1
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Perotti D, Williams RD, Wegert J, Brzezinski J, Maschietto M, Ciceri S, Gisselsson D, Gadd S, Walz AL, Furtwaengler R, Drost J, Al-Saadi R, Evageliou N, Gooskens SL, Hong AL, Murphy AJ, Ortiz MV, O'Sullivan MJ, Mullen EA, van den Heuvel-Eibrink MM, Fernandez CV, Graf N, Grundy PE, Geller JI, Dome JS, Perlman EJ, Gessler M, Huff V, Pritchard-Jones K. Hallmark discoveries in the biology of Wilms tumour. Nat Rev Urol 2024; 21:158-180. [PMID: 37848532 DOI: 10.1038/s41585-023-00824-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2023] [Indexed: 10/19/2023]
Abstract
The modern study of Wilms tumour was prompted nearly 50 years ago, when Alfred Knudson proposed the 'two-hit' model of tumour development. Since then, the efforts of researchers worldwide have substantially expanded our knowledge of Wilms tumour biology, including major advances in genetics - from cloning the first Wilms tumour gene to high-throughput studies that have revealed the genetic landscape of this tumour. These discoveries improve understanding of the embryonal origin of Wilms tumour, familial occurrences and associated syndromic conditions. Many efforts have been made to find and clinically apply prognostic biomarkers to Wilms tumour, for which outcomes are generally favourable, but treatment of some affected individuals remains challenging. Challenges are also posed by the intratumoural heterogeneity of biomarkers. Furthermore, preclinical models of Wilms tumour, from cell lines to organoid cultures, have evolved. Despite these many achievements, much still remains to be discovered: further molecular understanding of relapse in Wilms tumour and of the multiple origins of bilateral Wilms tumour are two examples of areas under active investigation. International collaboration, especially when large tumour series are required to obtain robust data, will help to answer some of the remaining unresolved questions.
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Affiliation(s)
- Daniela Perotti
- Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
| | - Richard D Williams
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Section of Genetics and Genomics, Faculty of Medicine, Imperial College London, London, UK
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, Wuerzburg, Germany
| | - Jack Brzezinski
- Division of Haematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Mariana Maschietto
- Research Center, Boldrini Children's Hospital, Campinas, São Paulo, Brazil
| | - Sara Ciceri
- Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - David Gisselsson
- Cancer Cell Evolution Unit, Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Skåne, Sweden
| | - Samantha Gadd
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Amy L Walz
- Division of Hematology,Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Rhoikos Furtwaengler
- Division of Pediatric Oncology and Hematology, Department of Pediatrics, Inselspital Bern University, Bern, Switzerland
| | - Jarno Drost
- Princess Máxima Center for Paediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Reem Al-Saadi
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Histopathology, Great Ormond Street Hospital for Children, London, UK
| | - Nicholas Evageliou
- Divisions of Hematology and Oncology, Children's Hospital of Philadelphia, CHOP Specialty Care Center, Vorhees, NJ, USA
| | - Saskia L Gooskens
- Princess Máxima Center for Paediatric Oncology, Utrecht, Netherlands
| | - Andrew L Hong
- Aflac Cancer and Blood Disorders Center, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Andrew J Murphy
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael V Ortiz
- Department of Paediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maureen J O'Sullivan
- Histology Laboratory, Children's Health Ireland at Crumlin, Dublin, Ireland
- Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - Elizabeth A Mullen
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | | | - Conrad V Fernandez
- Division of Paediatric Hematology Oncology, IWK Health Centre and Dalhousie University, Halifax, Nova Scotia, Canada
| | - Norbert Graf
- Department of Paediatric Oncology and Hematology, Saarland University Hospital, Homburg, Germany
| | - Paul E Grundy
- Department of Paediatrics Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - James I Geller
- Division of Oncology, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Jeffrey S Dome
- Division of Oncology, Center for Cancer and Blood Disorders, Children's National Hospital and the Department of Paediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Elizabeth J Perlman
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, Wuerzburg, Germany
- Comprehensive Cancer Center Mainfranken, Wuerzburg, Germany
| | - Vicki Huff
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathy Pritchard-Jones
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
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2
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Morton AR, Dogan-Artun N, Faber ZJ, MacLeod G, Bartels CF, Piazza MS, Allan KC, Mack SC, Wang X, Gimple RC, Wu Q, Rubin BP, Shetty S, Angers S, Dirks PB, Sallari RC, Lupien M, Rich JN, Scacheri PC. Functional Enhancers Shape Extrachromosomal Oncogene Amplifications. Cell 2019; 179:1330-1341.e13. [PMID: 31761532 DOI: 10.1016/j.cell.2019.10.039] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 09/20/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Non-coding regions amplified beyond oncogene borders have largely been ignored. Using a computational approach, we find signatures of significant co-amplification of non-coding DNA beyond the boundaries of amplified oncogenes across five cancer types. In glioblastoma, EGFR is preferentially co-amplified with its two endogenous enhancer elements active in the cell type of origin. These regulatory elements, their contacts, and their contribution to cell fitness are preserved on high-level circular extrachromosomal DNA amplifications. Interrogating the locus with a CRISPR interference screening approach reveals a diversity of additional elements that impact cell fitness. The pattern of fitness dependencies mirrors the rearrangement of regulatory elements and accompanying rewiring of the chromatin topology on the extrachromosomal amplicon. Our studies indicate that oncogene amplifications are shaped by regulatory dependencies in the non-coding genome.
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Affiliation(s)
- Andrew R Morton
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Nergiz Dogan-Artun
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Zachary J Faber
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Graham MacLeod
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Megan S Piazza
- Center for Human Genetics Laboratory, University Hospitals, Cleveland, OH 44106, USA
| | - Kevin C Allan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Stephen C Mack
- Department of Pediatrics, Division of Hematology and Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA
| | - Xiuxing Wang
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ryan C Gimple
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH 44120, USA
| | - Qiulian Wu
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Brian P Rubin
- Departments of Anatomic Pathology and Molecular Genetics, Cleveland Clinic, Lerner Research Institute and Taussig Cancer Center, Cleveland, OH 44195, USA
| | - Shashirekha Shetty
- Center for Human Genetics Laboratory, University Hospitals, Cleveland, OH 44106, USA
| | - Stephane Angers
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Peter B Dirks
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | | | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeremy N Rich
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92037, USA.
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA.
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3
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Correlations between Histological and Array Comparative Genomic Hybridization Characterizations of Wilms Tumor. Pathol Oncol Res 2019; 25:1199-1206. [DOI: 10.1007/s12253-019-00601-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/15/2019] [Indexed: 12/25/2022]
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Biological Drivers of Wilms Tumor Prognosis and Treatment. CHILDREN-BASEL 2018; 5:children5110145. [PMID: 30373137 PMCID: PMC6262554 DOI: 10.3390/children5110145] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/16/2018] [Accepted: 10/18/2018] [Indexed: 12/11/2022]
Abstract
Prior to the 1950s, survival from Wilms tumor (WT) was less than 10%. Today, a child diagnosed with WT has a greater than 90% chance of survival. These gains in survival rates from WT are attributed largely to improvements in multimodal therapy: Enhanced surgical techniques leading to decreased operative mortality, optimization of more effective chemotherapy regimens (specifically, dactinomycin and vincristine), and inclusion of radiation therapy in treatment protocols. More recent improvements in survival, however, can be attributed to a growing understanding of the molecular landscape of Wilms tumor. Particularly, identification of biologic markers portending poor prognosis has facilitated risk stratification to tailor therapy that achieves the best possible outcome with the least possible toxicity. The aim of this review is to (1) outline the specific biologic markers that have been associated with prognosis in WT and (2) provide an overview of the current use of biologic and other factors to stratify risk and assign treatment accordingly.
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5
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Ciceri S, Gamba B, Corbetta P, Mondini P, Terenziani M, Catania S, Nantron M, Bianchi M, D'Angelo P, Torri F, Macciardi F, Collini P, Di Martino M, Melchionda F, Di Cataldo A, Spreafico F, Radice P, Perotti D. Genetic and epigenetic analyses guided by high resolution whole-genome SNP array reveals a possible role of CHEK2 in Wilms tumour susceptibility. Oncotarget 2018; 9:34079-34089. [PMID: 30344923 PMCID: PMC6183341 DOI: 10.18632/oncotarget.26123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/01/2018] [Indexed: 01/25/2023] Open
Abstract
Wilms tumour (WT), the most frequent malignant childhood renal tumour, shows a high degree of genetic and epigenetic heterogeneity. Loss of imprinting on chromosome 11p15 is found in a large fraction of cases and mutations in a few genes, including WT1, CTNNB1, WTX, TP53 and, more recently, SIX1, SIX2 and micro RNA processing genes (miRNAPGs), have been observed. However, these alterations are not sufficient to describe the entire spectrum of genetic defects underlying WT development. We inspected data obtained from a previously performed genome-wide single nucleotide polymorphism (SNP) array analysis on 96 WT samples. By selecting focal regions commonly involved in chromosomal anomalies, we identified genes with a possible role in WT development, based on the prior knowledge of their biological relevance, including MYCN, DIS3L2, MIR562, HACE1, GLI3, CDKN2A and CDKN2B, PALB2, and CHEK2. The MYCN hotspot mutation c.131C>T was detected in seven cases (7.3%). Full sequencing of the remaining genes disclosed 16 rare missense variants and a splicing mutation. Most of these were present at the germline level. Promoter analysis of HACE1, CDKN2A and CDKN2B disclosed partial methylation affecting HACE1 in a consistent fraction of cases (85%). Interestingly, of the four missense variants identified in CHEK2, three were predicted to be deleterious by in silico analyses, while an additional variant was observed to alter mRNA splicing, generating a functionally defective protein. Our study adds additional information on putative WT genes, and adds evidences involving CHEK2 in WT susceptibility.
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Affiliation(s)
- Sara Ciceri
- Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Beatrice Gamba
- Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Paola Corbetta
- Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Patrizia Mondini
- Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Monica Terenziani
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Serena Catania
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Marilina Nantron
- Department of Hematology and Oncology, Istituto G. Gaslini, Genova, Italy
| | - Maurizio Bianchi
- Pediatric Onco-Hematology, Stem Cell Transplantation and Cellular Therapy Division, Regina Margherita Children's Hospital, Torino, Italy
| | - Paolo D'Angelo
- Pediatric Oncology Unit, A.R.N.A.S. Ospedali Civico, Di Cristina e Benfratelli, Palermo, Italy
| | - Federica Torri
- Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA
| | - Paola Collini
- Soft Tissue and Bone Pathology, Histopathology, and Pediatric Pathology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Martina Di Martino
- Pediatric Oncology Unit, Pediatric Department, II University, Naples, Italy
| | - Fraia Melchionda
- Pediatric Hematology and Oncology Unit, Bologna University, Bologna, Italy
| | - Andrea Di Cataldo
- Pediatric Hematology and Oncology Unit, Catania University, Catania, Italy
| | - Filippo Spreafico
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Paolo Radice
- Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Daniela Perotti
- Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
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Micale MA, Embrey B, Macknis JK, Harper CE, Aughton DJ. Constitutional 560.49 kb chromosome 2p24.3 duplication including the MYCN gene identified by SNP chromosome microarray analysis in a child with multiple congenital anomalies and bilateral Wilms tumor. Eur J Med Genet 2016; 59:618-623. [DOI: 10.1016/j.ejmg.2016.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/20/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022]
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7
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Deng C, Dai R, Li X, Liu F. Genetic variation frequencies in Wilms' tumor: A meta-analysis and systematic review. Cancer Sci 2016; 107:690-9. [PMID: 26892980 PMCID: PMC4970837 DOI: 10.1111/cas.12910] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 12/11/2022] Open
Abstract
Over the last few decades, numerous biomarkers in Wilms' tumor have been confirmed and shown variations in prevalence. Most of these studies were based on small sample sizes. We carried out a meta-analysis of the research published from 1992 to 2015 to obtain more precise and comprehensive outcomes for genetic tests. In the present study, 70 out of 5175 published reports were eligible for the meta-analysis, which was carried out using Stata 12.0 software. Pooled prevalence for gene mutations WT1, WTX, CTNNB1, TP53, MYCN, DROSHA, and DGCR8 was 0.141 (0.104, 0.178), 0.147 (0.110, 0.184), 0.140 (0.100, 0.190), 0.410 (0.214, 0.605), 0.071 (0.041, 0.100), 0.082 (0.048, 0.116), and 0.036 (0.026, 0.046), respectively. Pooled prevalence of loss of heterozygosity at 1p, 11p, 11q, 16q, and 22q was 0.109 (0.084, 0.133), 0.334 (0.295, 0.373), 0.199 (0.146, 0.252), 0.151 (0.129, 0.172), and 0.148 (0.108, 0.189), respectively. Pooled prevalence of 1q and chromosome 12 gain was 0.218 (0.161, 0.275) and 0.273 (0.195, 0.350), respectively. The limited prevalence of currently known genetic alterations in Wilms' tumors indicates that significant drivers of initiation and progression remain to be discovered. Subgroup analyses indicated that ethnicity may be one of the sources of heterogeneity. However, in meta-regression analyses, no study-level characteristics of indicators were found to be significant. In addition, the findings of our sensitivity analysis and possible publication bias remind us to interpret results with caution.
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Affiliation(s)
- Changkai Deng
- Department of Urology Surgery, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorder, Key Laboratory of Pediatrics in Chongqing (CSTC2009CA5002), Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China.,Chengdu Women and Children's Central Hospital, Chengdu, China
| | - Rong Dai
- Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Xuliang Li
- Department of Urology Surgery, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorder, Key Laboratory of Pediatrics in Chongqing (CSTC2009CA5002), Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
| | - Feng Liu
- Department of Urology Surgery, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorder, Key Laboratory of Pediatrics in Chongqing (CSTC2009CA5002), Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
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8
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Lovvorn HN, Pierce J, Libes J, Li B, Wei Q, Correa H, Gouffon J, Clark PE, Axt JR, Hansen E, Newton M, O'Neill JA. Genetic and chromosomal alterations in Kenyan Wilms Tumor. Genes Chromosomes Cancer 2015; 54:702-15. [PMID: 26274016 PMCID: PMC4567398 DOI: 10.1002/gcc.22281] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/08/2015] [Accepted: 06/08/2015] [Indexed: 12/31/2022] Open
Abstract
Wilms tumor (WT) is the most common childhood kidney cancer worldwide and poses a cancer health disparity to black children of sub-Saharan African ancestry. Although overall survival from WT at 5 years exceeds 90% in developed countries, this pediatric cancer is alarmingly lethal in sub-Saharan Africa and specifically in Kenya (36% survival at 2 years). Although multiple barriers to adequate WT therapy contribute to this dismal outcome, we hypothesized that a uniquely aggressive and treatment-resistant biology compromises survival further. To explore the biologic composition of Kenyan WT (KWT), we completed a next generation sequencing analysis targeting 10 WT-associated genes and evaluated whole-genome copy number variation. The study cohort was comprised of 44 KWT patients and their specimens. Fourteen children are confirmed dead at 2 years and 11 remain lost to follow-up despite multiple tracing attempts. TP53 was mutated most commonly in 11 KWT specimens (25%), CTNNB1 in 10 (23%), MYCN in 8 (18%), AMER1 in 5 (11%), WT1 and TOP2A in 4 (9%), and IGF2 in 3 (7%). Loss of heterozygosity (LOH) at 17p, which covers TP53, was detected in 18% of specimens examined. Copy number gain at 1q, a poor prognostic indicator of WT biology in developed countries, was detected in 32% of KWT analyzed, and 89% of these children are deceased. Similarly, LOH at 11q was detected in 32% of KWT, and 80% of these patients are deceased. From this genomic analysis, KWT biology appears uniquely aggressive and treatment-resistant.
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Affiliation(s)
- Harold N Lovvorn
- Department of Pediatric Surgery, Vanderbilt University School of Medicine, Nashville, TN
| | - Janene Pierce
- Department of Pediatric Surgery, Vanderbilt University School of Medicine, Nashville, TN
| | - Jaime Libes
- Department of Pediatrics, University of Illinois College of Medicine, Peoria, IL.,Division of Hematology/Oncology, University of Illinois College of Medicine, Peoria, IL
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Qiang Wei
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Hernan Correa
- Division of Pediatric Pathology, Vanderbilt University School of Medicine, Nashville, TN
| | | | - Peter E Clark
- Department of Urologic Surgery, Vanderbilt University School of Medicine, Nashville, TN
| | - Jason R Axt
- Department of Pediatric Surgery, Vanderbilt University School of Medicine, Nashville, TN
| | - Erik Hansen
- Department of Pediatric Surgery, Vanderbilt University School of Medicine, Nashville, TN
| | - Mark Newton
- Division of Pediatric Anesthesia, Vanderbilt University School of Medicine, Nashville, TN
| | - James A O'Neill
- Department of Pediatric Surgery, Vanderbilt University School of Medicine, Nashville, TN
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9
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Singh N, Sahu DK, Goel M, Kant R, Gupta DK. Retrospective analysis of FFPE based Wilms' Tumor samples through copy number and somatic mutation related Molecular Inversion Probe Based Array. Gene 2015; 565:295-308. [PMID: 25913740 DOI: 10.1016/j.gene.2015.04.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 04/13/2015] [Accepted: 04/20/2015] [Indexed: 01/18/2023]
Abstract
In this report, retrospectively, we analyzed fifteen histo-pathologically characterized FFPE based Wilms' Tumor (WT) samples following an integrative approach of copy number (CN) and loss of heterozygosity (LOH) imbalances. The isolated-DNA was tested on CN and somatic-mutation related Molecular-Inversion-Probe based-Oncoscan Array™ and was analyzed through Nexus-Express OncoScan-3.0 and 7.0 software. We identified gain of 3p13.0-q29, 4p16.3-14.0, 7, 12p13.33-q24.33, and losses of 1p36.11-q44, 11p15.5-q25, 21q 22.2-22.3 and 22q11.21-13.2 in six samples (W1-6) and validated them in nine more samples (W7-9, W12-15, W17-18). Some observed that discrete deletions (1p, 1q, 10p, 10q, 13q, 20p) were specific to our samples. Maximum-LOH was observed in Ch11 as reported in previous studies. However, LOH was also observed in different regions of Ch7 including some cancer genes. The identified LOH-regions (1q21.2-q21.3, 2p24.1-23.3, 2p24.3-24.3, 3p21.3-21.1, 4p16.3, 7p11.2-p11.1, 7q31.2-31.32, 7q34-q35 and Ch 8) in W1-W6 were also validated in W7-9, W12-15 and W18. In addition, previously reported LOH of 1p and 16q region was also observed in our cases. The proven and novel onco (OG)- and tumor-suppressor genes (TSGs) involved in the CNV regions affected the major pathways like Chromatin Modification, RAS, PI3K; RAS in 14/15 cases, NOTCH/TGF-β and Cell Cycle Apoptosis in 10/15 cases, APC in 9/15 cases and Transcriptional Regulation in 7/15 cases, PI3K and genome maintenance in 6/15 cases. This exhaustive profiling of OG and TG may help in prognosis and diagnosis of the disease after validation of all the relevant results, especially the novel ones, obtained in this research in a larger number of samples.
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Affiliation(s)
- Neetu Singh
- Advanced Molecular Science Research Center (Center for Advanced Research), King George's Medical University, Lucknow 226 003, India.
| | - Dinesh K Sahu
- Imperial Life Sciences, 463 Phase City 2nd, Sector 37, Gurgaon, Haryana 122001, India
| | - Madhumati Goel
- Department of Pathology, King George's Medical University, Lucknow 226 003, India
| | - Ravi Kant
- Department of Surgical Oncology, King George's Medical University, Lucknow, Uttar Pradesh, India226 003
| | - Devendra K Gupta
- Department of Pediatric Surgery, All India Institute of Medical Sciences, New Delhi 110029, India
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10
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Williams RD, Chagtai T, Alcaide-German M, Apps J, Wegert J, Popov S, Vujanic G, van Tinteren H, van den Heuvel-Eibrink MM, Kool M, de Kraker J, Gisselsson D, Graf N, Gessler M, Pritchard-Jones K. Multiple mechanisms of MYCN dysregulation in Wilms tumour. Oncotarget 2015; 6:7232-43. [PMID: 25749049 PMCID: PMC4466681 DOI: 10.18632/oncotarget.3377] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/14/2015] [Indexed: 12/20/2022] Open
Abstract
Genomic gain of the proto-oncogene transcription factor gene MYCN is associated with poor prognosis in several childhood cancers. Here we present a comprehensive copy number analysis of MYCN in Wilms tumour (WT), demonstrating that gain of this gene is associated with anaplasia and with poorer relapse-free and overall survival, independent of histology. Using whole exome and gene-specific sequencing, together with methylation and expression profiling, we show that MYCN is targeted by other mechanisms, including a recurrent somatic mutation, P44L, and specific DNA hypomethylation events associated with MYCN overexpression in tumours with high risk histologies. We describe parallel evolution of genomic copy number gain and point mutation of MYCN in the contralateral tumours of a remarkable bilateral case in which independent contralateral mutations of TP53 also evolve over time. We report a second bilateral case in which MYCN gain is a germline aberration. Our results suggest a significant role for MYCN dysregulation in the molecular biology of Wilms tumour. We conclude that MYCN gain is prognostically significant, and suggest that the novel P44L somatic variant is likely to be an activating mutation.
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Affiliation(s)
| | | | | | - John Apps
- UCL Institute of Child Health, London, UK
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry and Comprehensive Cancer Center Mainfranken, Wuerzburg University, Wuerzburg, Germany
| | - Sergey Popov
- Institute of Cancer Research, Sutton, Surrey, UK
| | - Gordan Vujanic
- Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Harm van Tinteren
- Biometrics Department, Netherlands Cancer Institute, Antonie van Leeuwenhoek Ziekenhuis, Amsterdam, The Netherlands
| | | | - Marcel Kool
- German Cancer Research Centre, Heidelberg, Germany
| | | | | | - Norbert Graf
- Department of Paediatric Oncology and Haematology, Saarland University Hospital, Homburg/Saar, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry and Comprehensive Cancer Center Mainfranken, Wuerzburg University, Wuerzburg, Germany
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11
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Comparative genomic hybridization of Wilms' tumor. Methods Mol Biol 2013; 973:249-65. [PMID: 23412795 DOI: 10.1007/978-1-62703-281-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Cytogenetic analysis of solid tumors including Wilms' tumor is challenging due to poor chromosome morphology, complexity of abnormalities, and to the possibility of stromal cell overgrowth in tissue culture. Molecular cytogenetic techniques such as chromosomal comparative genomic hybridization (CGH) have improved the diagnosis of chromosomal aberrations in Wilms' tumor since they can provide results based on the analysis of DNA from nondividing cells. However, chromosomal CGH provides only a limited resolution across the whole genome, which is not different than routine cytogenetic analysis (gains or losses of less than one chromosome band or 10 Mb are not detectable by routine cytogenetics or chromosomal CGH). More recently, the development of genomic arrays opened the possibility of assessing the whole genome at a much higher resolution at a sub-microscopic or sub-band level. Based on the principle of chromosomal CGH, this approach, frequently termed array-CGH, opens the possibility to find invisible changes at the whole genome level not only in abnormal but also in normal tumor karyotypes. Here, we discuss the main technical features, benefits, and limitations of the above three techniques as applied to Wilms' tumor and summarize the main advances in our knowledge about the genetic changes of Wilms' tumor and their clinical relevance.
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12
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Turnbull C, Perdeaux E, Pernet D, Naranjo A, Renwick A, Seal S, Xicola RMM, Hanks S, Slade I, Zachariou A, Warren-Perry M, Ruark E, Gerrard M, Hale J, Hewitt M, Kohler J, Lane S, Levitt G, Madi M, Morland B, Neefjes V, Nicholdson J, Picton S, Pizer B, Ronghe M, Stevens M, Traunecker H, Stiller CA, Pritchard-Jones K, Dome J, Grundy P, Rahman N. A genome-wide association study identifies susceptibility loci for Wilms tumor. Nat Genet 2012; 44:681-4. [PMID: 22544364 PMCID: PMC3400150 DOI: 10.1038/ng.2251] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 03/19/2012] [Indexed: 12/28/2022]
Abstract
Wilms tumor is the most common renal malignancy of childhood. To identify common variants that confer susceptibility to Wilms tumor, we conducted a genome-wide association study in 757 individuals with Wilms tumor (cases) and 1,879 controls. We evaluated ten SNPs in regions significantly associated at P < 5 × 10(-5) in two independent replication series from the UK (769 cases and 2,814 controls) and the United States (719 cases and 1,037 controls). We identified clear significant associations at 2p24 (rs3755132, P = 1.03 × 10(-14); rs807624, P = 1.32 × 10(-14)) and 11q14 (rs790356, P = 4.25 × 10(-15)). Both regions contain genes that are plausibly related to Wilms tumorigenesis. We also identified candidate association signals at 5q14, 22q12 and Xp22.
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Affiliation(s)
- Clare Turnbull
- Division of Genetics & Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Elizabeth Perdeaux
- Division of Genetics & Epidemiology, Institute of Cancer Research, Sutton, UK
| | - David Pernet
- Division of Genetics & Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Arlene Naranjo
- Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, USA
| | - Anthony Renwick
- Division of Genetics & Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology, Institute of Cancer Research, Sutton, UK
| | | | - Sandra Hanks
- Division of Genetics & Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Ingrid Slade
- Division of Genetics & Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Anna Zachariou
- Division of Genetics & Epidemiology, Institute of Cancer Research, Sutton, UK
| | | | - Elise Ruark
- Division of Genetics & Epidemiology, Institute of Cancer Research, Sutton, UK
| | | | - Juliet Hale
- Department of Paediatric Oncology, Royal Victoria Infirmary, Newcastle, UK
| | - Martin Hewitt
- Department of Paediatric Oncology, University Hospital Nottingham, Nottingham, UK
| | - Janice Kohler
- Regional Paediatric Oncology Centre. Southampton General Hospital, Southampton, UK
| | - Sheila Lane
- Department of Paediatric Oncology, Oxford Children's Hospital, John Radcliffe Hospital, Oxford, UK
| | - Gill Levitt
- Department of Paediatric Oncology, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Mabrook Madi
- Department of Paediatric Oncology, Leicester Royal Infirmary, Leicester, UK
| | - Bruce Morland
- Department of Paediatric Oncology, Birmingham Children's Hospital, Birmingham, UK
| | - Veronica Neefjes
- Department of Paediatric Oncology, Royal Aberdeen Children's Hospital, Aberdeen, UK
| | - James Nicholdson
- Department of Paediatric Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrookes Hospital, Cambridge, UK
| | - Susan Picton
- Paediatric Oncology Department, Leeds General Infirmary, Leeds, UK
| | - Barry Pizer
- Department of Paediatric Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Milind Ronghe
- Department of Paediatric Oncology, Royal Hospital for Sick Children, Glasgow, UK
| | - Michael Stevens
- Department of Paediatric Oncology, Bristol Royal Hospital for Children, Bristol, UK
| | - Heidi Traunecker
- Paediatric Oncology Unit, Children's Hospital for Wales, Cardiff, UK
| | | | - Kathy Pritchard-Jones
- Molecular Haematology and Cancer Biology Unit, University College London, Institute of Child Health, London, UK
| | - Jeffrey Dome
- Division of Oncology, Children's National Medical Center, Washington D.C., USA
| | - Paul Grundy
- Department of Pediatrics, University of Alberta, Edmonton, Canada
- Department of Oncology, University of Alberta, Edmonton, Canada
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, Institute of Cancer Research, Sutton, UK
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Zin R, Pham K, Ashleigh M, Ravine D, Waring P, Charles A. SNP-based arrays complement classic cytogenetics in the detection of chromosomal aberrations in Wilms’ tumor. Cancer Genet 2012; 205:80-93. [DOI: 10.1016/j.cancergen.2011.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 12/09/2011] [Accepted: 12/16/2011] [Indexed: 12/11/2022]
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Veeck J, Dahl E. Targeting the Wnt pathway in cancer: the emerging role of Dickkopf-3. Biochim Biophys Acta Rev Cancer 2011; 1825:18-28. [PMID: 21982838 DOI: 10.1016/j.bbcan.2011.09.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/16/2011] [Accepted: 09/16/2011] [Indexed: 11/19/2022]
Abstract
Aberrant activation of the Wnt signaling pathway is a major trait of many human cancers. Due to its vast implications in tumorigenesis and progression, the Wnt pathway has attracted considerable attention at several molecular levels, also with respect to developing novel cancer therapeutics. Indeed, research in Wnt biology has recently provided numerous clues, and evidence is accumulating that the secreted Wnt antagonist Dickkopf-related protein 3 (Dkk-3) and its regulators may constitute interesting therapeutic targets in the most important human cancers. Based on the currently available literature, we here review the knowledge on the biological role of Dkk-3 as an antagonist of the Wnt signaling pathway, the involvement of Dkk-3 in several stages of tumor development, the genetic and epigenetic mechanisms disrupting DKK3 gene function in cancerous cells, and the potential clinical value of Dkk-3 expression/DKK3 promoter methylation as a biomarker and molecular target in cancer diseases. In conclusion, Dkk-3 rapidly emerges as a key player in human cancer with auspicious tumor suppressive capacities, most of all affecting apoptosis and proliferation. Its gene expression is frequently downregulated by promoter methylation in almost any solid and hematological tumor entity. Clinically, evidence is accumulating of Dkk-3 being both a potential tumor biomarker and effective anti-cancer agent. Although further research is needed, re-establishing Dkk-3 expression in cancer cells holds promise as novel targeted molecular tumor therapy.
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Affiliation(s)
- Jürgen Veeck
- Division of Medical Oncology, Department of Internal Medicine, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands.
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Williams RD, Al-Saadi R, Natrajan R, Mackay A, Chagtai T, Little S, Hing SN, Fenwick K, Ashworth A, Grundy P, Anderson JR, Dome JS, Perlman EJ, Jones C, Pritchard-Jones K. Molecular profiling reveals frequent gain of MYCN and anaplasia-specific loss of 4q and 14q in Wilms tumor. Genes Chromosomes Cancer 2011; 50:982-95. [PMID: 21882282 DOI: 10.1002/gcc.20907] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 06/22/2011] [Indexed: 11/08/2022] Open
Abstract
Anaplasia in Wilms tumor, a distinctive histology characterized by abnormal mitoses, is associated with poor patient outcome. While anaplastic tumors frequently harbour TP53 mutations, little is otherwise known about their molecular biology. We have used array comparative genomic hybridization (aCGH) and cDNA microarray expression profiling to compare anaplastic and favorable histology Wilms tumors to determine their common and differentiating features. In addition to changes on 17p, consistent with TP53 deletion, recurrent anaplasia-specific genomic loss and under-expression were noted in several other regions, most strikingly 4q and 14q. Further aberrations, including gain of 1q and loss of 16q were common to both histologies. Focal gain of MYCN, initially detected by high resolution aCGH profiling in 6/61 anaplastic samples, was confirmed in a significant proportion of both tumor types by a genomic quantitative PCR survey of over 400 tumors. Overall, these results are consistent with a model where anaplasia, rather than forming an entirely distinct molecular entity, arises from the general continuum of Wilms tumor by the acquisition of additional genomic changes at multiple loci.
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Affiliation(s)
- Richard D Williams
- Molecular Haematology and Cancer Biology Unit, University College London, Institute of Child Health, London, UK
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Abstract
Neonatal renal tumours are rare, with only 7% of all neonatal tumours arising from the kidney. Presentation is usually as a flank mass or as a coincidental finding on either antenatal or postnatal ultrasound. Mesoblastic nephroma is the most common tumour to be found at this age, but Wilms' tumour and other malignant and benign tumours occur. Cross sectional imaging is useful to delineate the extent of the disease. Given the low malignant potential of these tumours, treatment is by radical nephroureterctomy, except in cases with bilateral disease or syndromic patients with a high incidence of metachronous tumours. Chemotherapy is rarely indicated. Survival is generally excellent for all tumour types in this age group, the exception being malignant rhabdoid tumour of the kidney which may have metastases at presentation.
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17
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Williams RD, Al-Saadi R, Chagtai T, Popov S, Messahel B, Sebire N, Gessler M, Wegert J, Graf N, Leuschner I, Hubank M, Jones C, Vujanic G, Pritchard-Jones K. Subtype-specific FBXW7 mutation and MYCN copy number gain in Wilms' tumor. Clin Cancer Res 2010; 16:2036-45. [PMID: 20332316 DOI: 10.1158/1078-0432.ccr-09-2890] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
PURPOSE Wilms' tumor (WT), the most common pediatric renal malignancy, is associated with mutations in several well-characterized genes, most notably WT1, CTNNB1, WTX, and TP53. However, the majority of cases do not harbor mutations in these genes. We hypothesized that additional drivers of tumor behavior would be contained within areas of consistent genomic copy number change, especially those associated with the WT risk groups defined by the International Society of Paediatric Oncology (SIOP). EXPERIMENTAL DESIGN We analyzed high-resolution (Affymetrix 250K single nucleotide polymorphism array) genomic copy number profiles of over 100 tumors from selected risk groups treated under the SIOP protocols, further characterizing genes of interest by sequencing, Multiplex Ligation-dependent Probe Amplification, or fluorescence in situ hybridization. RESULTS We identified FBXW7, an E3 ubiquitin ligase component, as a novel Wilms' tumor gene, mutated or deleted in approximately 4% of tumors examined. Strikingly, 3 of 14 (21%) of tumors with epithelial type histology after neoadjuvant chemotherapy had FBXW7 aberrations, whereas a fourth WT patient had germline mutations in both FBXW7 and WT1. We also showed that MYCN copy number gain, detected in 9 of 104 (8.7%) of cases, is relatively common in WT and significantly more so in tumors of the high risk diffuse anaplastic subtype (6 of 19, 32%). CONCLUSIONS Because MYCN is itself a target of FBXW7-mediated ubiquitination and degradation, these results suggest that a common pathway is dysregulated by different mechanisms in various WT subtypes. Emerging therapies that target MYCN, which is amplified in several other pediatric cancers, may therefore be of value in high risk Wilms' tumor.
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Affiliation(s)
- Richard D Williams
- Section of Paediatric Oncology, Institute of Cancer Research, Sutton, Surrey, United Kingdom
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Xue YB, Song X. [Progresses on the methods of tumor chromosome aberration analysis]. YI CHUAN = HEREDITAS 2008; 30:1529-1535. [PMID: 19073565 DOI: 10.3724/sp.j.1005.2008.01529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Most cancers are known to be associated with chromosome aberration, and chromosome analysis is essential to understand the relationships between chromosome aberration and cancer. Here we briefly introduce several methods of chromosome aberration detection, including G-banding, fluorescence in situ hybridization (FISH), spectral karyotyping (SKY), multi-fluorescence in situ hybridization (M-FISH), cross-species color banding (Rx-FISH), comparative genomic hybridization (CGH)and Array comparative genomic hybridization (Array CGH).
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Affiliation(s)
- Yuan-Bo Xue
- Center of Cancer Biotherapy, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650018, China.
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Rassekh SR, Chan S, Harvard C, Dix D, Qiao Y, Rajcan-Separovic E. Screening for submicroscopic chromosomal rearrangements in Wilms tumor using whole-genome microarrays. ACTA ACUST UNITED AC 2008; 182:84-94. [DOI: 10.1016/j.cancergencyto.2007.12.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 12/19/2007] [Accepted: 12/28/2007] [Indexed: 12/22/2022]
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