrosis) prognostic scoring system. These models were subjected to internal validation using bootstrap. RESULTS Median followup in survivors was 45 months. Several markers correlated with adverse cancer specific survival and time to recurrence on univariate analysis. However, most of them lost significance when controlling for tumor size with or without age in the preoperative models or for SSIGN score in the postoperative setting. Adding multiple genomic markers selected by the elastic net algorithm failed to substantially add to the predictive accuracy of any preoperative or postoperative model for cancer specific survival or time to recurrence. CONCLUSIONS While recurrent copy number alterations and cancer gene mutations are biologically significant, they do not appear to improve the predictive accuracy of existing models of clinical cancer specific survival or time to recurrence for clear cell renal cell carcinoma.
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Affiliation(s)
- A Ari Hakimi
- Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York.
| | - Roy Mano
- Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Giovanni Ciriello
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Mithat Gonen
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Nina Mikkilineni
- Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - John P Sfakianos
- Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Philip H Kim
- Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Robert J Motzer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Paul Russo
- Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - James J Hsieh
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York
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Gutenberg A, Nischwitz MD, Gunawan B, Enders C, Jung K, Bergmann M, Feiden W, Egensperger R, Keyvani K, Stolke D, Sure U, Schroeder HWS, Warzok R, Schober R, Meixensberger J, Paulus W, Wassmann H, Stummer W, Blumcke I, Buchfelder M, van Landeghem FKH, Vajkoczy P, Günther M, Bedke J, Giese A, Rohde V, Brück W, Füzesi L, Sander B. Predictive chromosomal clusters of synchronous and metachronous brain metastases in clear cell renal cell carcinoma. Cancer Genet 2014; 207:206-13. [PMID: 25027636 DOI: 10.1016/j.cancergen.2014.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 05/01/2014] [Accepted: 05/10/2014] [Indexed: 01/21/2023]
Abstract
Synchronous (early) and metachronous (late) brain metastasis (BM) events of sporadic clear cell renal cell carcinoma (ccRCC) (n = 148) were retrospectively analyzed using comparative genomic hybridization (CGH). Using oncogenetic tree models and cluster analyses, chromosomal imbalances related to recurrence-free survival until BM (RFS-BM) were analyzed. Losses at 9p and 9q appeared to be hallmarks of metachronous BM events, whereas an absence of detectable chromosomal changes at 3p was often associated with synchronous BM events. Correspondingly, k-means clustering showed that cluster 1 cases generally exhibited low copy number chromosomal changes that did not involve 3p. Cluster 2 cases had a high occurrence of -9p/-9q (94-98%) deletions, whereas cluster 3 cases had a higher frequency of copy number changes, including loss at chromosome 14 (80%). The higher number of synchronous cases in cluster 1 was also associated with a significantly shorter RFS-BM compared with clusters 2 and 3 (P = 0.02). Conversely, a significantly longer RFS-BM was observed for cluster 2 versus clusters 1 and 3 (P = 0.02). Taken together, these data suggest that metachronous BM events of ccRCC are characterized by loss of chromosome 9, whereas synchronous BM events may form independently of detectable genetic changes at chromosomes 9 and 3p.
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Affiliation(s)
- Angelika Gutenberg
- Department of Neurosurgery, Georg August University, Göttingen, Germany; Department of Neurosurgery, Johannes Gutenberg University, Mainz, Germany.
| | - Martin D Nischwitz
- Department of Gastroenteropathology, Georg August University, Göttingen, Germany
| | - Bastian Gunawan
- Department of Gastroenteropathology, Georg August University, Göttingen, Germany
| | - Christina Enders
- Department of Gastroenteropathology, Georg August University, Göttingen, Germany
| | - Klaus Jung
- Department of Medical Statistics, Georg August University, Göttingen, Germany
| | - Markus Bergmann
- Department of Neuropathology, Klinikum Bremen-Mitte, Bremen, Germany
| | - Wolfgang Feiden
- Departments of Gastroenteropathology and Neuropathology, University of the Saarland, Homburg, Germany
| | - Rupert Egensperger
- Institute of Neuropathology, University of Duisburg-Essen, Essen, Germany
| | - Kathy Keyvani
- Institute of Neuropathology, University of Duisburg-Essen, Essen, Germany
| | - Dietmar Stolke
- Department of Neurosurgery, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Sure
- Department of Neurosurgery, University of Duisburg-Essen, Essen, Germany
| | - Henry W S Schroeder
- Department of Neurosurgery, Ernst Moritz Arndt University, Greifswald, Germany
| | - Rolf Warzok
- Department of Neuropathology, Ernst Moritz Arndt University, Greifswald, Germany
| | - Ralf Schober
- Department of Neuropathology, University of Leipzig, Leipzig, Germany
| | | | - Werner Paulus
- Department of Neuropathology, Westphalian Wilhelm University, Münster, Germany
| | - Hansdetlef Wassmann
- Department of Neurosurgery, Westphalian Wilhelm University, Münster, Germany
| | - Wolfgang Stummer
- Department of Neurosurgery, Westphalian Wilhelm University, Münster, Germany
| | - Ingmar Blumcke
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Michael Buchfelder
- Department of Neurosurgery, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Frank K H van Landeghem
- Department of Neuropathology, Charité University Medicine, Berlin, Germany; Department of Neuropathology, University of Alberta, Edmonton, Canada
| | - Peter Vajkoczy
- Department of Neurosurgery, Charité University Medicine, Berlin, Germany
| | - Marlis Günther
- Department of Pathology, Health Care Center Brandenburg, Brandenburg, Germany
| | - Jens Bedke
- Department of Urology, Eberhard Karls University, Tübingen, Germany
| | - Alf Giese
- Department of Neurosurgery, Johannes Gutenberg University, Mainz, Germany
| | - Veit Rohde
- Department of Neurosurgery, Georg August University, Göttingen, Germany
| | - Wolfgang Brück
- Department of Neuropathology, Georg August University, Göttingen, Germany
| | - Laszlo Füzesi
- Department of Gastroenteropathology, Georg August University, Göttingen, Germany
| | - Bjoern Sander
- Stereology and Electron Microscopy Laboratory, Department of Clinical Medicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
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Dugay F, Le Goff X, Rioux-Leclerq N, Chesnel F, Jouan F, Henry C, Cabillic F, Verhoest G, Vigneau C, Arlot-Bonnemains Y, Belaud-Rotureau MA. Overexpression of the polarity protein PAR-3 in clear cell renal cell carcinoma is associated with poor prognosis. Int J Cancer 2014; 134:2051-60. [PMID: 24136590 DOI: 10.1002/ijc.28548] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 10/10/2013] [Indexed: 01/09/2023]
Abstract
The partition-defective 3 (PAR-3) protein is implicated in the development and maintenance of cell polarity and is associated with proteins that mediate the changes in cytoskeleton organization required for cell polarity establishment. In this work, we used two original primary cell lines (R-180 and R-305) derived from clear cell Renal Cell Carcinoma (ccRCC) surgical specimens of a patient with unfavorable clinical course (R-180 cells) and a patient with favorable prognosis (R-305 cells) to identify genetic and molecular features that may explain the survival difference of the two patients. The cytogenetic analysis of these cell lines revealed that the PARD3 gene was amplified only in the R-180 cell line that was derived from an aggressive ccRCC. PARD3 gene amplification was associated with overexpression of the encoded protein and altered cytoskeleton organization. Consistently, PARD3 knockdown in R-180 cells restored the cytoskeleton organization and reduced cell migration in comparison to non-transfected cells. Immunohistochemical analysis of ccRCC samples from a cohort of 96 patients with a follow-up of 6 years revealed that PAR-3 overexpression was correlated with poor survival. Our results suggest that PAR-3 has a role in the clinical aggressiveness of ccRCC, possibly by promoting cell migration.
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Dugay F, Dagher J, Verhoest G, Henry C, Jaillard S, Arlot-Bonnemains Y, Bensalah K, Vigneau C, Rioux-Leclercq N, Belaud-Rotureau MA. [Cytogenetics profiles of renal carcinoma]. Morphologie 2014; 98:1-7. [PMID: 24656859 DOI: 10.1016/j.morpho.2014.02.006] [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: 02/04/2013] [Accepted: 02/12/2014] [Indexed: 11/29/2022]
Abstract
Renal carcinomas are histologically and prognostically heterogeneous. Genomic as well as chromosomal studies of these tumors have permitted a better comprehension of molecular mechanisms implicated in their development and progression. The most frequent histological subtypes are characterized by recurrent cytogenetic abnormalities, such as the loss of the chromosome 3 short arm involving a VHL gene copy in clear cell renal carcinomas, or trisomies 7 and 17 in papillary renal cell carcinomas. New histological subtypes like renal carcinomas associated with Xp11.2 translocations have also been individualized. Besides diagnosis, some chromosomal aberrations like the loss of a short arm of chromosome 9 in different renal carcinoma histological subtypes have a worse prognostic impact. The identification of chromosomal shuffles contributes in backing histological diagnosis and in precising the individual prognosis of patients. This review describes chromosomal abnormalities associated to renal carcinomas and their impact for an accurate classification of these tumors and the evaluation of their prognosis.
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Affiliation(s)
- F Dugay
- Service de cytogénétique et biologie cellulaire, hôpital Pontchaillou, CHU de Rennes, 2, rue Henri-Le-Guilloux, 35033 Rennes cedex, France; UMR 6290 IGDR, cancer du rein-BIOSIT, faculté de médecine-Rennes, 35000 Rennes, France
| | - J Dagher
- Service d'anatomie et cytologie pathologiques, CHU de Rennes, 35000 Rennes, France; UMR 6290 IGDR, cancer du rein-BIOSIT, faculté de médecine-Rennes, 35000 Rennes, France
| | - G Verhoest
- Service d'urologie, CHU de Rennes, 35000 Rennes, France; UMR 6290 IGDR, cancer du rein-BIOSIT, faculté de médecine-Rennes, 35000 Rennes, France
| | - C Henry
- Service de cytogénétique et biologie cellulaire, hôpital Pontchaillou, CHU de Rennes, 2, rue Henri-Le-Guilloux, 35033 Rennes cedex, France
| | - S Jaillard
- Service de cytogénétique et biologie cellulaire, hôpital Pontchaillou, CHU de Rennes, 2, rue Henri-Le-Guilloux, 35033 Rennes cedex, France
| | - Y Arlot-Bonnemains
- UMR 6290 IGDR, cancer du rein-BIOSIT, faculté de médecine-Rennes, 35000 Rennes, France
| | - K Bensalah
- Service d'urologie, CHU de Rennes, 35000 Rennes, France
| | - C Vigneau
- Service de néphrologie, CHU de Rennes, 35000 Rennes, France; UMR 6290 IGDR, cancer du rein-BIOSIT, faculté de médecine-Rennes, 35000 Rennes, France
| | - N Rioux-Leclercq
- Service d'anatomie et cytologie pathologiques, CHU de Rennes, 35000 Rennes, France; UMR 6290 IGDR, cancer du rein-BIOSIT, faculté de médecine-Rennes, 35000 Rennes, France
| | - M-A Belaud-Rotureau
- Service de cytogénétique et biologie cellulaire, hôpital Pontchaillou, CHU de Rennes, 2, rue Henri-Le-Guilloux, 35033 Rennes cedex, France; UMR 6290 IGDR, cancer du rein-BIOSIT, faculté de médecine-Rennes, 35000 Rennes, France.
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Hypertension-related, calcium-regulated gene (HCaRG/COMMD5) and kidney diseases: HCaRG accelerates tubular repair. J Nephrol 2014; 27:351-60. [PMID: 24515317 PMCID: PMC4104007 DOI: 10.1007/s40620-014-0054-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 11/21/2013] [Indexed: 12/22/2022]
Abstract
Hypertension is a risk factor for renal impairment. While treatment of hypertension provides significant renal protection, there is still an unmet need requiring further exploration of additional pathogenetic mechanisms. We have found that the hypertension-related, calcium-regulated gene (HCaRG/COMMD5) is involved in renal repair. HCaRG is a small intracellular protein of 225 amino acids and its gene expression is negatively regulated by extracellular calcium concentrations. HCaRG is mostly expressed in the kidneys, with higher levels found in the spontaneously hypertensive rat than in normotensive rats. In an acute kidney injury model, HCaRG expression decreases immediately after injury but increases above baseline during the repair phase. In cell cultures, HCaRG has been shown to facilitate differentiation and to inhibit cell proliferation via p21 transactivation through the p53-independent signaling pathway. Induction of p21 independently of p53 is also observed in transgenic mice overexpressing HCaRG during the repair phase after ischemia/reperfusion injury, resulting in their improved renal function and survival with rapid re-differentiation of proximal tubular epithelial cells. In addition, transgenic mice recover rapidly from the inflammatory burst most likely as a result of maintenance of the tubular epithelial barrier. Recent studies indicate that facilitating re-differentiation and cell cycle regulation in injured renal proximal tubules might be important functions of HCaRG. We have proposed that HCaRG is a component of differential genetic susceptibility to renal impairment in response to hypertension.
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Abstract
Currently approved treatments for metastatic renal cell carcinoma (RCC) include vascular endothelial growth factor (VEGF)-blocking agents, mammalian target of rapamycin (mTOR) inhibitors, and cytokine therapy. In the near future, we are likely to add immune checkpoint blocking agents to this list. As we develop treatment platforms around each therapeutic class, determining which drug is best for a particular patient becomes increasingly important. At this point, we do not have validated predictive biomarkers for patients with RCC. Here, we discuss the logistical challenges surrounding biomarker development, summarize the current crop of biomarker candidates, and explore potential avenues for the development of more effective predictive tools for patients with advanced RCC.
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Affiliation(s)
- Jesus Garcia-Donas
- Genitourinary Tumors Programme Centro Integral Oncologico Clara Campal CIOCC, Madrid, Spain
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Histologic prognostic factors associated with chromosomal imbalances in a contemporary series of 89 clear cell renal cell carcinomas. Hum Pathol 2013; 44:2106-15. [PMID: 23806527 DOI: 10.1016/j.humpath.2013.03.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 11/21/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cancer. The aim of this study was to define specific chromosomal imbalances in ccRCC that could be related to clinical or histologic prognostic factors. Tumors and karyotypes of 89 patients who underwent nephrectomy for ccRCC were analyzed from April 2009 to July 2012. The mean number of chromosomal aberrations was significantly higher (7.8; P < .05) in Fuhrman grade 4 (F4) than in F3 (4) and F2 (3.4) cases. The results were similar, considering separately the mean number of chromosomal losses and gains. The F4 cases had a distinct pattern with more frequent losses of chromosomes 9, 13, 14, 18, 21, 22, and Y and gains of chromosome 20. Necrosis was associated with losses of chromosomes 7, 9, 18, and 22; sarcomatoid component, losses of chromosomes 7, 9, and 14 and gains of 20; and T stage, losses of chromosomes 18 and Y. After multivariate analysis, renal fat invasion, renal vein emboli, and microscopic vascular invasion were, respectively, associated with losses of chromosomes 13 and Y, loss of chromosome 13, and loss of chromosome 14 and gains of chromosomes 7 and 20. F4 was independently associated with losses of chromosomes 9 and Y; sarcomatoid component, loss of chromosome 9 and gain of 20; necrosis, loss of chromosome 18; and T stage, loss of chromosome Y. These chromosomal imbalances can be detected routinely by karyotype or fluorescence in situ hybridization analyses to stratify patients for risk of progression.
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Kroeger N, Klatte T, Chamie K, Rao PN, Birkhäuser FD, Sonn GA, Riss J, Kabbinavar FF, Belldegrun AS, Pantuck AJ. Deletions of chromosomes 3p and 14q molecularly subclassify clear cell renal cell carcinoma. Cancer 2013; 119:1547-54. [PMID: 23335244 DOI: 10.1002/cncr.27947] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 12/05/2012] [Accepted: 12/10/2012] [Indexed: 11/08/2022]
Abstract
BACKGROUND The short arm of chromosome 3 (3p) harbors the von Hippel-Lindau (VHL) tumor suppressor gene, and the long arm of chromosome 14 (14q) harbors the hypoxia-inducible factor 1α (HIF-1α) gene. The objective of this study was to evaluate the significance of 3p loss (loss VHL gene) and 14q loss (loss HIF-1α gene) in clear cell renal cell carcinoma (ccRCC). METHODS In total, 288 ccRCC tumors underwent a prospective cytogenetic analysis for alterations in chromosomes 3p and 14q. Tumors were assigned to 1 of 4 possible chromosomal alterations: VHL +3p/+14q (VHL wild type [VHL-WT]), VHL +3p/-14q (VHL-WT plus HIF2α [WT/H2]), -3p/+14q (HIF1α and HIF2α [H1H2]), and -3p/-14q (HIF2α [H2]). RESULTS Among patients who had loss of 3p, tumors with -3p/-14q (H2) alterations were larger (P = .002), had higher grade (P = .002) and stage (P = .001), and more often were metastatic (P = .029) than tumors that retained 14q (H1H2). All patients who had tumors with -3p/-14q (H2) had worse cancer-specific survival (P = .014), and patients who had localized disease (P = .012) and primary T1 (pT1) tumors (P = .008) had worse recurrence-free survival. In patients who had pT1 tumors, combined 3p/14q loss was an independent predictor of recurrence-free survival (hazard ratio, 11.19; 95% confidence interval, 1.91-65.63) and cancer-specific survival (hazard ratio, 15.93; 95% confidence interval, 3.09-82.16). The current investigation was limited by its retrospective design, single-center experience, and a lack of confirmatory protein analyses. CONCLUSIONS Loss of chromosome 3p (the VHL gene) was associated with improved survival in patients with ccRCC, whereas loss of chromosome 14q (the HIF-1α gene) was associated with worse outcomes. The results of the current study support the hypothesis that HIF-1α functions as an important tumor suppressor gene in ccRCC.
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Affiliation(s)
- Nils Kroeger
- Institute of Urologic Oncology, Department of Urology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California, USA
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