1
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Yamada M, Keller RR, Gutierrez RL, Cameron D, Suzuki H, Sanghrajka R, Vaynshteyn J, Gerwin J, Maura F, Hooper W, Shah M, Robine N, Demarest P, Bayin NS, Zapater LJ, Reed C, Hébert S, Masilionis I, Chaligne R, Socci ND, Taylor MD, Kleinman CL, Joyner AL, Raju GP, Kentsis A. Childhood cancer mutagenesis caused by transposase-derived PGBD5. SCIENCE ADVANCES 2024; 10:eadn4649. [PMID: 38517960 PMCID: PMC10959420 DOI: 10.1126/sciadv.adn4649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
Genomic rearrangements are a hallmark of most childhood tumors, including medulloblastoma, one of the most common brain tumors in children, but their causes remain largely unknown. Here, we show that PiggyBac transposable element derived 5 (Pgbd5) promotes tumor development in multiple developmentally accurate mouse models of Sonic Hedgehog (SHH) medulloblastoma. Most Pgbd5-deficient mice do not develop tumors, while maintaining normal cerebellar development. Ectopic activation of SHH signaling is sufficient to enforce cerebellar granule cell progenitor-like cell states, which exhibit Pgbd5-dependent expression of distinct DNA repair and neurodevelopmental factors. Mouse medulloblastomas expressing Pgbd5 have increased numbers of somatic structural DNA rearrangements, some of which carry PGBD5-specific sequences at their breakpoints. Similar sequence breakpoints recurrently affect somatic DNA rearrangements of known tumor suppressors and oncogenes in medulloblastomas in 329 children. This identifies PGBD5 as a medulloblastoma mutator and provides a genetic mechanism for the generation of oncogenic DNA rearrangements in childhood cancer.
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Affiliation(s)
- Makiko Yamada
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Ross R. Keller
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Daniel Cameron
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Reeti Sanghrajka
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Jake Vaynshteyn
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Gerwin
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesco Maura
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - William Hooper
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Minita Shah
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Nicolas Robine
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Phillip Demarest
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - N. Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge University, Cambridge, UK
| | - Luz Jubierre Zapater
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Casie Reed
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Steven Hébert
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ignas Masilionis
- Single-Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligne
- Single-Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D. Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael D. Taylor
- Department of Pediatrics—Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, USA
- Hematology-Oncology Section, Texas Children’s Cancer Center, Houston, TX, USA
- The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Claudia L. Kleinman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Biochemistry, Cell and Molecular Biology Program and Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - G. Praveen Raju
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alex Kentsis
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA
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2
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A View on Uterine Leiomyoma Genesis through the Prism of Genetic, Epigenetic and Cellular Heterogeneity. Int J Mol Sci 2023; 24:ijms24065752. [PMID: 36982825 PMCID: PMC10056617 DOI: 10.3390/ijms24065752] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Uterine leiomyomas (ULs), frequent benign tumours of the female reproductive tract, are associated with a range of symptoms and significant morbidity. Despite extensive research, there is no consensus on essential points of UL initiation and development. The main reason for this is a pronounced inter- and intratumoral heterogeneity resulting from diverse and complicated mechanisms underlying UL pathobiology. In this review, we comprehensively analyse risk and protective factors for UL development, UL cellular composition, hormonal and paracrine signalling, epigenetic regulation and genetic abnormalities. We conclude the need to carefully update the concept of UL genesis in light of the current data. Staying within the framework of the existing hypotheses, we introduce a possible timeline for UL development and the associated key events—from potential prerequisites to the beginning of UL formation and the onset of driver and passenger changes.
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3
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de Groot D, Spanjaard A, Hogenbirk MA, Jacobs H. Chromosomal Rearrangements and Chromothripsis: The Alternative End Generation Model. Int J Mol Sci 2023; 24:ijms24010794. [PMID: 36614236 PMCID: PMC9821053 DOI: 10.3390/ijms24010794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
Chromothripsis defines a genetic phenomenon where up to hundreds of clustered chromosomal rearrangements can arise in a single catastrophic event. The phenomenon is associated with cancer and congenital diseases. Most current models on the origin of chromothripsis suggest that prior to chromatin reshuffling numerous DNA double-strand breaks (DSBs) have to exist, i.e., chromosomal shattering precedes rearrangements. However, the preference of a DNA end to rearrange in a proximal accessible region led us to propose chromothripsis as the reaction product of successive chromatin rearrangements. We previously coined this process Alternative End Generation (AEG), where a single DSB with a repair-blocking end initiates a domino effect of rearrangements. Accordingly, chromothripsis is the end product of this domino reaction taking place in a single catastrophic event.
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Affiliation(s)
- Daniel de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Aldo Spanjaard
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Marc A. Hogenbirk
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Agendia NV, Radarweg 60, 1043 NT Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Correspondence: ; Tel.: +31-20-512-2065
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4
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Espejo Valle-Inclan J, Besselink NJ, de Bruijn E, Cameron DL, Ebler J, Kutzera J, van Lieshout S, Marschall T, Nelen M, Priestley P, Renkens I, Roemer MG, van Roosmalen MJ, Wenger AM, Ylstra B, Fijneman RJ, Kloosterman WP, Cuppen E. A multi-platform reference for somatic structural variation detection. CELL GENOMICS 2022; 2:100139. [PMID: 36778136 PMCID: PMC9903816 DOI: 10.1016/j.xgen.2022.100139] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 05/06/2021] [Accepted: 05/06/2022] [Indexed: 10/18/2022]
Abstract
Accurate detection of somatic structural variation (SV) in cancer genomes remains a challenging problem. This is in part due to the lack of high-quality, gold-standard datasets that enable the benchmarking of experimental approaches and bioinformatic analysis pipelines. Here, we performed somatic SV analysis of the paired melanoma and normal lymphoblastoid COLO829 cell lines using four different sequencing technologies. Based on the evidence from multiple technologies combined with extensive experimental validation, we compiled a comprehensive set of carefully curated and validated somatic SVs, comprising all SV types. We demonstrate the utility of this resource by determining the SV detection performance as a function of tumor purity and sequence depth, highlighting the importance of assessing these parameters in cancer genomics projects. The truth somatic SV dataset as well as the underlying raw multi-platform sequencing data are freely available and are an important resource for community somatic benchmarking efforts.
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Affiliation(s)
| | - Nicolle J.M. Besselink
- Center for Molecular Medicine and Oncode Institute, UMC Utrecht, Utrecht, the Netherlands
| | | | - Daniel L. Cameron
- Hartwig Medical Foundation, Amsterdam, the Netherlands,Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Joachim Kutzera
- Center for Molecular Medicine and Oncode Institute, UMC Utrecht, Utrecht, the Netherlands
| | | | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marcel Nelen
- Department of Human Genetics, Radboud UMC, Nijmegen, the Netherlands
| | | | - Ivo Renkens
- Center for Molecular Medicine and Oncode Institute, UMC Utrecht, Utrecht, the Netherlands
| | - Margaretha G.M. Roemer
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | | | | - Bauke Ylstra
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Remond J.A. Fijneman
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Wigard P. Kloosterman
- Center for Molecular Medicine and Oncode Institute, UMC Utrecht, Utrecht, the Netherlands,Corresponding author
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, UMC Utrecht, Utrecht, the Netherlands,Hartwig Medical Foundation, Amsterdam, the Netherlands,Corresponding author
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5
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Takita J. Molecular Basis and Clinical Features of Neuroblastoma. JMA J 2021; 4:321-331. [PMID: 34796286 PMCID: PMC8580727 DOI: 10.31662/jmaj.2021-0077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/02/2021] [Indexed: 12/05/2022] Open
Abstract
Neuroblastoma, a neoplasm of the sympathetic nervous system, originates from neuroblastoma stem cells during embryogenesis. It exhibits unique clinical features including a tendency for spontaneous regression of tumors in infants and a high frequency of metastatic disease at diagnosis in patients aged over 18 months. Genetic risk factors and epigenetic dysregulation also play a significant role in the development of neuroblastoma. Over the past decade, our understanding of this disease has advanced considerably. This has included the identification of chromosomal copy number aberrations specific to neuroblastoma development, risk groups, and disease stage. However, high-risk neuroblastoma remains a therapeutic challenge for pediatric oncologists. New therapeutic approaches have been developed, either as alternatives to conventional chemotherapy or in combination, to overcome the dismal prognosis. Particularly promising strategies are targeted therapies that directly affect cancer cells or cancer stem cells while exhibiting minimal effect on healthy cells. This review summarizes our understanding of neuroblastoma biology and prognostic features and focuses on novel therapeutic strategies for this intractable disease.
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Affiliation(s)
- Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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6
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Goto K, Pissaloux D, Tirode F, de la Fouchardière A. Spitz nevus with a novel TFG-NTRK2 fusion: The first case report of NTRK2-rearranged Spitz/Reed nevus. J Cutan Pathol 2021; 48:1193-1196. [PMID: 33979462 DOI: 10.1111/cup.14062] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 12/11/2022]
Abstract
Fusions of ALK, ROS1, NTRK1, NTRK3, RET, MET, MERTK, FGFR1, ERBB4, LCK, BRAF, MAP3K8, MAP3K3, and PRKDC and mutation of HRAS have so far been discovered as the genetic alterations associated with the pathogenesis of Spitz neoplasms. This report presents the first case of NTRK2-rearranged Spitz/Reed nevus. The patient was a 39-year-old male with a pigmented macule rapidly growing on his shoulder. Histopathologically, the lesion was a junctional melanocytic nevus composed of large nests of spindled melanocytes with abundant eosinophilic cytoplasm associated with a hyperplastic epidermis. These findings fulfilled the diagnostic criteria of a pigmented spindle cell nevus of Reed (variant of Spitz nevus). Immunohistochemistry for pan-Trk revealed diffuse cytoplasmic positivity in the tumor cells, but immunoexpression of ALK, ROS1, and BRAF V600E was not seen. A novel, in-frame, TFG-NTRK2 fusion was identified by RNA sequencing. This case report expands the list of genetic alterations in Spitz neoplasms and the spectrum of NTRK2-rearranged tumors.
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Affiliation(s)
- Keisuke Goto
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Disease Center Komagome Hospital, Tokyo, Japan.,Department of Pathology, Itabashi Central Clinical Laboratory, Tokyo, Japan.,Department of Diagnostic Pathology, Shizuoka Cancer Center Hospital, Sunto, Japan.,Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan.,Department of Diagnostic Pathology, Osaka National Hospital, Osaka, Japan.,Department of Dermatology, Hyogo Cancer Center, Akashi, Japan
| | - Daniel Pissaloux
- Department of Biopathology, Center Léon Bérard, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Lyon, France
| | - Franck Tirode
- Department of Biopathology, Center Léon Bérard, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Lyon, France
| | - Arnaud de la Fouchardière
- Department of Biopathology, Center Léon Bérard, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Lyon, France
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7
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Siri SO, Martino J, Gottifredi V. Structural Chromosome Instability: Types, Origins, Consequences, and Therapeutic Opportunities. Cancers (Basel) 2021; 13:3056. [PMID: 34205328 PMCID: PMC8234978 DOI: 10.3390/cancers13123056] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 01/04/2023] Open
Abstract
Chromosomal instability (CIN) refers to an increased rate of acquisition of numerical and structural changes in chromosomes and is considered an enabling characteristic of tumors. Given its role as a facilitator of genomic changes, CIN is increasingly being considered as a possible therapeutic target, raising the question of which variables may convert CIN into an ally instead of an enemy during cancer treatment. This review discusses the origins of structural chromosome abnormalities and the cellular mechanisms that prevent and resolve them, as well as how different CIN phenotypes relate to each other. We discuss the possible fates of cells containing structural CIN, focusing on how a few cell duplication cycles suffice to induce profound CIN-mediated genome alterations. Because such alterations can promote tumor adaptation to treatment, we discuss currently proposed strategies to either avoid CIN or enhance CIN to a level that is no longer compatible with cell survival.
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Affiliation(s)
- Sebastián Omar Siri
- Cell Cycle and Genome Stability Laboratory, Fundación Instituto Leloir, C1405 BWE Buenos Aires, Argentina;
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405 BWE Buenos Aires, Argentina
| | - Julieta Martino
- Cell Cycle and Genome Stability Laboratory, Fundación Instituto Leloir, C1405 BWE Buenos Aires, Argentina;
| | - Vanesa Gottifredi
- Cell Cycle and Genome Stability Laboratory, Fundación Instituto Leloir, C1405 BWE Buenos Aires, Argentina;
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405 BWE Buenos Aires, Argentina
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8
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Simovic M, Bolkestein M, Moustafa M, Wong JKL, Körber V, Benedetto S, Khalid U, Schreiber HS, Jugold M, Korshunov A, Hübschmann D, Mack N, Brons S, Wei PC, Breckwoldt MO, Heiland S, Bendszus M, Jürgen D, Höfer T, Zapatka M, Kool M, Pfister SM, Abdollahi A, Ernst A. Carbon ion radiotherapy eradicates medulloblastomas with chromothripsis in an orthotopic Li-Fraumeni patient-derived mouse model. Neuro Oncol 2021; 23:2028-2041. [PMID: 34049392 PMCID: PMC8643436 DOI: 10.1093/neuonc/noab127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Medulloblastomas with chromothripsis developing in children with Li-Fraumeni Syndrome (germline TP53 mutations) are highly aggressive brain tumors with dismal prognosis. Conventional photon radiotherapy and DNA-damaging chemotherapy are not successful for these patients and raise the risk of secondary malignancies. We hypothesized that the pronounced homologous recombination deficiency in these tumors might offer vulnerabilities that can be therapeutically utilized in combination with high linear energy transfer carbon ion radiotherapy. Methods We tested high-precision particle therapy with carbon ions and protons as well as topotecan with or without PARP inhibitor in orthotopic primary and matched relapsed patient-derived xenograft models. Tumor and normal tissue underwent longitudinal morphological MRI, cellular (markers of neurogenesis and DNA damage-repair), and molecular characterization (whole-genome sequencing). Results In the primary medulloblastoma model, carbon ions led to complete response in 79% of animals irrespective of PARP inhibitor within a follow-up period of 300 days postirradiation, as detected by MRI and histology. No sign of neurologic symptoms, impairment of neurogenesis or in-field carcinogenesis was detected in repair-deficient host mice. PARP inhibitors further enhanced the effect of proton irradiation. In the postradiotherapy relapsed tumor model, median survival was significantly increased after carbon ions (96 days) versus control (43 days, P < .0001). No major change in the clonal composition was detected in the relapsed model. Conclusion The high efficacy and favorable toxicity profile of carbon ions warrants further investigation in primary medulloblastomas with chromothripsis. Postradiotherapy relapsed medulloblastomas exhibit relative resistance compared to treatment-naïve tumors, calling for exploration of multimodal strategies.
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Affiliation(s)
- Milena Simovic
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ).,Faculty of Biosciences, Heidelberg University
| | - Michiel Bolkestein
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ)
| | - Mahmoud Moustafa
- Division of Molecular & Translational Radiation Oncology,Heidelberg Ion-Beam Therapy Center (HIT).,Heidelberg Institute for Radiation Oncology (HIRO).,National Center for Radiation Oncology (NCRO).,National Center for Tumor Diseases (NCT).,Heidelberg University Hospital (UKHD) and DKFZ.,German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Department of Clinical Pathology, Suez Canal University, Ismailia-Egypt
| | - John K L Wong
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Division of Molecular Genetics, DKFZ
| | | | | | - Umar Khalid
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ).,Faculty of Biosciences, Heidelberg University
| | - Hannah Sophia Schreiber
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ).,Faculty of Medicine, Heidelberg University
| | | | - Andrey Korshunov
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Clinical Cooperation Unit Neuropathology, DKFZ, Department of Neuropathology, UKHD
| | - Daniel Hübschmann
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Computational Oncology Group, Molecular Diagnostics Program at the NCT and DKFZ.,Heidelberg Institute for Stem cell Technology and Experimental Medicine.,Department of Pediatric Oncology, Hematology and Immunology, UKHD
| | - Norman Mack
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Division of Molecular Genetics, DKFZ.,Department of Pediatric Oncology, Hematology and Immunology, UKHD.,Hopp Children's Cancer Center, NCT Heidelberg (KiTZ).,Division of Pediatric Neurooncology, DKFZ
| | | | | | | | | | | | - Debus Jürgen
- Heidelberg Institute for Radiation Oncology (HIRO).,National Center for Tumor Diseases (NCT).,German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Department of Radiation Oncology, UKHD.,Department of Radiation Oncology, Eberhard-Karls-University Tuebingen.,Clinical Cooperation Unit Radiation Oncology, DKFZ
| | | | - Marc Zapatka
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Division of Molecular Genetics, DKFZ
| | - Marcel Kool
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Hopp Children's Cancer Center, NCT Heidelberg (KiTZ).,Division of Pediatric Neurooncology, DKFZ.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Stefan M Pfister
- German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ.,Department of Pediatric Oncology, Hematology and Immunology, UKHD.,Hopp Children's Cancer Center, NCT Heidelberg (KiTZ).,Division of Pediatric Neurooncology, DKFZ
| | - Amir Abdollahi
- Division of Molecular & Translational Radiation Oncology,Heidelberg Ion-Beam Therapy Center (HIT).,Heidelberg Institute for Radiation Oncology (HIRO).,National Center for Radiation Oncology (NCRO).,National Center for Tumor Diseases (NCT).,Heidelberg University Hospital (UKHD) and DKFZ.,German Cancer Consortium (DKTK), partner site Heidelberg, DKFZ
| | - Aurélie Ernst
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ)
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9
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Chromothripsis-Explosion in Genetic Science. Cells 2021; 10:cells10051102. [PMID: 34064429 PMCID: PMC8147837 DOI: 10.3390/cells10051102] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/27/2021] [Accepted: 05/01/2021] [Indexed: 12/13/2022] Open
Abstract
Chromothripsis has been defined as complex patterns of alternating genes copy number changes (normal, gain or loss) along the length of a chromosome or chromosome segment (International System for Human Cytogenomic Nomenclature 2020). The phenomenon of chromothripsis was discovered in 2011 and changed the concept of genome variability, mechanisms of oncogenic transformation, and hereditary diseases. This review describes the phenomenon of chromothripsis, its prevalence in genomes, the mechanisms underlying this phenomenon, and methods of its detection. Due to the fact that most often the phenomenon of chromothripsis occurs in cancer cells, in this review, we will separately discuss the issue of the contribution of chromothripsis to the process of oncogenesis.
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10
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Pellestor F, Gaillard JB, Schneider A, Puechberty J, Gatinois V. Chromoanagenesis, the mechanisms of a genomic chaos. Semin Cell Dev Biol 2021; 123:90-99. [PMID: 33608210 DOI: 10.1016/j.semcdb.2021.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023]
Abstract
Designated under the name of chromoanagenesis, the phenomena of chromothripsis, chromanasynthesis and chromoplexy constitute new types of complex rearrangements, including many genomic alterations localized on a few chromosomal regions, and whose discovery over the last decade has changed our perception about the formation of chromosomal abnormalities and their etiology. Although exhibiting specific features, these new catastrophic mechanisms generally occur within a single cell cycle and their emergence is closely linked to genomic instability. Various non-exclusive exogenous or cellular mechanisms capable of generating chromoanagenesis have been evoked. However, recent experimental data shed light on 2 major processes, which following a defect in the mitotic segregation of chromosomes, can generate a cascade of cellular events leading to chromoanagenesis. These mechanisms are the formation of micronuclei integrating isolated chromosomal material, and the occurrence of chromatin bridges around chromosomal material resulting from telomeric fusions. In both cases, the cellular and molecular mechanisms of fragmentation, repair and transmission of damaged chromosomal material are consistent with the features of chromoanagenesis-related complex chromosomal rearrangements. In this review, we introduce each type of chromoanagenesis, and describe the experimental models that have allowed to validate the existence of chromoanagenesis events and to better understand their cellular mechanisms of formation and transmission, as well as their impact on the stability and the plasticity of the genome.
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Affiliation(s)
- F Pellestor
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France; INSERM 1183 Unit "Genome and Stem Cell Plasticity in Development and Aging" Institute of Regenerative Medecine and Biotherapies, St Eloi Hospital, Montpellier, France.
| | - J B Gaillard
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - A Schneider
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - J Puechberty
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - V Gatinois
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France; INSERM 1183 Unit "Genome and Stem Cell Plasticity in Development and Aging" Institute of Regenerative Medecine and Biotherapies, St Eloi Hospital, Montpellier, France
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11
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The glycosphingolipid GD2 as an effective but enigmatic target of passive immunotherapy in children with aggressive neuroblastoma (HR-NBL). Cancer Lett 2020; 503:220-230. [PMID: 33271265 DOI: 10.1016/j.canlet.2020.11.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/02/2020] [Accepted: 11/26/2020] [Indexed: 11/20/2022]
Abstract
Neuroblastoma (NBL), the most frequent and lethal pediatric cancer of children in pre-school age, is considered enigmatic in view of its extreme heterogeneity, from spontaneous regression in the IV-S form to incurable disease in approx. 40% of cases (High Risk, HR-NBL). It has an embryonal origin and a very heterogeneous genomic landscape, hampering the success of targeted strategies. The glycosphingolipid GD2 was shown to be expressed on NBL cells and utilized as target for passive immunotherapy with anti-GD2 antibodies (GD2-IMT). An international protocol was established with GD2-IMT, which increases remission length and survival in HR-NBL. By reviewing the different biological and molecular aspects of NBL and GD2-IMT, this mini-review questions the present lack of association between GD2-IMT and the underlying molecular landscape. The alternative model of Micro-Foci inducing virus (MFV) is presented, since MFV infection can induce extensive genomic aberrations (100X NMYC DNA-amplification). Since this family of viruses uses molecules for cell penetration similar to GD2 (i.e., GM2), it is hypothesized that GD2 is the port-of-entry for MFV and that success of anti-GD2 therapies is also associated to inhibition of this clastogenic virus in HR-NBL.
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12
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Williams LS, Caro J, Razzo B, Boyle EM, Morgan GJ. Deep sequencing as an approach to understanding the complexity and improving the treatment of multiple myeloma. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2020. [DOI: 10.1080/23808993.2020.1792285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Louis S. Williams
- Department of Hematology & Medical Oncology, NYU Langone Medical Center, New York, NY, USA
| | - Jessica Caro
- Department of Hematology & Medical Oncology, NYU Langone Medical Center, New York, NY, USA
| | - Beatrice Razzo
- Department of Internal Medicine, NYU Langone Medical Center, New York, NY, USA
| | - Eileen M. Boyle
- Department of Hematology & Medical Oncology, Multiple Myeloma Research Program, NYU Langone Medical Center, New York, NY, USA
| | - Gareth J. Morgan
- Department of Hematology & Medical Oncology, Multiple Myeloma Research Program, NYU Langone Medical Center, New York, NY, USA
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13
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Fuse K, Tanaka T, Shibasaki Y, Furukawa T, Narita M, Sone H, Masuko M. Marker chromosome is a strong poor prognosis factor after allogeneic HSCT for adverse-risk AML patients. Eur J Haematol 2020; 105:616-625. [PMID: 32705716 DOI: 10.1111/ejh.13495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Chromosome analysis is necessary for the risk classification of acute myeloid leukemia (AML). Marker chromosome (MC) is a fragmented chromosome whose origin cannot be identified from other chromosomes and originates from marked genomic instability. Although AML with MC (MC+) has a poor prognosis even after intensive chemotherapy, its influence on the outcome after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is unclear. OBJECTIVE AND METHODS We retrospectively analyzed 162 AML patients after allo-HSCT. To evaluate the significance of MC, we compared it with other chromosomal abnormalities. RESULT Marker chromosome was detected in 14 (8.6%, MC+) patients (vs MC-, n = 158). The 2-year overall survival (OS) in MC+ vs MC- was 26.8% vs 62.2% (P = .0098). The 2-year cumulative incidence of relapse (CIR) in MC+ vs MC- was 80.4% vs 35.5% (P = .0004). Among adverse-risk AML (AD-AML, n = 36), AD-AML/MC+ (n = 11) demonstrated a poorer 2-year OS (9.1%, vs AD-AML/MC- n = 25, 58.3%, P = .0031) and higher 2-year CIR (89.6%, vs AD-AML/MC- 44.7%, P = .002). In multivariate analysis, MC (HR 3.08, 95% CI; 1.02-9.29, P = .046) and HCT-CI (HR 3.23, 95% CI; 1.00-10.4, P = .049) were independent risk factors for CIR among AD-AML. CONCLUSION Our study suggests MC as a new independent factor for chromosome risk classification to further classify AD-AML.
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Affiliation(s)
- Kyoko Fuse
- Department of Hematology, Endocrinology and Metabolism, Faculty of Medicine Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Tomoyuki Tanaka
- Department of Hematology, Endocrinology and Metabolism, Faculty of Medicine Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Yasuhiko Shibasaki
- Department of Hematopoietic Cell Transplantation, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Tatsuo Furukawa
- Department of Hematology, Nagaoka Red Cross Hospital, Nagaoka, Japan
| | - Miwako Narita
- Laboratory of Hematology and Oncology, Graduate School of Health Sciences, Niigata University, Niigata, Japan
| | - Hirohito Sone
- Department of Hematology, Endocrinology and Metabolism, Faculty of Medicine Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Masayoshi Masuko
- Department of Hematopoietic Cell Transplantation, Niigata University Medical and Dental Hospital, Niigata, Japan
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14
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Kneissig M, Keuper K, de Pagter MS, van Roosmalen MJ, Martin J, Otto H, Passerini V, Campos Sparr A, Renkens I, Kropveld F, Vasudevan A, Sheltzer JM, Kloosterman WP, Storchova Z. Micronuclei-based model system reveals functional consequences of chromothripsis in human cells. eLife 2019; 8:e50292. [PMID: 31778112 PMCID: PMC6910827 DOI: 10.7554/elife.50292] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/23/2019] [Indexed: 01/18/2023] Open
Abstract
Cancer cells often harbor chromosomes in abnormal numbers and with aberrant structure. The consequences of these chromosomal aberrations are difficult to study in cancer, and therefore several model systems have been developed in recent years. We show that human cells with extra chromosome engineered via microcell-mediated chromosome transfer often gain massive chromosomal rearrangements. The rearrangements arose by chromosome shattering and rejoining as well as by replication-dependent mechanisms. We show that the isolated micronuclei lack functional lamin B1 and become prone to envelope rupture, which leads to DNA damage and aberrant replication. The presence of functional lamin B1 partly correlates with micronuclei size, suggesting that the proper assembly of nuclear envelope might be sensitive to membrane curvature. The chromosomal rearrangements in trisomic cells provide growth advantage compared to cells without rearrangements. Our model system enables to study mechanisms of massive chromosomal rearrangements of any chromosome and their consequences in human cells.
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Affiliation(s)
- Maja Kneissig
- Department of Molecular GeneticsTU KaiserslauternKaiserslauternGermany
| | - Kristina Keuper
- Department of Molecular GeneticsTU KaiserslauternKaiserslauternGermany
| | - Mirjam S de Pagter
- Department of Genetics, Center for Molecular MedicineUniversity Medical CenterUniversiteitswegNetherlands
| | - Markus J van Roosmalen
- Department of Genetics, Center for Molecular MedicineUniversity Medical CenterUniversiteitswegNetherlands
| | - Jana Martin
- Department of Molecular GeneticsTU KaiserslauternKaiserslauternGermany
| | - Hannah Otto
- Department of Molecular GeneticsTU KaiserslauternKaiserslauternGermany
| | | | | | - Ivo Renkens
- Department of Genetics, Center for Molecular MedicineUniversity Medical CenterUniversiteitswegNetherlands
| | - Fenna Kropveld
- Department of Genetics, Center for Molecular MedicineUniversity Medical CenterUniversiteitswegNetherlands
| | - Anand Vasudevan
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | | | - Wigard P Kloosterman
- Department of Genetics, Center for Molecular MedicineUniversity Medical CenterUniversiteitswegNetherlands
| | - Zuzana Storchova
- Department of Molecular GeneticsTU KaiserslauternKaiserslauternGermany
- Max Planck Institute of BiochemistryMartinsriedGermany
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15
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Haploid Induction and Genome Instability. Trends Genet 2019; 35:791-803. [DOI: 10.1016/j.tig.2019.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/26/2019] [Accepted: 07/10/2019] [Indexed: 11/24/2022]
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16
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Berry NK, Scott RJ, Rowlings P, Enjeti AK. Clinical use of SNP-microarrays for the detection of genome-wide changes in haematological malignancies. Crit Rev Oncol Hematol 2019; 142:58-67. [PMID: 31377433 DOI: 10.1016/j.critrevonc.2019.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 12/17/2022] Open
Abstract
Single nucleotide polymorphism (SNP) microarrays are commonly used for the clinical investigation of constitutional genomic disorders; however, their adoption for investigating somatic changes is being recognised. With increasing importance being placed on defining the cancer genome, a shift in technology is imperative at a clinical level. Microarray platforms have the potential to become frontline testing, replacing or complementing standard investigations such as FISH or karyotype. This 'molecular karyotype approach' exemplified by SNP-microarrays has distinct advantages in the investigation of several haematological malignancies. A growing body of literature, including guidelines, has shown support for the use of SNP-microarrays in the clinical laboratory to aid in a more accurate definition of the cancer genome. Understanding the benefits of this technology along with discussing the barriers to its implementation is necessary for the development and incorporation of SNP-microarrays in a clinical laboratory for the investigation of haematological malignancies.
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Affiliation(s)
- Nadine K Berry
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology, Newcastle, New South Wales, Australia.
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology, Newcastle, New South Wales, Australia
| | - Philip Rowlings
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia
| | - Anoop K Enjeti
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia
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17
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Pellestor F. Chromoanagenesis: cataclysms behind complex chromosomal rearrangements. Mol Cytogenet 2019; 12:6. [PMID: 30805029 PMCID: PMC6371609 DOI: 10.1186/s13039-019-0415-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background During the last decade, genome sequencing projects in cancer genomes as well as in patients with congenital diseases and healthy individuals have led to the identification of new types of massive chromosomal rearrangements arising during single chaotic cellular events. These unanticipated catastrophic phenomenon are termed chromothripsis, chromoanasynthesis and chromoplexis., and are grouped under the name of “chromoanagenesis”. Results For each process, several specific features have been described, allowing each phenomenon to be distinguished from each other and to understand its mechanism of formation and to better understand its aetiology. Thus, chromothripsis derives from chromosome shattering followed by the random restitching of chromosomal fragments with low copy-number change whereas chromoanasynthesis results from erroneous DNA replication of a chromosome through serial fork stalling and template switching with variable copy-number gains, and chromoplexy refers to the occurrence of multiple inter-and intra-chromosomal translocations and deletions with little or no copy-number alterations in prostate cancer. Cumulating data and experimental models have shown that chromothripsis and chromoanasynthesis may essentially result from lagging chromosome encapsulated in micronuclei or telomere attrition and end-to-end telomere fusion. Conclusion The concept of chromanagenesis has provided new insight into the aetiology of complex structural rearrangements, the connection between defective cell cycle progression and genomic instability, and the complexity of cancer evolution. Increasing reported chromoanagenesis events suggest that these chaotic mechanisms are probably much more frequent than anticipated.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371, avenue du Doyen Gaston Giraud, 34295 Montpellier cedex 5, France.,INSERM 1183 Unit «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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18
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Abstract
Somatic structural variants undoubtedly play important roles in driving tumourigenesis. This is evident despite the substantial technical challenges that remain in accurately detecting structural variants and their breakpoints in tumours and in spite of our incomplete understanding of the impact of structural variants on cellular function. Developments in these areas of research contribute to the ongoing discovery of structural variation with a clear impact on the evolution of the tumour and on the clinical importance to the patient. Recent large whole genome sequencing studies have reinforced our impression of each tumour as a unique combination of mutations but paradoxically have also discovered similar genome-wide patterns of single-nucleotide and structural variation between tumours. Statistical methods have been developed to deconvolute mutation patterns, or signatures, that recur across samples, providing information about the mutagens and repair processes that may be active in a given tumour. These signatures can guide treatment by, for example, highlighting vulnerabilities in a particular tumour to a particular chemotherapy. Thus, although the complete reconstruction of the full evolutionary trajectory of a tumour genome remains currently out of reach, valuable data are already emerging to improve the treatment of cancer.
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Affiliation(s)
- Ailith Ewing
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH42XU, UK
| | - Colin Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH42XU, UK
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19
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Boisselier B, Dugay F, Belaud-Rotureau MA, Coutolleau A, Garcion E, Menei P, Guardiola P, Rousseau A. Whole genome duplication is an early event leading to aneuploidy in IDH-wild type glioblastoma. Oncotarget 2018; 9:36017-36028. [PMID: 30542515 PMCID: PMC6267593 DOI: 10.18632/oncotarget.26330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/24/2018] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma, the most frequent and lethal form of glioma, displays chromosome instability and recurrent somatic copy number alterations (SCNA). Chromothripsis and whole genome duplication (WGD) have been recently identified in cancer. In the present study, we analyzed SCNA and determine the ploidy pattern in 123 IDH-wild-type glioblastomas, using SNP array data. WGD and chromothripsis events were validated using, respectively, FISH and CTLPScanner. WGD was detected in 11.4% glioblastomas (14/123) and was associated with TP53 mutation (p = 0.0068). It was an early event occurring after the recurrent SCNA observed in diffuse high-grade gliomas. Glioblastomas with WGD were more aneuploid compared to glioblastomas without WGD (p < 0.0001). Chromothripsis occurred in 29.3% glioblastomas (36/123) and mostly affected chromosomes 7, 9 and 12, with amplification of oncogenes (EGFR, MDM2/CDK4), and homozygous deletion of tumor suppressor genes (CDKN2A). There was a significant association between chromothripsis and gene rearrangement at a given locus. WGD is an early genetic event significantly associated to TP53 mutation and leading to chromosome instability and aneuploidy in IDH-wild-type glioblastoma. Chromothripsis recurrently targets oncogenes and tumor suppressor genes that are key players in gliomagenesis and tumor progression. The occurrence of chromothripsis points to underlying gene rearrangements (including gene fusions), potential therapeutic targets in glioblastoma.
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Affiliation(s)
- Blandine Boisselier
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, Angers, France.,CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Frédéric Dugay
- Laboratoire de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | | | | | - Emmanuel Garcion
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Philippe Menei
- Département de Neurochirurgie, CHU Angers, Angers, France
| | | | - Audrey Rousseau
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, Angers, France.,CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
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20
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Maass KK, Rosing F, Ronchi P, Willmund KV, Devens F, Hergt M, Herrmann H, Lichter P, Ernst A. Altered nuclear envelope structure and proteasome function of micronuclei. Exp Cell Res 2018; 371:353-363. [PMID: 30149001 DOI: 10.1016/j.yexcr.2018.08.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/15/2018] [Accepted: 08/23/2018] [Indexed: 11/18/2022]
Abstract
Micronuclei are extra-nuclear bodies containing whole chromosomes that were not incorporated into the nucleus after cell division or damaged chromosome fragments. Even though the link between micronuclei and DNA damage is described for a long time, little is known about the functional organization of micronuclei and their contribution to tumorigenesis. We showed fusions between micronuclear membranes and lysosomes by electron microscopy and linked lysosome function to DNA damage levels in micronuclei. In addition, micronuclei drastically differ from primary nuclei in nuclear envelope composition, with a significant increase in the relative amount of nuclear envelope proteins LBR and emerin and a decrease in nuclear pore proteins. Strikingly, micronuclei lack active proteasomes, as the processing subunits and other factors of the ubiquitin proteasome system. Moreover, micronuclear chromatin shows a higher degree of compaction as compared to primary nuclei. The specific aberrations identified in micronuclei and the potential functional consequences of these defects may contribute to the role of micronuclei in catastrophic genomic rearrangements.
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Affiliation(s)
- Kendra K Maass
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Germany
| | - Fabian Rosing
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paolo Ronchi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Karolin V Willmund
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frauke Devens
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michaela Hergt
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Harald Herrmann
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aurélie Ernst
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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21
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Cai M, Zhang H, Hou L, Gao W, Song Y, Cui X, Li C, Guan R, Ma J, Wang X, Han Y, Lv Y, Chen F, Wang P, Meng X, Fu S. Inhibiting homologous recombination decreases extrachromosomal amplification but has no effect on intrachromosomal amplification in methotrexate-resistant colon cancer cells. Int J Cancer 2018; 144:1037-1048. [PMID: 30070702 PMCID: PMC6586039 DOI: 10.1002/ijc.31781] [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: 09/12/2017] [Revised: 02/23/2018] [Accepted: 07/24/2018] [Indexed: 01/08/2023]
Abstract
Gene amplification, which involves the two major topographical structures double minutes (DMs) and homegeneously stained region (HSR), is a common mechanism of treatment resistance in cancer and is initiated by DNA double‐strand breaks. NHEJ, one of DSB repair pathways, is involved in gene amplification as we demonstrated previously. However, the involvement of homologous recombination, another DSB repair pathway, in gene amplification remains to be explored. To better understand the association between HR and gene amplification, we detected HR activity in DM‐ and HSR‐containing MTX‐resistant HT‐29 colon cancer cells. In DM‐containing MTX‐resistant cells, we found increased homologous recombination activity compared with that in MTX‐sensitive cells. Therefore, we suppressed HR activity by silencing BRCA1, the key player in the HR pathway. The attenuation of HR activity decreased the numbers of DMs and DM‐form amplified gene copies and increased the exclusion of micronuclei and nuclear buds that contained DM‐form amplification; these changes were accompanied by cell cycle acceleration and increased MTX sensitivity. In contrast, BRCA1 silencing did not influence the number of amplified genes and MTX sensitivity in HSR‐containing MTX‐resistant cells. In conclusion, our results suggest that the HR pathway plays different roles in extrachromosomal and intrachromosomal gene amplification and may be a new target to improve chemotherapeutic outcome by decreasing extrachromosomal amplification in cancer. What's new? Double‐strand DNA breaks (DSBs) initiate gene amplification, a phenomenon associated with therapeutic resistance in cancer that involves two topographical structures, double minutes (DMs) and homogeneously staining regions (HSRs). Whether DSB repair pathways, particularly homologous recombination (HR), also influence gene amplification is unknown. Here, in methotrexate‐resistant colon cancer cells, HR inhibition effectively reduced gene amplification, specifically the DM‐form, by blocking DM formation and promoting DM exclusion via micronuclei. HR inhibition had no influence on the HSR‐form of gene amplification. Loss of gene amplification by HR inhibition, through partial reversal of methotrexate resistance, may contribute to improved chemotherapeutic outcome.
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Affiliation(s)
- Mengdi Cai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Huishu Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Liqing Hou
- Department of Genetics, Inner Mongolia Maternal and Child Care Hospital, Hohhot, Inner Mongolia Autonomous Region, China
| | - Wei Gao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Ying Song
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Xiaobo Cui
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Chunxiang Li
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Rongwei Guan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Jinfa Ma
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Xu Wang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Yue Han
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Yafan Lv
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Feng Chen
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Ping Wang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Xiangning Meng
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
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22
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Identification of Chromothripsis in Biopsy Using SNP-Based Microarray. Methods Mol Biol 2018. [PMID: 29564820 DOI: 10.1007/978-1-4939-7780-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
One of the well-known hallmarks of cancer is genomic instability. Although gradualism is a well-established process of cancer evolution, recent studies have shown that chromothripsis or chromoanasynthesis can result in complex genomic rearrangements by a single catastrophic event rather than several incremental steps. These two novel phenomena suggest an evolutionary modality for cancer cells to circumvent individual mutational events with one simultaneous shattering of chromosomes or chromosome regions resulting in the random reassembling of shattered genetic material to form complex derivative chromosomes. Although sequencing methods are ideal for the detection of chromothripsis, single-nucleotide polymorphism (SNP)-based microarray methods are also useful in detecting chromothripsis in biopsy samples. Issues related to sample collection, storage, and transport, especially with tumor biopsies, may limit the options for sequencing studies, and in such cases, SNP-based microarray may be a viable alternative for detecting chromothripsis.
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23
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Chromothripsis in acute myeloid leukemia: biological features and impact on survival. Leukemia 2018; 32:1609-1620. [PMID: 29472722 PMCID: PMC6035145 DOI: 10.1038/s41375-018-0035-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/31/2017] [Accepted: 11/21/2017] [Indexed: 12/12/2022]
Abstract
Chromothripsis is a one-step genome-shattering catastrophe resulting from disruption of one or few chromosomes in multiple fragments and consequent random rejoining and repair. This study defines incidence of chromothripsis in 395 newly diagnosed adult acute myeloid leukemia (AML) patients from three institutions, its impact on survival and its genomic background. SNP 6.0 or CytoscanHD Array (Affymetrix®) were performed on all samples. We detected chromothripsis with a custom algorithm in 26/395 patients. Patients harboring chromothripsis had higher age (p = 0.002), ELN high risk (HR) (p < 0.001), lower white blood cell (WBC) count (p = 0.040), TP53 loss, and/or mutations (p < 0.001) while FLT3 (p = 0.025), and NPM1 (p = 0.032) mutations were mutually exclusive with chromothripsis. Chromothripsis-positive patients showed a worse overall survival (OS) (p < 0.001) compared with HR patients (p = 0.011) and a poor prognosis in a COX-HR optimal regression model. Chromothripsis presented the hallmarks of chromosome instability [i.e., TP53 alteration, 5q deletion, higher mean of copy number alteration (CNA), complex karyotype, alterations in DNA repair, and cell cycle] and focal deletions on chromosomes 4, 7, 12, 16, and 17. CBA. FISH showed that chromothripsis is associated with marker, derivative, and ring chromosomes. In conclusion, chromothripsis frequently occurs in AML (6.6%) and influences patient prognosis and disease biology.
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24
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Smetana J, Oppelt J, Štork M, Pour L, Kuglík P. Chromothripsis 18 in multiple myeloma patient with rapid extramedullary relapse. Mol Cytogenet 2018; 11:7. [PMID: 29375670 PMCID: PMC5774134 DOI: 10.1186/s13039-018-0357-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/10/2018] [Indexed: 12/15/2022] Open
Abstract
Background Catastrophic chromosomal event known as chromothripsis was proven to be a significant hallmark of poor prognosis in several cancer diseases. While this phenomenon is very rare in among multiple myeloma (MM) patients, its presence in karyotype is associated with very poor prognosis. Case presentation In our case, we report a 62 year female patient with rapid progression of multiple myeloma (MM) into extramedullary disease and short overall survival (OS = 23 months). I-FISH investigation revealed presence of gain 1q21 and hyperdiploidy (+ 5,+ 9,+ 15) in 82% and 86%, respectively, while IgH rearrangements, del(17)(p13) and del(13)(q14) were evaluated as negative.Whole-genome profiling using array-CGH showed complex genomic changes including hyperdiploidy (+ 3,+ 5,+ 9,+ 11, + 15,+ 19), monosomy X, structural gains (1q21-1q23.1, 1q32-1q44, 16p13.13-16p11.2) and losses (1q23.1-1q32.1; 8p23.3-8p11.21) of genetic material and chromothripsis in chromosome 18 with 6 breakpoint areas. Next-generation sequencing showed a total of 338 variants with 1.8% (6/338) of pathological mutations in NRAS (c.181C > A; p.Gln61Lys) or variants of unknown significance in TP53, CUX1 and POU4F1. Conclusions Our findings suggest that presence of chromothripsis should be considered as another important genetic hallmark of poor prognosis in MM patients and utilization of genome-wide screening techniques such as array-CGH and NGS improves the clinical diagnostics of the disease.
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Affiliation(s)
- Jan Smetana
- 1Laboratory of Molecular Cytogenetics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic.,2Department of Medical Genetics, University Hospital, Brno, Czech Republic, Černopolní 9, Brno, Czech Republic
| | - Jan Oppelt
- 3CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,4National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Martin Štork
- 5Department of Internal Medicine-Hematooncology, University Hospital Brno, Jihlavská 20, 62500 Brno, Czech Republic
| | - Luděk Pour
- 5Department of Internal Medicine-Hematooncology, University Hospital Brno, Jihlavská 20, 62500 Brno, Czech Republic
| | - Petr Kuglík
- 1Laboratory of Molecular Cytogenetics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic.,2Department of Medical Genetics, University Hospital, Brno, Czech Republic, Černopolní 9, Brno, Czech Republic
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25
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Oesper L, Dantas S, Raphael BJ. Identifying simultaneous rearrangements in cancer genomes. Bioinformatics 2018; 34:346-352. [PMID: 29186385 PMCID: PMC5860217 DOI: 10.1093/bioinformatics/btx745] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/17/2017] [Accepted: 11/24/2017] [Indexed: 11/15/2022] Open
Abstract
Motivation The traditional view of cancer evolution states that a cancer genome accumulates a sequential ordering of mutations over a long period of time. However, in recent years it has been suggested that a cancer genome may instead undergo a one-time catastrophic event, such as chromothripsis, where a large number of mutations instead occur simultaneously. A number of potential signatures of chromothripsis have been proposed. In this work, we provide a rigorous formulation and analysis of the ‘ability to walk the derivative chromosome’ signature originally proposed by Korbel and Campbell. In particular, we show that this signature, as originally envisioned, may not always be present in a chromothripsis genome and we provide a precise quantification of under what circumstances it would be present. We also propose a variation on this signature, the H/T alternating fraction, which allows us to overcome some of the limitations of the original signature. Results We apply our measure to both simulated data and a previously analyzed real cancer dataset and find that the H/T alternating fraction may provide useful signal for distinguishing genomes having acquired mutations simultaneously from those acquired in a sequential fashion. Availability and implementation An implementation of the H/T alternating fraction is available at https://bitbucket.org/oesperlab/ht-altfrac. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Layla Oesper
- Department of Computer Science, Carleton College, Northfield, MN, USA
| | - Simone Dantas
- Institute of Mathematics and Statistics, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA
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26
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Fukami M, Kurahashi H. Clinical Consequences of Chromothripsis and Other Catastrophic Cellular Events. Methods Mol Biol 2018; 1769:21-33. [PMID: 29564815 DOI: 10.1007/978-1-4939-7780-2_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Chromothripsis was initially described as a novel cause of chromosomal rearrangements in cancer cells and was subsequently implicated in the development of gross chromosomal rearrangements in the germline. Other catastrophic cellular events such as chromoanasynthesis and chromoplexy have also been observed in human cells. Such events have been associated with various phenotypes including mental retardation and congenital malformations. Here, we introduce representative cases of human disorders arising from somatic or germline chromothripsis or similar catastrophic events. In this chapter, we use the term "chromoanagenesis" to indicate all catastrophic events including chromothripsis.
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Affiliation(s)
- Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan.
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27
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Marcozzi A, Pellestor F, Kloosterman WP. The Genomic Characteristics and Origin of Chromothripsis. Methods Mol Biol 2018; 1769:3-19. [PMID: 29564814 DOI: 10.1007/978-1-4939-7780-2_1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In 2011 a phenomenon involving complex chromosomal rearrangements was discovered in cancer genomes. This phenomenon has been termed chromothripsis, on the basis of its chromosomal hallmarks, which point to an underlying process involving chromosome (chromo) shattering (thripsis). The prevailing hypothesis of cancer genome evolution as a gradual process of mutation and selection was challenged by the discovery of chromothripsis, because its patterns of chromosome rearrangement rather indicated an one-off catastrophic burst of genome rearrangement. The initial discovery of chromothripsis has led to many more examples of chromothripsis both in cancer genomes as well as in patients with congenital diseases and in the genomes of healthy individuals. Since then, a burning topic has been the study of the molecular mechanism that leads to chromothripsis. Cumulating evidence has shown that chromothripsis may result from lagging chromosomes encapsulated in micronuclei, as well as from telomere fusions followed by chromosome bridge formation. In this chapter, we will outline the genomic characteristics of chromothripsis, and we present genomic methodologies that enable the detection of chromothripsis. Furthermore, we will give an overview of recent insights into the mechanisms underlying chromothripsis.
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Affiliation(s)
- Alessio Marcozzi
- Division of Biomedical Genetics, Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Franck Pellestor
- Laboratory of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, Montpellier, France.,INSERM Unit Plasticity of the Genome and Aging, Institute of Functional Genomics, Montpellier, France
| | - Wigard P Kloosterman
- Division of Biomedical Genetics, Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.
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28
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Abou-El-Ardat K, Seifert M, Becker K, Eisenreich S, Lehmann M, Hackmann K, Rump A, Meijer G, Carvalho B, Temme A, Schackert G, Schröck E, Krex D, Klink B. Comprehensive molecular characterization of multifocal glioblastoma proves its monoclonal origin and reveals novel insights into clonal evolution and heterogeneity of glioblastomas. Neuro Oncol 2017; 19:546-557. [PMID: 28201779 PMCID: PMC5464316 DOI: 10.1093/neuonc/now231] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Background The evolution of primary glioblastoma (GBM) is poorly understood. Multifocal GBM (ie, multiple synchronous lesions in one patient) could elucidate GBM development. Methods We present the first comprehensive study of 12 GBM foci from 6 patients using array-CGH, spectral karyotyping, gene expression arrays, and next-generation sequencing. Results Multifocal GBMs genetically resemble primary GBMs. Comparing foci from the same patient proved their monoclonal origin. All tumors harbored alterations in the 3 GBM core pathways: RTK/PI3K, p53, and RB regulatory pathways with aberrations of EGFR and CDKN2A/B in all (100%) patients. This unexpected high frequency reflects a distinct genetic signature of multifocal GBMs and might account for their highly malignant and invasive phenotype. Surprisingly, the types of mutations in these genes/pathways were different in tumor foci from the same patients. For example, we found distinct mutations/aberrations in PTEN, TP53, EGFR, and CDKN2A/B, which therefore must have occurred independently and late during tumor development. We also identified chromothripsis as a late event and in tumors with wild-type TP53. Only 2 events were found to be early in all patients: single copy loss of PTEN and TERT promoter point mutations. Conclusions Multifocal GBMs develop through parallel genetic evolution. The high frequency of alterations in 3 main pathways suggests that these are essential steps in GBM evolution; however, their late occurrence indicates that they are not founder events but rather subclonal drivers. This might account for the marked genetic heterogeneity seen in primary GBM and therefore has important implications for GBM therapy.
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Affiliation(s)
- Khalil Abou-El-Ardat
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Michael Seifert
- German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany.,Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Kerstin Becker
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sophie Eisenreich
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Matthias Lehmann
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karl Hackmann
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Andreas Rump
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Gerrit Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Beatriz Carvalho
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Achim Temme
- German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany.,Klinik und Poliklinik für Neurochirurgie, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Gabriele Schackert
- German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany.,Klinik und Poliklinik für Neurochirurgie, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Evelin Schröck
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Dietmar Krex
- German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany.,Klinik und Poliklinik für Neurochirurgie, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Barbara Klink
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
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Rücker FG, Dolnik A, Blätte TJ, Teleanu V, Ernst A, Thol F, Heuser M, Ganser A, Döhner H, Döhner K, Bullinger L. Chromothripsis is linked to TP53 alteration, cell cycle impairment, and dismal outcome in acute myeloid leukemia with complex karyotype. Haematologica 2017; 103:e17-e20. [PMID: 29079594 DOI: 10.3324/haematol.2017.180497] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Frank G Rücker
- Department of Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, Germany
| | - Anna Dolnik
- Department of Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, Germany
| | - Tamara J Blätte
- Department of Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, Germany
| | - Veronica Teleanu
- Department of Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, Germany
| | - Aurélie Ernst
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Berlin, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Berlin, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Berlin, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, Germany
| | - Lars Bullinger
- Department of Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, Germany.,Department of Hematology, Oncology and Tumor Immunology, Charité-University Medicine Berlin, Campus Virchow Klinikum, Berlin, Germany
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30
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Abstract
Genetic abnormalities are present in all tumor types, although the frequency and type can vary. Chromosome abnormalities include highly aberrant structures, particularly chromothriptic chromosomes. The generation of massive sequencing data has illuminated the scope of the mutational burden in cancer genomes, identifying patterns of mutations (mutation signatures), which have the potential to shed light on the relatedness and etiologies of cancers and impact therapy response. Some mutation patterns are clearly attributable to disruptions in pathways that maintain genomic integrity. Here we review recent advances in our understanding of genetic changes occurring in cancers and the roles of genome maintenance pathways.
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Affiliation(s)
- Elizabeth M Kass
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Mary Ellen Moynahan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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31
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Mandahl N, Magnusson L, Nilsson J, Viklund B, Arbajian E, von Steyern FV, Isaksson A, Mertens F. Scattered genomic amplification in dedifferentiated liposarcoma. Mol Cytogenet 2017; 10:25. [PMID: 28652867 PMCID: PMC5483303 DOI: 10.1186/s13039-017-0325-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/08/2017] [Indexed: 01/07/2023] Open
Abstract
Background Atypical lipomatous tumor (ALT), well differentiated liposarcoma (WDLS) and dedifferentiated liposarcoma (DDLS) are cytogenetically characterized by near-diploid karyotypes with no or few other aberrations than supernumerary ring or giant marker chromosomes, although DDLS tend to have somewhat more complex rearrangements. In contrast, pleomorphic liposarcomas (PLS) have highly aberrant and heterogeneous karyotypes. The ring and giant marker chromosomes contain discontinuous amplicons, in particular including multiple copies of the target genes CDK4, HMGA2 and MDM2 from 12q, but often also sequences from other chromosomes. Results The present study presents a DDLS with an atypical hypertriploid karyotype without any ring or giant marker chromosomes. SNP array analyses revealed amplification of almost the entire 5p and discontinuous amplicons of 12q including the classical target genes, in particular CDK4. In addition, amplicons from 1q, 3q, 7p, 9p, 11q and 20q, covering from 2 to 14 Mb, were present. FISH analyses showed that sequences from 5p and 12q were scattered, separately or together, over more than 10 chromosomes of varying size. At RNA sequencing, significantly elevated expression, compared to myxoid liposarcomas, was seen for TRIO and AMACR in 5p and of CDK4, HMGA2 and MDM2 in 12q. Conclusions The observed pattern of scattered amplification does not show the characteristics of chromothripsis, but is novel and differs from the well known cytogenetic manifestations of amplification, i.e., double minutes, homogeneously staining regions and ring chromosomes. Possible explanations for this unusual distribution of amplified sequences might be the mechanism of alternative lengthening of telomeres that is frequently active in DDLS and events associated with telomere crisis. Electronic supplementary material The online version of this article (doi:10.1186/s13039-017-0325-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Jenny Nilsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Björn Viklund
- Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Elsa Arbajian
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Fredrik Vult von Steyern
- Department of Orthopedics, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
| | - Anders Isaksson
- Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
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32
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Das S, Kelly D, Moran B, Han K, Mulligan N, Barrett C, Buckley PG, McMahon P, McCaffrey J, Van Essen HF, Connor K, Lambrechts D, Ylstra B, Gallagher WM, O'Connor DP, Kelly CM. Postmortem Examination of an Aggressive Case of Medullary Thyroid Carcinoma Characterized by Catastrophic Genomic Abnormalities. JCO Precis Oncol 2017; 1:1600063. [PMID: 32913965 DOI: 10.1200/po.16.00063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Sudipto Das
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Deirdre Kelly
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Bruce Moran
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Kathleen Han
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Niall Mulligan
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Ciara Barrett
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Patrick G Buckley
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Peter McMahon
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - John McCaffrey
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Hendrik F Van Essen
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Kate Connor
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Diether Lambrechts
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Bauke Ylstra
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - William M Gallagher
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Darran P O'Connor
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
| | - Catherine M Kelly
- , , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium
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New Insights in the Cytogenetic Practice: Karyotypic Chaos, Non-Clonal Chromosomal Alterations and Chromosomal Instability in Human Cancer and Therapy Response. Genes (Basel) 2017; 8:genes8060155. [PMID: 28587191 PMCID: PMC5485519 DOI: 10.3390/genes8060155] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 05/26/2017] [Accepted: 05/31/2017] [Indexed: 12/17/2022] Open
Abstract
Recently, non-clonal chromosomal alterations previously unappreciated are being proposed to be included in cytogenetic practice. The aim of this inclusion is to obtain a greater understanding of chromosomal instability (CIN) and tumor heterogeneity and their role in cancer evolution and therapy response. Although several genetic assays have allowed the evaluation of the variation in a population of cancer cells, these assays do not provide information at the level of individual cells, therefore limiting the information of the genomic diversity within tumors (heterogeneity). The karyotype is one of the few available cytogenetic techniques that allow us not only to identify the chromosomal alterations present within a single cell, but also allows us to profile both clonal (CCA) and non-clonal chromosomal alterations (NCCAs). A greater understanding of CIN and tumor heterogeneity in cancer could not only improve existing therapeutic regimens but could also be used as targets for the design of new therapeutic approaches. In this review we indicate the importance and significance of karyotypic chaos, NCCAs and CIN in the prognosis of human cancers.
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Ortega V, Chaubey A, Mendiola C, Ehman W, Vadlamudi K, Dupont B, Velagaleti G. Complex Chromosomal Rearrangements in B-Cell Lymphoma: Evidence of Chromoanagenesis? A Case Report. Neoplasia 2017; 18:223-8. [PMID: 27108385 PMCID: PMC4840270 DOI: 10.1016/j.neo.2016.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/08/2016] [Accepted: 02/15/2016] [Indexed: 11/19/2022] Open
Abstract
Genomic instability is a well-known hallmark of cancer. Recent genome sequencing studies have led to the identification of novel phenomena called chromothripsis and chromoanasynthesis in which complex genomic rearrangements are thought to be derived from a single catastrophic event rather than by several incremental steps. A new term chromoanagenesis or chromosomal rebirth was coined recently to group these two one-step catastrophic events together. These phenomena suggest an evolutionary modality for cancer cells to circumvent individual mutational events with one simultaneous shattering of chromosomes resulting in the random reassembling of segmented genetic material to form complex derivative chromosomes. We report a case of possible chromoanagenesis in a patient with diffuse large B-cell lymphoma. Chromosome analysis from the biopsy showed a complex karyotype with multiple numerical and structural rearrangements including a translocation of chromosomes 3 and 7 involving the BCL6 gene region, with the derivative chromosome further rearranging with chromosomes 14, 7, and 22 with involvement of the IGH gene region. Fluorescence in situ hybridization studies confirmed these findings. Chromosomal microarray studies showed multiple complex copy number variations including a chromosome 12 abnormality, the complexity of which appears to suggest the phenomenon of chromoanagenesis. Our case further illustrates that lymphomagenesis can be complex and may arise from a catastrophic event resulting in multiple complex chromosome rearrangements.
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Affiliation(s)
- Veronica Ortega
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX
| | | | - Christina Mendiola
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX
| | - William Ehman
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX
| | - Kumari Vadlamudi
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX
| | | | - Gopalrao Velagaleti
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX.
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Fukami M, Shima H, Suzuki E, Ogata T, Matsubara K, Kamimaki T. Catastrophic cellular events leading to complex chromosomal rearrangements in the germline. Clin Genet 2017; 91:653-660. [PMID: 27888607 DOI: 10.1111/cge.12928] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 12/28/2022]
Abstract
Although complex chromosomal rearrangements were thought to reflect the accumulation of DNA damage over time, recent studies have shown that such rearrangements frequently arise from 'all-at-once' catastrophic cellular events. These events, designated chromothripsis, chromoanasynthesis, and chromoanagenesis, were first documented in the cancer genome and subsequently observed in the germline. These events likely result from micronucleus-mediated chromosomal shattering and subsequent random reassembly of DNA fragments, although several other mechanisms have also been proposed. Typically, only one or a few chromosomes of paternal origin are affected per event. These events can produce intrachromosomal deletions, duplications, inversions, and translocations, as well as interchromosomal translocations. Germline complex rearrangements of autosomes often result in developmental delay and dysmorphic features, whereas X chromosomal rearrangements are usually associated with relatively mild clinical manifestations. The concept of these catastrophic events provides novel insights into the etiology of human genomic disorders. This review introduces the molecular characteristics and phenotypic outcomes of catastrophic cellular events in the germline.
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Affiliation(s)
- M Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - H Shima
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - E Suzuki
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - T Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - K Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - T Kamimaki
- Department of Pediatrics, Shizuoka City Shimizu Hospital, Shizuoka, Japan
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Chen H, Singh RR, Lu X, Huo L, Yao H, Aldape K, Abraham R, Virani S, Mehrotra M, Mishra BM, Bousamra A, Albarracin C, Wu Y, Roy-Chowdhuri S, Shamanna RK, Routbort MJ, Medeiros LJ, Patel KP, Broaddus R, Sahin A, Luthra R. Genome-wide copy number aberrations and HER2 and FGFR1 alterations in primary breast cancer by molecular inversion probe microarray. Oncotarget 2017; 8:10845-10857. [PMID: 28125801 PMCID: PMC5355228 DOI: 10.18632/oncotarget.14802] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/10/2017] [Indexed: 11/25/2022] Open
Abstract
Breast cancer remains the second leading cause of cancer-related death in women despite stratification based on standard hormonal receptor (HR) and HER2 testing. Additional prognostic markers are needed to improve breast cancer treatment. Chromothripsis, a catastrophic genome rearrangement, has been described recently in various cancer genomes and affects cancer progression and prognosis. However, little is known about chromothripsis in breast cancer. To identify novel prognostic biomarkers in breast cancer, we used molecular inversion probe (MIP) microarray to explore genome-wide copy number aberrations (CNA) and breast cancer-related gene alterations in DNA extracted from formalin-fixed paraffin-embedded tissue. We examined 42 primary breast cancers with known HR and HER2 status assessed via immunohistochemistry and FISH and analyzed MIP microarray results for correlation with standard tests and survival outcomes. Global genome-wide CNA ranged from 0.2% to 65.7%. Chromothripsis-like patterns were observed in 23/38 (61%) cases and were more prevalent in cases with ≥10% CNA (20/26, 77%) than in cases with <10% CNA (3/12, 25%; p<0.01). Most frequently involved chromosomal segment was 17q12-q21, the HER2 locus. Chromothripsis-like patterns involving 17q12 were observed in 8/19 (42%) of HER2-amplified tumors but not in any of the tumors without HER2 amplification (0/19; p<0.01). HER2 amplification detected by MIP microarray was 95% concordant with conventional testing (39/41). Interestingly, 21% of patients (9/42) had fibroblast growth factor receptor 1 (FGFR1)amplification and had a 460% higher risk for mortality than those without FGFR1 amplification (p<0.01). In summary, MIP microarray provided a robust assessment of genomic CNA of breast cancer.
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MESH Headings
- Adult
- Aged
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Breast Neoplasms, Male/genetics
- Breast Neoplasms, Male/metabolism
- Breast Neoplasms, Male/pathology
- Chromosomes, Human, Pair 17/genetics
- Chromothripsis
- DNA Copy Number Variations
- Female
- Gene Amplification
- Genome-Wide Association Study/methods
- High-Throughput Nucleotide Sequencing
- Humans
- Immunohistochemistry
- In Situ Hybridization, Fluorescence
- Male
- Microarray Analysis/methods
- Middle Aged
- Molecular Probes/genetics
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Survival Analysis
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Affiliation(s)
- Hui Chen
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajesh R. Singh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinyan Lu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lei Huo
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenneth Aldape
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Ronald Abraham
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shumaila Virani
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bal Mukund Mishra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alex Bousamra
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Allegheny Health Network, Pittsburgh, PA, USA
| | - Constance Albarracin
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yun Wu
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sinchita Roy-Chowdhuri
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rashmi Kanagal Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark J. Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L. Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Russell Broaddus
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aysegul Sahin
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Chromothripsis in Two Patients With Renal Cell Carcinoma: A Case Series. Clin Genitourin Cancer 2017; 15:e137-e143. [DOI: 10.1016/j.clgc.2016.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/11/2016] [Indexed: 12/11/2022]
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Phillips T, Devata S, Wilcox RA. Challenges and opportunities for checkpoint blockade in T-cell lymphoproliferative disorders. J Immunother Cancer 2016; 4:95. [PMID: 28031823 PMCID: PMC5170899 DOI: 10.1186/s40425-016-0201-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/01/2016] [Indexed: 01/05/2023] Open
Abstract
The T-cell lymphoproliferative disorders are a heterogeneous group of non-Hodgkin’s lymphomas (NHL) for which current therapeutic strategies are inadequate, as most patients afflicted with these NHL will succumb to disease progression within 2 years of diagnosis. Appreciation of the genetic and immunologic landscape of these aggressive NHL, including PD-L1 (B7-H1, CD274) expression by malignant T cells and within the tumor microenvironment, provides a strong rationale for therapeutic targeting this immune checkpoint. While further studies are needed, the available data suggests that responses with PD-1 checkpoint blockade alone will unlikely approach those achieved in other lymphoproliferative disorders. Herein, we review the unique challenges posed by the T-cell lymphoproliferative disorders and discuss potential strategies to optimize checkpoint blockade in these T-cell derived malignancies.
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Affiliation(s)
- Tycel Phillips
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI USA
| | - Sumana Devata
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI USA
| | - Ryan A Wilcox
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI USA ; University of Michigan Comprehensive Cancer Center, 4310 Cancer Center, 1500 East Medical Center Drive, Ann Arbor, MI 48109 USA
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Niu ZS, Niu XJ, Wang WH. Genetic alterations in hepatocellular carcinoma: An update. World J Gastroenterol 2016; 22:9069-9095. [PMID: 27895396 PMCID: PMC5107590 DOI: 10.3748/wjg.v22.i41.9069] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/20/2016] [Accepted: 10/19/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Although recent advances in therapeutic approaches for treating HCC have improved the prognoses of patients with HCC, this cancer is still associated with a poor survival rate mainly due to late diagnosis. Therefore, a diagnosis must be made sufficiently early to perform curative and effective treatments. There is a need for a deeper understanding of the molecular mechanisms underlying the initiation and progression of HCC because these mechanisms are critical for making early diagnoses and developing novel therapeutic strategies. Over the past decade, much progress has been made in elucidating the molecular mechanisms underlying hepatocarcinogenesis. In particular, recent advances in next-generation sequencing technologies have revealed numerous genetic alterations, including recurrently mutated genes and dysregulated signaling pathways in HCC. A better understanding of the genetic alterations in HCC could contribute to identifying potential driver mutations and discovering novel therapeutic targets in the future. In this article, we summarize the current advances in research on the genetic alterations, including genomic instability, single-nucleotide polymorphisms, somatic mutations and deregulated signaling pathways, implicated in the initiation and progression of HCC. We also attempt to elucidate some of the genetic mechanisms that contribute to making early diagnoses of and developing molecularly targeted therapies for HCC.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Genomic Instability
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Molecular Diagnostic Techniques
- Molecular Targeted Therapy
- Mutation
- Patient Selection
- Phenotype
- Polymorphism, Single Nucleotide
- Precision Medicine
- Predictive Value of Tests
- Signal Transduction
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Abáigar M, Robledo C, Benito R, Ramos F, Díez-Campelo M, Hermosín L, Sánchez-del-Real J, Alonso JM, Cuello R, Megido M, Rodríguez JN, Martín-Núñez G, Aguilar C, Vargas M, Martín AA, García JL, Kohlmann A, del Cañizo MC, Hernández-Rivas JM. Chromothripsis Is a Recurrent Genomic Abnormality in High-Risk Myelodysplastic Syndromes. PLoS One 2016; 11:e0164370. [PMID: 27741277 PMCID: PMC5065168 DOI: 10.1371/journal.pone.0164370] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 09/23/2016] [Indexed: 11/18/2022] Open
Abstract
To explore novel genetic abnormalities occurring in myelodysplastic syndromes (MDS) through an integrative study combining array-based comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) in a series of MDS and MDS/myeloproliferative neoplasms (MPN) patients. 301 patients diagnosed with MDS (n = 240) or MDS/MPN (n = 61) were studied at the time of diagnosis. A genome-wide analysis of DNA copy number abnormalities was performed. In addition, a mutational analysis of DNMT3A, TET2, RUNX1, TP53 and BCOR genes was performed by NGS in selected cases. 285 abnormalities were identified in 71 patients (23.6%). Three high-risk MDS cases (1.2%) displayed chromothripsis involving exclusively chromosome 13 and affecting some cancer genes: FLT3, BRCA2 and RB1. All three cases carried TP53 mutations as revealed by NGS. Moreover, in the whole series, the integrative analysis of aCGH and NGS enabled the identification of cryptic recurrent deletions in 2p23.3 (DNMT3A; n = 2.8%), 4q24 (TET2; n = 10%) 17p13 (TP53; n = 8.5%), 21q22 (RUNX1; n = 7%), and Xp11.4 (BCOR; n = 2.8%), while mutations in the non-deleted allele where found only in DNMT3A (n = 1), TET2 (n = 3), and TP53 (n = 4). These cryptic abnormalities were detected mainly in patients with normal (45%) or non-informative (15%) karyotype by conventional cytogenetics, except for those with TP53 deletion and mutation (15%), which had a complex karyotype. In addition to well-known copy number defects, the presence of chromothripsis involving chromosome 13 was a novel recurrent change in high-risk MDS patients. Array CGH analysis revealed the presence of cryptic abnormalities in genomic regions where MDS-related genes, such as TET2, DNMT3A, RUNX1 and BCOR, are located.
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Affiliation(s)
- María Abáigar
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Cristina Robledo
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Rocío Benito
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Fernando Ramos
- IBIOMED, Instituto de Biomedicina, Universidad de León, León, Spain
- Servicio de Hematología, Hospital Universitario de León, León, Spain
| | - María Díez-Campelo
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Lourdes Hermosín
- Servicio de Hematología, Hospital Jerez de la Frontera, Cádiz, Spain
| | | | - Jose M. Alonso
- Servicio de Hematología, Hospital Río Carrión, Palencia, Spain
| | - Rebeca Cuello
- Servicio de Hematología, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Marta Megido
- Servicio de Hematología, Hospital del Bierzo, Ponferrada, Spain
| | | | | | - Carlos Aguilar
- Servicio de Hematología, Hospital General de Soria, Soria, Spain
| | - Manuel Vargas
- Servicio de Hematología, Hospital Comarcal de Jarrio, Jarrio-Coaña, Spain
| | - Ana A. Martín
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Juan L. García
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Alexander Kohlmann
- AstraZeneca, Personalized Healthcare and Biomarkers, Innovative Medicines and Early Development, Cambridge, United Kingdom
| | - M. Consuelo del Cañizo
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- IBSAL, Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
| | - Jesús M. Hernández-Rivas
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- IBSAL, Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- * E-mail:
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Lee JC, Lu TP, Changou CA, Liang CW, Huang HN, Lauria A, Huang HY, Lin CY, Chiang YC, Davidson B, Lin MC, Kuo KT. Genomewide copy number analysis of Müllerian adenosarcoma identified chromosomal instability in the aggressive subgroup. Mod Pathol 2016; 29:1070-82. [PMID: 27255164 DOI: 10.1038/modpathol.2016.99] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/23/2016] [Accepted: 04/24/2016] [Indexed: 12/19/2022]
Abstract
Müllerian adenosarcomas are malignant gynecologic neoplasms. Advanced staging and sarcomatous overgrowth predict poor prognosis. Because the genomic landscape remains poorly understood, we conducted this study to characterize the genomewide copy number variations in adenosarcomas. Sixteen tumors, including eight with and eight without sarcomatous overgrowth, were subjected to a molecular inversion probe array analysis. Copy number variations, particularly losses, were significantly higher in cases with sarcomatous overgrowth. Frequent gains of chromosomal 12q were noted, often involving cancer-associated genes CDK4 (six cases), MDM2, CPM, YEATS4, DDIT3, GLI1 (five each), HMGA2 and STAT6 (four), without association with sarcomatous overgrowth status. The most frequent losses involved chromosomes 13q (five cases), 9p, 16q and 17q (four cases each) and were almost limited to cases with sarcomatous overgrowth. MDM2 and CDK4 amplification, as well as losses of RB1 (observed in two cases) and CDKN2A/B (one case), was verified by FISH. By immunohistochemistry, all MDM2/CDK4-coamplified cases were confirmed to overexpress both encoded proteins, whereas all four cases with (plus an additional four without) gain of HMGA2 overexpressed the HMGA2 protein. Both cases with RB1 loss were negative for the immunostaining of the encoded protein. Chromothripsis-like copy number profiles involving chromosome 12 or 14 were observed in three fatal cases, all of which harbored sarcomatous overgrowth. With whole chromosome painting and deconvolution fluorescent microscopy, dividing tumor cells in all three cases were shown to have scattered extrachromosomal materials derived from chromosomes involved by chromothripsis, suggesting that this phenomenon may serve as visual evidence for chromothripsis in paraffin tissue. In conclusion, we identified frequent chromosome 12q amplifications, including loci containing potential pharmacological targets. Global chromosomal instability and chromothripsis were more frequent in cases with sarcomatous overgrowth. To our knowledge, this is the first time that evidence of chromothripsis has been demonstrated in paraffin-embedded clinical tissues and in adenosarcomas.
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Affiliation(s)
- Jen-Chieh Lee
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tzu-Pin Lu
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun A Changou
- Integrated Laboratory, Center of Translational Medicine, Graduate Institute of Translational Medicine, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Taipei, Taiwan
| | - Cher-Wei Liang
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsien-Neng Huang
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Pathology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Alexandra Lauria
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hsuan-Ying Huang
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chin-Yao Lin
- Department of Pathology, Cardinal Tien Hospital Yung-Ho Branch, New Taipei City, Taiwan
| | - Ying-Cheng Chiang
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ben Davidson
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ming-Chieh Lin
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Kuan-Ting Kuo
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
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Kovtun IV, Murphy SJ, Johnson SH, Cheville JC, Vasmatzis G. Chromosomal catastrophe is a frequent event in clinically insignificant prostate cancer. Oncotarget 2016; 6:29087-96. [PMID: 26337081 PMCID: PMC4745713 DOI: 10.18632/oncotarget.4900] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/11/2015] [Indexed: 11/27/2022] Open
Abstract
Massive genomic rearrangements, a result of single catastrophic event termed chromothrispsis or chromosomal catastrophe, have been identified in a variety of human cancers. In a few cancer types, chromothripsis was found to be associated with poor prognosis. We performed mate-pair sequencing and analysis of structural rearrangements in 132 prostate cancer cases which included clinically insignificant Gleason score 6 tumors, clinically significant tumors of higher grade (7+) and high grade prostatic intraepithelial neoplasia. Chromothripsis was observed at least 30 per cent of the samples across different grades. Surprisingly, it was frequently observed in clinically insignificant Gleason score 6 tumors, indicating that chromothripsis does not define more aggressive phenotype. The degree of chromothripsis did not increase significantly in tumors of advanced grades and did not appear to contribute to tumor progression. Our data showed that distribution of chromothriptic rearrangements differed from that of fragile sites but correlated with the size of chromosomes. We also provided evidence that rearrangements resulting from chromothripsis were present in the cells of neighboring Gleason patterns of the same tumor. Our data suggest that that chromothripsis plays role in prostate cancer initiation.
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Affiliation(s)
- Irina V Kovtun
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA.,Department of Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen J Murphy
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah H Johnson
- Department of Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - John C Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.,Department of Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Yang J, Liu J, Ouyang L, Chen Y, Liu B, Cai H. CTLPScanner: a web server for chromothripsis-like pattern detection. Nucleic Acids Res 2016; 44:W252-8. [PMID: 27185889 PMCID: PMC4987951 DOI: 10.1093/nar/gkw434] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/08/2016] [Indexed: 02/05/2023] Open
Abstract
Chromothripsis is a recently observed phenomenon in cancer cells in which one or several chromosomes shatter into pieces with subsequent inaccurate reassembly and clonal propagation. This type of event generates a potentially vast number of mutations within a relatively short-time period, and has been considered as a new paradigm in cancer development. Despite recent advances, much work is still required to better understand the molecular mechanisms of this phenomenon, and thus an easy-to-use tool is in urgent need for automatically detecting and annotating chromothripsis. Here we present CTLPScanner, a web server for detection of chromothripsis-like pattern (CTLP) in genomic array data. The output interface presents intuitive graphical representations of detected chromosome pulverization region, as well as detailed results in table format. CTLPScanner also provides additional information for associated genes in chromothripsis region to help identify the potential candidates involved in tumorigenesis. To assist in performing meta-data analysis, we integrated over 50 000 pre-processed genomic arrays from The Cancer Genome Atlas and Gene Expression Omnibus into CTLPScanner. The server allows users to explore the presence of chromothripsis signatures from public data resources, without carrying out any local data processing. CTLPScanner is freely available at http://cgma.scu.edu.cn/CTLPScanner/.
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Affiliation(s)
- Jian Yang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Jixiang Liu
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, Sichuan, China
| | - Yi Chen
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, Sichuan, China Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Bo Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, Sichuan, China
| | - Haoyang Cai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
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Wang L, Zehir A, Nafa K, Zhou N, Berger MF, Casanova J, Sadowska J, Lu C, Allis CD, Gounder M, Chandhanayingyong C, Ladanyi M, Boland PJ, Hameed M. Genomic aberrations frequently alter chromatin regulatory genes in chordoma. Genes Chromosomes Cancer 2016; 55:591-600. [PMID: 27072194 DOI: 10.1002/gcc.22362] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023] Open
Abstract
Chordoma is a rare primary bone neoplasm that is resistant to standard chemotherapies. Despite aggressive surgical management, local recurrence and metastasis is not uncommon. To identify the specific genetic aberrations that play key roles in chordoma pathogenesis, we utilized a genome-wide high-resolution SNP-array and next generation sequencing (NGS)-based molecular profiling platform to study 24 patient samples with typical histopathologic features of chordoma. Matching normal tissues were available for 16 samples. SNP-array analysis revealed nonrandom copy number losses across the genome, frequently involving 3, 9p, 1p, 14, 10, and 13. In contrast, copy number gain is uncommon in chordomas. Two minimum deleted regions were observed on 3p within a ∼8 Mb segment at 3p21.1-p21.31, which overlaps SETD2, BAP1 and PBRM1. The minimum deleted region on 9p was mapped to CDKN2A locus at 9p21.3, and homozygous deletion of CDKN2A was detected in 5/22 chordomas (∼23%). NGS-based molecular profiling demonstrated an extremely low level of mutation rate in chordomas, with an average of 0.5 mutations per sample for the 16 cases with matched normal. When the mutated genes were grouped based on molecular functions, many of the mutation events (∼40%) were found in chromatin regulatory genes. The combined copy number and mutation profiling revealed that SETD2 is the single gene affected most frequently in chordomas, either by deletion or by mutations. Our study demonstrated that chordoma belongs to the C-class (copy number changes) tumors whose oncogenic signature is non-random multiple copy number losses across the genome and genomic aberrations frequently alter chromatin regulatory genes. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nengyi Zhou
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacklyn Casanova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chao Lu
- Department of Laboratory of Chromatin Biology and Epigenetics, the Rockefeller University, New York, NY
| | - C David Allis
- Department of Laboratory of Chromatin Biology and Epigenetics, the Rockefeller University, New York, NY
| | - Mrinal Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Patrick J Boland
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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45
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Chromothripsis and epigenomics complete causality criteria for cannabis- and addiction-connected carcinogenicity, congenital toxicity and heritable genotoxicity. Mutat Res 2016; 789:15-25. [PMID: 27208973 DOI: 10.1016/j.mrfmmm.2016.05.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/17/2016] [Accepted: 05/01/2016] [Indexed: 12/30/2022]
Abstract
The recent demonstration that massive scale chromosomal shattering or pulverization can occur abruptly due to errors induced by interference with the microtubule machinery of the mitotic spindle followed by haphazard chromosomal annealing, together with sophisticated insights from epigenetics, provide profound mechanistic insights into some of the most perplexing classical observations of addiction medicine, including cancerogenesis, the younger and aggressive onset of addiction-related carcinogenesis, the heritability of addictive neurocircuitry and cancers, and foetal malformations. Tetrahydrocannabinol (THC) and other addictive agents have been shown to inhibit tubulin polymerization which perturbs the formation and function of the microtubules of the mitotic spindle. This disruption of the mitotic machinery perturbs proper chromosomal segregation during anaphase and causes micronucleus formation which is the primary locus and cause of the chromosomal pulverization of chromothripsis and downstream genotoxic events including oncogene induction and tumour suppressor silencing. Moreover the complementation of multiple positive cannabis-cancer epidemiological studies, and replicated dose-response relationships with established mechanisms fulfils causal criteria. This information is also consistent with data showing acceleration of the aging process by drugs of addiction including alcohol, tobacco, cannabis, stimulants and opioids. THC shows a non-linear sigmoidal dose-response relationship in multiple pertinent in vitro and preclinical genotoxicity assays, and in this respect is similar to the serious major human mutagen thalidomide. Rising community exposure, tissue storage of cannabinoids, and increasingly potent phytocannabinoid sources, suggests that the threshold mutagenic dose for cancerogenesis will increasingly be crossed beyond the developing world, and raise transgenerational transmission of teratogenicity as an increasing concern.
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46
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Schiffman JD, Breen M. Comparative oncology: what dogs and other species can teach us about humans with cancer. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0231. [PMID: 26056372 DOI: 10.1098/rstb.2014.0231] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Over 1.66 million humans (approx. 500/100,000 population rate) and over 4.2 million dogs (approx. 5300/100,000 population rate) are diagnosed with cancer annually in the USA. The interdisciplinary field of comparative oncology offers a unique and strong opportunity to learn more about universal cancer risk and development through epidemiology, genetic and genomic investigations. Working across species, researchers from human and veterinary medicine can combine scientific findings to understand more quickly the origins of cancer and translate these findings to novel therapies to benefit both human and animals. This review begins with the genetic origins of canines and their advantage in cancer research. We next focus on recent findings in comparative oncology related to inherited, or genetic, risk for tumour development. We then detail the somatic, or genomic, changes within tumours and the similarities between species. The shared cancers between humans and dogs that we discuss include sarcoma (osteosarcoma, soft tissue sarcoma, histiocytic sarcoma, hemangiosarcoma), haematological malignancies (lymphoma, leukaemia), bladder cancer, intracranial neoplasms (meningioma, glioma) and melanoma. Tumour risk in other animal species is also briefly discussed. As the field of genomics advances, we predict that comparative oncology will continue to benefit both humans and the animals that live among us.
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Affiliation(s)
- Joshua D Schiffman
- Department of Pediatrics and Oncological Sciences, Primary Children's Hospital, Intermountain Healthcare, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, Center for Comparative Medicine and Translational Research, Center for Human Health and the Environment, Cancer Genetics, UNC Lineberger Comprehensive Cancer Center, North Carolina State University, Raleigh, NC, USA
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Storchová Z, Kloosterman WP. The genomic characteristics and cellular origin of chromothripsis. Curr Opin Cell Biol 2016; 40:106-113. [PMID: 27023493 DOI: 10.1016/j.ceb.2016.03.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/19/2016] [Accepted: 03/05/2016] [Indexed: 01/25/2023]
Abstract
Human genomes are continuously subjected to mutations, which can drive genetic diseases and cancer. An intriguing recent finding has been the discovery of chromothripsis, a spectacular and complex form of chromosome rearrangement that can occur in the genomes of cancer cells and patients with congenital diseases. Chromothripsis has been described in a large array of human cancers and various types of chromothripsis have appeared, which differ in complexity and genomic hallmarks. From the combined genomic data a consensus hypothesis has been inferred, involving aberrant DNA replication and chromosome shattering as the underlying processes explaining chromothripsis. In addition, recent work has established several cellular models that recapitulate chromothripsis under defined experimental conditions. One of these models indicates that chromothripsis can originate from DNA damage in micronuclei, providing an elegant explanation for the restriction of chromothriptic rearrangements to a single chromosome. Alternatively, chromothripsis can be caused by telomere crisis, a process that involves formation of dicentric chromosomes and chromatin bridges. Here, we summarize the genomic features of chromothripsis and we discuss experimental approaches that allow dissection of the chromothripsis process.
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Affiliation(s)
- Zuzana Storchová
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Molecular Genetics, University of Kaiserslautern, Paul-Ehrlich Str. 24, 67653 Kaiserslautern, Germany
| | - Wigard P Kloosterman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands.
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48
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Forero-Castro M, Robledo C, Benito R, Abáigar M, África Martín A, Arefi M, Fuster JL, de las Heras N, Rodríguez JN, Quintero J, Riesco S, Hermosín L, de la Fuente I, Recio I, Ribera J, Labrador J, Alonso JM, Olivier C, Sierra M, Megido M, Corchete-Sánchez LA, Ciudad Pizarro J, García JL, Ribera JM, Hernández-Rivas JM. Genome-Wide DNA Copy Number Analysis of Acute Lymphoblastic Leukemia Identifies New Genetic Markers Associated with Clinical Outcome. PLoS One 2016; 11:e0148972. [PMID: 26872047 PMCID: PMC4752220 DOI: 10.1371/journal.pone.0148972] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/26/2016] [Indexed: 01/13/2023] Open
Abstract
Identifying additional genetic alterations associated with poor prognosis in acute lymphoblastic leukemia (ALL) is still a challenge. Aims: To characterize the presence of additional DNA copy number alterations (CNAs) in children and adults with ALL by whole-genome oligonucleotide array (aCGH) analysis, and to identify their associations with clinical features and outcome. Array-CGH was carried out in 265 newly diagnosed ALLs (142 children and 123 adults). The NimbleGen CGH 12x135K array (Roche) was used to analyze genetic gains and losses. CNAs were analyzed with GISTIC and aCGHweb software. Clinical and biological variables were analyzed. Three of the patients showed chromothripsis (cth6, cth14q and cth15q). CNAs were associated with age, phenotype, genetic subtype and overall survival (OS). In the whole cohort of children, the losses on 14q32.33 (p = 0.019) and 15q13.2 (p = 0.04) were related to shorter OS. In the group of children without good- or poor-risk cytogenetics, the gain on 1p36.11 was a prognostic marker independently associated with shorter OS. In adults, the gains on 19q13.2 (p = 0.001) and Xp21.1 (p = 0.029), and the loss of 17p (p = 0.014) were independent markers of poor prognosis with respect to OS. In summary, CNAs are frequent in ALL and are associated with clinical parameters and survival. Genome-wide DNA copy number analysis allows the identification of genetic markers that predict clinical outcome, suggesting that detection of these genetic lesions will be useful in the management of patients newly diagnosed with ALL.
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Affiliation(s)
- Maribel Forero-Castro
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- School of Biological Sciences (GEBIMOL), Pedagogical and Technological University of Colombia (UPTC), Tunja, Colombia
| | - Cristina Robledo
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - Rocío Benito
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - María Abáigar
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - Ana África Martín
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Maryam Arefi
- Department of Hematology, Clinical University Hospital of Valladolid, Valladolid, Spain
| | - José Luis Fuster
- Department of Pediatric Oncohematology, Clinical University Hospital Virgen de la Arrixaca, Murcia, Spain
| | | | - Juan N. Rodríguez
- Department of Hematology, Juan Ramón Jiménez Hospital, Huelva, Spain
| | | | - Susana Riesco
- Department of Pediatric Oncohematology, University Hospital of Salamanca, Salamanca, Spain
| | - Lourdes Hermosín
- Department of Hematology, Jerez Hospital, Jerez de la Frontera, Cádiz, Spain
| | | | - Isabel Recio
- Department of Hematology, Nuestra Señora de Sonsoles Hospital, Avila, Spain
| | - Jordi Ribera
- Department of Hematology, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Jorge Labrador
- Department of Hematology, University Hospital of Burgos, Burgos, Spain
| | - José M. Alonso
- Department of Hematology, Rio Carrión Hospital, Palencia, Spain
| | - Carmen Olivier
- Department of Hematology, General Hospital of Segovia, Segovia, Spain
| | - Magdalena Sierra
- Department of Hematology, Virgen de la Concha Hospital, Zamora, Spain
| | - Marta Megido
- Department of Hematology, Bierzo Hospital, León/Ponferrada, Spain
| | | | - Juana Ciudad Pizarro
- Cytometry Service (NUCLEUS Research Support Platform), University of Salamanca (USAL), Salamanca, Spain
| | - Juan Luis García
- Institute of Health Science Studies of Castile and León (IESCYL), Salamanca, Spain
| | - José M. Ribera
- Department of Hematology, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Jesús M. Hernández-Rivas
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
- * E-mail:
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49
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The Challenge of Cancer Genomics in Rare Nervous System Neoplasms: Malignant Peripheral Nerve Sheath Tumors as a Paradigm for Cross-Species Comparative Oncogenomics. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 186:464-77. [PMID: 26740486 DOI: 10.1016/j.ajpath.2015.10.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/20/2015] [Indexed: 12/12/2022]
Abstract
Comprehensive genomic analyses of common nervous system cancers provide new insights into their pathogenesis, diagnosis, and treatment. Although analogous studies of rare nervous system tumors are needed, there are major barriers to performing such studies. Cross-species comparative oncogenomics, identifying driver mutations in mouse cancer models and validating them in human tumors, is a promising alternative. Although still in its infancy, this approach is being applied to malignant peripheral nerve sheath tumors (MPNSTs), rare Schwann cell-derived malignancies that occur sporadically, after radiotherapy, and in neurofibromatosis type 1. Studies of human neurofibromatosis type 1-associated tumors suggest that NF1 tumor suppressor loss in Schwann cells triggers cell-autonomous and intercellular changes, resulting in development of benign neurofibromas; subsequent neurofibroma-MPNST progression is caused by aberrant growth factor signaling and mutations affecting the p16(INK4A)-cyclin D1-CDK4-Rb and p19(ARF)-Mdm2-p53 cell cycle pathways. Mice with Nf1, Trp53, and/or Cdkn2a mutations that overexpress the Schwann cell mitogen neuregulin-1 or overexpress the epidermal growth factor receptor validate observations in human tumors and, to various degrees, model human tumorigenesis. Genomic analyses of MPNSTs arising in neuregulin-1 and epidermal growth factor receptor-overexpressing mice and forward genetic screens with Sleeping Beauty transposons implicate additional signaling cascades in MPNST pathogenesis. These studies confirm the utility of mouse models for MPNST driver gene discovery and provide new insights into the complexity of MPNST pathogenesis.
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50
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Leibowitz ML, Zhang CZ, Pellman D. Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. Annu Rev Genet 2015; 49:183-211. [DOI: 10.1146/annurev-genet-120213-092228] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mitchell L. Leibowitz
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
| | - Cheng-Zhong Zhang
- Department of Pediatric Oncology,
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
| | - David Pellman
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
- Howard Hughes Medical Institute, Boston, Massachusetts 02115
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