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Poot M. The Legacy of George M. Martin: From Segmental Progeroid Syndromes to Antigeroid Syndromes. Cytogenet Genome Res 2024; 163:231-235. [PMID: 38522422 DOI: 10.1159/000537967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024] Open
Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Biozentrum, Am Hubland, Würzburg, Germany
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2
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Bailey SM, Cross EM, Kinner-Bibeau L, Sebesta HC, Bedford JS, Tompkins CJ. Monitoring Genomic Structural Rearrangements Resulting from Gene Editing. J Pers Med 2024; 14:110. [PMID: 38276232 PMCID: PMC10817574 DOI: 10.3390/jpm14010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
The cytogenomics-based methodology of directional genomic hybridization (dGH) enables the detection and quantification of a more comprehensive spectrum of genomic structural variants than any other approach currently available, and importantly, does so on a single-cell basis. Thus, dGH is well-suited for testing and/or validating new advancements in CRISPR-Cas9 gene editing systems. In addition to aberrations detected by traditional cytogenetic approaches, the strand specificity of dGH facilitates detection of otherwise cryptic intra-chromosomal rearrangements, specifically small inversions. As such, dGH represents a powerful, high-resolution approach for the quantitative monitoring of potentially detrimental genomic structural rearrangements resulting from exposure to agents that induce DNA double-strand breaks (DSBs), including restriction endonucleases and ionizing radiations. For intentional genome editing strategies, it is critical that any undesired effects of DSBs induced either by the editing system itself or by mis-repair with other endogenous DSBs are recognized and minimized. In this paper, we discuss the application of dGH for assessing gene editing-associated structural variants and the potential heterogeneity of such rearrangements among cells within an edited population, highlighting its relevance to personalized medicine strategies.
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Affiliation(s)
- Susan M. Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Erin M. Cross
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | | | - Henry C. Sebesta
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Joel S. Bedford
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
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3
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Poot M. Methods of Detection and Mechanisms of Origin of Complex Structural Genome Variations. Methods Mol Biol 2024; 2825:39-65. [PMID: 38913302 DOI: 10.1007/978-1-0716-3946-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Based on classical karyotyping, structural genome variations (SVs) have generally been considered to be either "simple" (with one or two breakpoints) or "complex" (with more than two breakpoints). Studying the breakpoints of SVs at nucleotide resolution revealed additional, subtle structural variations, such that even "simple" SVs turned out to be "complex." Genome-wide sequencing methods, such as fosmid and paired-end mapping, short-read and long-read whole genome sequencing, and single-molecule optical mapping, also indicated that the number of SVs per individual was considerably larger than expected from karyotyping and high-resolution chromosomal array-based studies. Interestingly, SVs were detected in studies of cohorts of individuals without clinical phenotypes. The common denominator of all SVs appears to be a failure to accurately repair DNA double-strand breaks (DSBs) or to halt cell cycle progression if DSBs persist. This review discusses the various DSB response mechanisms during the mitotic cell cycle and during meiosis and their regulation. Emphasis is given to the molecular mechanisms involved in the formation of translocations, deletions, duplications, and inversions during or shortly after meiosis I. Recently, CRISPR-Cas9 studies have provided unexpected insights into the formation of translocations and chromothripsis by both breakage-fusion-bridge and micronucleus-dependent mechanisms.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Wuerzburg, Wuerzburg, Germany
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4
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Insight into the Molecular Basis Underlying Chromothripsis. Int J Mol Sci 2022; 23:ijms23063318. [PMID: 35328739 PMCID: PMC8948871 DOI: 10.3390/ijms23063318] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
Chromoanagenesis constitutes a group of events that arise from single cellular events during early development. This particular class of complex rearrangements is a newfound occurrence that may lead to chaotic and complex genomic realignments. By that, chromoanagenesis is thought to be a crucial factor regarding macroevolution of the genome, and consequently is affecting the karyotype revolution together with genomic plasticity. One of chromoanagenesis-type of events is chromothripsis. It is characterised by the breakage of the chromosomal structure and its reassembling in random order and orientation which results in the establishment of derivative forms of chromosomes. Molecular mechanisms that underlie this phenomenon are mostly related to chromosomal sequestration throughout the micronuclei formation process. Chromothripsis is linked both to congenital and cancer diseases, moreover, it might be detected in subjects characterised by a normal phenotype. Chromothripsis, as well as the other chromoanagenetic variations, may be confined to one or more chromosomes, which makes up a non-uniform variety of karyotypes among chromothriptic patients. The detection of chromothripsis is enabled via tools like microarray-based comparative genomic hybridisation, next generation sequencing or authorial protocols aimed for the recognition of structural variations.
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Mosquera Orgueira A, Cid López M, Peleteiro Raíndo A, Díaz Arias JÁ, Antelo Rodríguez B, Bao Pérez L, Alonso Vence N, Bendaña López Á, Abuin Blanco A, Melero Valentín P, Ferreiro Ferro R, Aliste Santos C, Fraga Rodríguez MF, González Pérez MS, Pérez Encinas MM, Bello López JL. Detection of Rare Germline Variants in the Genomes of Patients with B-Cell Neoplasms. Cancers (Basel) 2021; 13:cancers13061340. [PMID: 33809641 PMCID: PMC8001490 DOI: 10.3390/cancers13061340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The global importance of rare variants in tumorigenesis has been addressed by some pan-cancer analysis, revealing significant enrichments in protein-truncating variants affecting genes such as ATM, BRCA1/2, BRIP1, and MSH6. Germline variants can influence treatment response and contribute to the development of treatment-related second neoplasms, especially in childhood leukemia. We aimed to analyze the genomes of patients with B-cell lymphoproliferative disorders for the discovery of genes enriched in rare pathogenic variants. We discovered a significant enrichment for two genes in germline rare and dysfunctional variants. Additionally, we detected rare and likely pathogenic variants associated with disease prognosis and potential druggability, indicating a relevant role of these events in the variability of cancer phenotypes. Abstract There is growing evidence indicating the implication of germline variation in cancer predisposition and prognostication. Here, we describe an analysis of likely disruptive rare variants across the genomes of 726 patients with B-cell lymphoid neoplasms. We discovered a significant enrichment for two genes in rare dysfunctional variants, both of which participate in the regulation of oxidative stress pathways (CHMP6 and GSTA4). Additionally, we detected 1675 likely disrupting variants in genes associated with cancer, of which 44.75% were novel events and 7.88% were protein-truncating variants. Among these, the most frequently affected genes were ATM, BIRC6, CLTCL1A, and TSC2. Homozygous or germline double-hit variants were detected in 28 cases, and coexisting somatic events were observed in 17 patients, some of which affected key lymphoma drivers such as ATM, KMT2D, and MYC. Finally, we observed that variants in six different genes were independently associated with shorter survival in CLL. Our study results support an important role for rare germline variation in the pathogenesis and prognosis of B-cell lymphoid neoplasms.
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Affiliation(s)
- Adrián Mosquera Orgueira
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
- Correspondence: ; Tel.: +34-981-950-191
| | - Miguel Cid López
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - Andrés Peleteiro Raíndo
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - José Ángel Díaz Arias
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Beatriz Antelo Rodríguez
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - Laura Bao Pérez
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Natalia Alonso Vence
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Ángeles Bendaña López
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - Aitor Abuin Blanco
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Paula Melero Valentín
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Roi Ferreiro Ferro
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Carlos Aliste Santos
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - Máximo Francisco Fraga Rodríguez
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
- Department of Medicine, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Marta Sonia González Pérez
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Manuel Mateo Pérez Encinas
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - José Luis Bello López
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Department of Medicine, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
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Simovic M, Ernst A. Chromothripsis, DNA repair and checkpoints defects. Semin Cell Dev Biol 2021; 123:110-114. [PMID: 33589336 DOI: 10.1016/j.semcdb.2021.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/05/2021] [Indexed: 11/28/2022]
Abstract
Chromothripsis is a unique form of genome instability characterized by tens to hundreds of DNA double-strand breaks on one or very few chromosomes, followed by error-prone repair. The derivative chromosome(s) display massive rearrangements, which lead to the loss of tumor suppressor function and to the activation of oncogenes. Chromothripsis plays a major role in cancer as well as in other conditions, such as congenital diseases. In this review, we discuss the repair processes involved in the rejoining of the chromosome fragments, the role of DNA repair and checkpoint defects as a cause for chromothripsis as well as DNA repair defects resulting from chromothripsis. Finally, we consider clinical implications and potential therapeutic vulnerabilities that could be utilized to eliminate tumor cells with chromothripsis.
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Affiliation(s)
- Milena Simovic
- Group Genome Instability in Tumors, German Cancer Research Centre (DKFZ), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Germany
| | - Aurélie Ernst
- Group Genome Instability in Tumors, German Cancer Research Centre (DKFZ), Heidelberg, Germany.
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7
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Poot M. Chromothripsis and Duplications as Underappreciated Genomic Gremlins. Mol Syndromol 2021; 11:239-242. [PMID: 33510597 DOI: 10.1159/000512565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 11/19/2022] Open
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Abstract
Bladder cancer has been successfully treated with immunotherapy, whereas prostate cancer is a cold tumor with inadequate immune-related treatment response. A greater understanding of the tumor microenvironment and methods for harnessing the immune system to address tumor growth will be needed to improve immunotherapies for both prostate and bladder cancer. Here, we provide an overview of prostate and bladder cancer, including fundamental aspects of the disease and treatment, the elaborate cellular makeup of the tumor microenvironment, and methods for exploiting relevant pathways to develop more effective treatments.
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9
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Sessa M, Cavazzini F, Cavallari M, Rigolin GM, Cuneo A. A Tangle of Genomic Aberrations Drives Multiple Myeloma and Correlates with Clinical Aggressiveness of the Disease: A Comprehensive Review from a Biological Perspective to Clinical Trial Results. Genes (Basel) 2020; 11:E1453. [PMID: 33287156 PMCID: PMC7761770 DOI: 10.3390/genes11121453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/24/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Multiple myeloma (MM) is a genetically heterogeneous disease, in which the process of tumorigenesis begins and progresses through the appearance and accumulation of a tangle of genomic aberrations. Several are the mechanisms of DNA damage in MM, varying from single nucleotide substitutions to complex genomic events. The timing of appearance of aberrations is well studied due to the natural history of the disease, that usually progress from pre-malignant to malignant phase. Different kinds of aberrations carry different prognostic significance and have been associated with drug resistance in some studies. Certain genetic events are well known to be associated with prognosis and are incorporated in risk evaluation in MM at diagnosis in the revised International Scoring System (R-ISS). The significance of some other aberrations needs to be further explained. Since now, few phase 3 randomized trials included analysis on patient's outcomes according to genetic risk, and further studies are needed to obtain useful data to stratify the choice of initial and subsequent treatment in MM.
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Affiliation(s)
- Mariarosaria Sessa
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S.Anna, University of Ferrara, 44121 Ferrara, Italy
| | - Francesco Cavazzini
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S.Anna, University of Ferrara, 44121 Ferrara, Italy
| | - Maurizio Cavallari
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S.Anna, University of Ferrara, 44121 Ferrara, Italy
| | - Gian Matteo Rigolin
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S.Anna, University of Ferrara, 44121 Ferrara, Italy
| | - Antonio Cuneo
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S.Anna, University of Ferrara, 44121 Ferrara, Italy
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10
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Anoshkin KI, Karandasheva KO, Goryacheva KM, Pyankov DV, Koshkin PA, Pavlova TV, Bobin AN, Shpot EV, Chernov YN, Vinarov AZ, Zaletaev DV, Kutsev SI, Strelnikov VV. Multiple Chromoanasynthesis in a Rare Case of Sporadic Renal Leiomyosarcoma: A Case Report. Front Oncol 2020; 10:1653. [PMID: 32974204 PMCID: PMC7466669 DOI: 10.3389/fonc.2020.01653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/28/2020] [Indexed: 01/25/2023] Open
Abstract
We present the genetic profile of kidney giant leiomyosarcoma characterized by sequencing of 409 cancer related genes and chromosomal microarray analysis. Renal leiomyosarcomas are extremely rare neoplasms with aggressive behavior and poor survival prognosis. Most frequent somatic events in leiomyosarcomas are mutations in the TP53, RB1, ATRX, and PTEN genes, chromosomal instability (CIN) and chromoanagenesis. 67-year-old woman presented with a right kidney completely replaced by tumor. Immunohistochemical reaction on surgical material was positive to desmin and smooth muscle actin. Molecular genetic analysis revealed that tumor harbored monosomy of chromosomes 3 and 11, gain of Xp (ATRX) arm and three chromoanasynthesis regions (6q21-q27, 7p22.3-p12.1, and 12q13.11-q21.2), with MDM2 and CDK4 oncogenes copy number gains, whereas no copy number variations (CNVs) or tumor specific single nucleotide variants (SNVs) in TP53, RB1, and PTEN genes were present. We hypothesize that chromoanasynthesis in 12q13.11-q21.2 could be a trigger of observed CIN in this tumor.
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11
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Hattori A, Fukami M. Established and Novel Mechanisms Leading to de novo Genomic Rearrangements in the Human Germline. Cytogenet Genome Res 2020; 160:167-176. [DOI: 10.1159/000507837] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/31/2020] [Indexed: 01/05/2023] Open
Abstract
During gametogenesis, the human genome can acquire various de novo rearrangements. Most constitutional genomic rearrangements are created through 1 of the 4 well-known mechanisms, i.e., nonallelic homologous recombination, erroneous repair after double-strand DNA breaks, replication errors, and retrotransposition. However, recent studies have identified 2 types of extremely complex rearrangements that cannot be simply explained by these mechanisms. The first type consists of chaotic structural changes in 1 or a few chromosomes that result from “chromoanagenesis (an umbrella term that covers chromothripsis, chromoanasynthesis, and chromoplexy).” The other type is large independent rearrangements in multiple chromosomes indicative of “transient multifocal genomic crisis.” Germline chromoanagenesis (chromothripsis) likely occurs predominantly during spermatogenesis or postzygotic embryogenesis, while multifocal genomic crisis appears to be limited to a specific time window during oogenesis and early embryogenesis or during spermatogenesis. This review article introduces the current understanding of the molecular basis of de novo rearrangements in the germline.
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Fucic A, Druzhinin V, Aghajanyan A, Slijepcevic P, Bakanova M, Baranova E, Minina V, Golovina T, Kourdakov K, Timofeeva A, Titov V. Rogue versus chromothriptic cell as biomarker of cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 784:108299. [PMID: 32430100 DOI: 10.1016/j.mrrev.2020.108299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 11/30/2022]
Abstract
New molecular cytogenetic biomarkers may significantly contribute to biodosimetry, whose application is still globally diverse and not fully standardized. In 2011, a new term, chromothripsis, was introduced raising great interest among researchers and soon motivating further investigations of the phenomenon. Chromothripsis is described as a single event in which one or more chromosomes go through severe DNA damage very much resembling rogue cells (RC) described more than 50 years ago. In this review, we for the first time compare these two multi-aberrant cells types, RC versus chromothriptic cells, giving insight into the similarities of the mechanisms involved in their etiology. In order to make a better comparison, data on RC in 3366 subjects from studies on cancer patients, Chernobyl liquidators, child victims of the Chernobyl nuclear plant accident, residentially and occupationally exposed population have been summarized for the first time. Results of experimental and epidemiological analysis show that chromothriptic cells and RC may be caused by exposure to high LET ionizing radiation. Experience and knowledge collected on RC may be used in future for further investigations of chromothripsis, introducing a new class of cells which include both chromothriptic and RC, and better insight into the frequency of chromothriptic cell per subject, which is currently absent. Both cell types are relevant in investigations of cancer etiology, biomonitoring of accidentally exposed population to ionizing radiation and biomonitoring of astronauts due to their exposure to high LET ionizing radiation during interplanetary voyages.
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Affiliation(s)
- Aleksandra Fucic
- Institute for Medical Research and Occupational Health, Zagreb, Croatia.
| | | | - Anna Aghajanyan
- Medical Institute Peoples' Friendship University of Russia (RUDN University), Moscow, Russia Federation
| | - Predrag Slijepcevic
- Brunel University London, Department of Life Sciences, College of Health and Life Sciences, Uxbridge, UK
| | | | | | | | | | | | | | - Victor Titov
- Kemerovo Regional Oncology Center, Kemerovo, Russian Federation
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Poot M. Genomic Earthquakes in the Human Germline and Their Ramifications. Mol Syndromol 2020; 10:291-293. [PMID: 32021602 DOI: 10.1159/000503366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2019] [Indexed: 02/05/2023] Open
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14
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Altıner Ş, Yürür Kutlay N, Ilgın Ruhi H. Mosaic Small Supernumerary Marker Chromosome Derived from Five Discontinuous Regions of Chromosome 8 in a Patient with Neutropenia and Oral Aphthous Ulcer. Cytogenet Genome Res 2020; 160:11-17. [PMID: 31982875 DOI: 10.1159/000505805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2019] [Indexed: 11/19/2022] Open
Abstract
Small supernumerary marker chromosomes (sSMCs) are characterized as additional centric chromosome fragments which are too small to be classified by cytogenetic banding alone and smaller than or equal to the size of chromosome 20 of the same metaphase spread. Here, we report a patient who presented with slight neutropenia and oral aphthous ulcers. A mosaic de novo sSMC, which originated from 5 discontinuous regions of chromosome 8, was detected in the patient. Formation of the sSMC(8) can probably be explained by a multi-step process beginning with maternal meiotic nondisjunction, followed by post-zygotic anaphase lag, and resulting in chromothripsis. Chromothripsis is a chromosomal rearrangement which occurs by breakage of one or more chromosomes leading to a fusion of surviving chromosome pieces. This case is a good example for emphasizing the importance of conventional karyotyping from PHA-induced peripheral blood lymphocytes and examining tissues other than bone marrow in patients with inconsistent genotype and phenotype.
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15
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Poot M. Concurrent Structural and Single Nucleotide Variation Resulting from a Single Replication-Based Mechanism. Mol Syndromol 2019; 10:183-185. [PMID: 31602189 DOI: 10.1159/000501382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 11/19/2022] Open
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16
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Maierhofer A, Flunkert J, Oshima J, Martin GM, Poot M, Nanda I, Dittrich M, Müller T, Haaf T. Epigenetic signatures of Werner syndrome occur early in life and are distinct from normal epigenetic aging processes. Aging Cell 2019; 18:e12995. [PMID: 31259468 PMCID: PMC6718529 DOI: 10.1111/acel.12995] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/24/2019] [Accepted: 06/05/2019] [Indexed: 12/11/2022] Open
Abstract
Werner Syndrome (WS) is an adult-onset segmental progeroid syndrome. Bisulfite pyrosequencing of repetitive DNA families revealed comparable blood DNA methylation levels between classical (18 WRN-mutant) or atypical WS (3 LMNA-mutant and 3 POLD1-mutant) patients and age- and sex-matched controls. WS was not associated with either age-related accelerated global losses of ALU, LINE1, and α-satellite DNA methylations or gains of rDNA methylation. Single CpG methylation was analyzed with Infinium MethylationEPIC arrays. In a correspondence analysis, atypical WS samples clustered together with the controls and were clearly separated from classical WS, consistent with distinct epigenetic pathologies. In classical WS, we identified 659 differentially methylated regions (DMRs) comprising 3,656 CpG sites and 613 RefSeq genes. The top DMR was located in the HOXA4 promoter. Additional DMR genes included LMNA, POLD1, and 132 genes which have been reported to be differentially expressed in WRN-mutant/depleted cells. DMRs were enriched in genes with molecular functions linked to transcription factor activity and sequence-specific DNA binding to promoters transcribed by RNA polymerase II. We propose that transcriptional misregulation of downstream genes by the absence of WRN protein contributes to the variable premature aging phenotypes of WS. There were no CpG sites showing significant differences in DNA methylation changes with age between WS patients and controls. Genes with both WS- and age-related methylation changes exhibited a constant offset of methylation between WRN-mutant patients and controls across the entire analyzed age range. WS-specific epigenetic signatures occur early in life and do not simply reflect an acceleration of normal epigenetic aging processes.
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Affiliation(s)
- Anna Maierhofer
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Julia Flunkert
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Junko Oshima
- Department of Pathology University of Washington Seattle Washington USA
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine Chiba University Chiba Japan
| | - George M. Martin
- Department of Pathology University of Washington Seattle Washington USA
| | - Martin Poot
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Indrajit Nanda
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Marcus Dittrich
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
- Department of Bioinformatics Julius Maximilians University Würzburg Germany
| | - Tobias Müller
- Department of Bioinformatics Julius Maximilians University Würzburg Germany
| | - Thomas Haaf
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
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17
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Hattori A, Okamura K, Terada Y, Tanaka R, Katoh-Fukui Y, Matsubara Y, Matsubara K, Kagami M, Horikawa R, Fukami M. Transient multifocal genomic crisis creating chromothriptic and non-chromothriptic rearrangements in prezygotic testicular germ cells. BMC Med Genomics 2019; 12:77. [PMID: 31138192 PMCID: PMC6540402 DOI: 10.1186/s12920-019-0526-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/10/2019] [Indexed: 12/15/2022] Open
Abstract
Background The co-occurrence of multiple de novo copy number variations (CNVs) is a rare phenomenon in the human genome. Recently, an “organismal CNV mutator phenotype” has been reported to result in transient genomic instability introducing multiple de novo CNVs in primary oocytes and early-stage zygotes. These findings opened a new area of human genome research. Methods We performed genome-wide copy number analysis for ~ 2100 individuals with various congenital defects. Furthermore, extensive molecular analyses, including synthetic long-read whole-genome sequencing and haplotype-phasing, were carried out for an individual with multiple de novo CNVs. Results A boy was found to have de novo rearrangements on five chromosomes. The rearrangements comprised simple duplication and inversion as well as chaotic changes, all of which affected paternally derived chromosomes. Postzygotic genomic instability was ruled out. The duplicated regions on 6q and 13q contained both diallelic and triallelic loci, indicating that the genomic rearrangements were initially created during premeiotic mitosis and subsequently modified by physiological cross-over during meiosis I. Breakpoints of the rearrangements were indicative of non-homologous end joining, replication-based errors, and/or chromothripsis. The mutagenic event was independent of specific local DNA motifs or de novo point mutations, but may be driven by spermatogenesis-specific factors. Conclusions These results indicate that during spermatogenesis, a transient multifocal genomic crisis can introduce several chromothriptic and non-chromothriptic changes into the genome. These findings broaden the concept of the “organismal CNV mutator phenotype”. This study provides insights into mechanisms for altering the global chromosomal architecture of human embryos. Electronic supplementary material The online version of this article (10.1186/s12920-019-0526-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Atsushi Hattori
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.,Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, 157-8535, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Yumiko Terada
- Division of Endocrinology and Metabolism, National Medical Center for Children and Mothers, Tokyo, 157-8535, Japan
| | - Rika Tanaka
- Department of Neonatology, Aiiku Hospital, Tokyo, 105-8321, Japan
| | - Yuko Katoh-Fukui
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Yoichi Matsubara
- National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Reiko Horikawa
- Division of Endocrinology and Metabolism, National Medical Center for Children and Mothers, Tokyo, 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.
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18
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Koltsova AS, Pendina AA, Efimova OA, Chiryaeva OG, Kuznetzova TV, Baranov VS. On the Complexity of Mechanisms and Consequences of Chromothripsis: An Update. Front Genet 2019; 10:393. [PMID: 31114609 PMCID: PMC6503150 DOI: 10.3389/fgene.2019.00393] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/11/2019] [Indexed: 12/28/2022] Open
Abstract
In the present review, we focus on the phenomenon of chromothripsis, a new type of complex chromosomal rearrangements. We discuss the challenges of chromothripsis detection and its distinction from other chromoanagenesis events. Along with already known causes and mechanisms, we introduce aberrant epigenetic regulation as a possible pathway to chromothripsis. We address the issue of chromothripsis characteristics in cancers and benign tumours, as well as chromothripsis inheritance in cases of its occurrence in germ cells, zygotes and early embryos. Summarising the presented data on different phenotypic effect of chromothripsis, we assume that its consequences are most likely determined not by the chromosome shattering and reassembly themselves, but by the genome regions involved in the rearrangement.
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Affiliation(s)
- Alla S Koltsova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Anna A Pendina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Olga A Efimova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Olga G Chiryaeva
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Tatyana V Kuznetzova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Vladislav S Baranov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
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19
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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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20
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Kaur G, Gupta R, Mathur N, Rani L, Kumar L, Sharma A, Singh V, Gupta A, Sharma OD. Clinical impact of chromothriptic complex chromosomal rearrangements in newly diagnosed multiple myeloma. Leuk Res 2018; 76:58-64. [PMID: 30576858 DOI: 10.1016/j.leukres.2018.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/12/2018] [Accepted: 12/14/2018] [Indexed: 11/26/2022]
Abstract
Complex Chromosomal Rearrangements (CCRs) are increasingly being reported as genetic risk factors of clinical significance in cancer owing to their identification using high resolution whole genome profiling technologies. This study employed high resolution CGH + SNP microarrays for whole genome copy number variations (CNV) profiling and identified CCRs in 11/107(10%) newly diagnosed Multiple Myeloma (MM) patients. Six patients exhibited Chromothripsis (CTH) among seven chromosomes that were confirmed with automated CTLPscanner web tool and; five cases displayed chromoplexy (CPL) which involved multiple chromosomes. Presence of chromothripsis in chromosome 17 in three out of six patients indicate a link between TP53 aberrations and incidence of CTH. Multivariable Cox regression model demonstrated a significant association of CTH with poor PFS (HR = 3.09, p = 0.010) and OS (HR = 3.31, p = 0.024) which suggests that CTH is an additional independent prognostic marker in multiple myeloma. Addition of CTH in risk stratification models in clinical setting in multiple myeloma may help in upfront identification of high risk patients for suitable customized therapy.
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Affiliation(s)
- Gurvinder Kaur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India.
| | - Nitin Mathur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Lata Rani
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Lalit Kumar
- Department of Medical Oncology, Dr. B.R.A.IRCH, AIIMS, New Delhi, India
| | - Atul Sharma
- Department of Medical Oncology, Dr. B.R.A.IRCH, AIIMS, New Delhi, India
| | | | - Anubha Gupta
- Department of Electronics & Communications, Indraprastha Institute of Information Technology (IIIT), New Delhi, India
| | - Om Dutt Sharma
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
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21
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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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22
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Nazaryan-Petersen L, Eisfeldt J, Pettersson M, Lundin J, Nilsson D, Wincent J, Lieden A, Lovmar L, Ottosson J, Gacic J, Mäkitie O, Nordgren A, Vezzi F, Wirta V, Käller M, Hjortshøj TD, Jespersgaard C, Houssari R, Pignata L, Bak M, Tommerup N, Lundberg ES, Tümer Z, Lindstrand A. Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization. PLoS Genet 2018; 14:e1007780. [PMID: 30419018 PMCID: PMC6258378 DOI: 10.1371/journal.pgen.1007780] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/26/2018] [Accepted: 10/23/2018] [Indexed: 01/25/2023] Open
Abstract
Clustered copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) are often reported as germline chromothripsis. However, such cases might need further investigations by massive parallel whole genome sequencing (WGS) in order to accurately define the underlying complex rearrangement, predict the occurrence mechanisms and identify additional complexities. Here, we utilized WGS to delineate the rearrangement structure of 21 clustered CNV carriers first investigated by CMA and identified a total of 83 breakpoint junctions (BPJs). The rearrangements were further sub-classified depending on the patterns observed: I) Cases with only deletions (n = 8) often had additional structural rearrangements, such as insertions and inversions typical to chromothripsis; II) cases with only duplications (n = 7) or III) combinations of deletions and duplications (n = 6) demonstrated mostly interspersed duplications and BPJs enriched with microhomology. In two cases the rearrangement mutational signatures indicated both a breakage-fusion-bridge cycle process and haltered formation of a ring chromosome. Finally, we observed two cases with Alu- and LINE-mediated rearrangements as well as two unrelated individuals with seemingly identical clustered CNVs on 2p25.3, possibly a rare European founder rearrangement. In conclusion, through detailed characterization of the derivative chromosomes we show that multiple mechanisms are likely involved in the formation of clustered CNVs and add further evidence for chromoanagenesis mechanisms in both “simple” and highly complex chromosomal rearrangements. Finally, WGS characterization adds positional information, important for a correct clinical interpretation and deciphering mechanisms involved in the formation of these rearrangements. Clustered copy number variants (CNVs) as detected by chromosomal microarray are often reported as germline chromoanagenesis. However, such cases might need further investigation by whole genome sequencing (WGS) to accurately resolve the complexity of the structural rearrangement and predict underlying mutational mechanisms. Here, we used WGS to characterize 83 breakpoint-junctions (BPJs) from 21 clustered CNVs, and outlined the rearrangement connectivity pictures. Cases with only deletions often had additional structural rearrangements, such as insertions and inversions, which could be a result of multiple double-strand DNA breaks followed by non-homologous repair, typical to chromothripsis. In contrast, cases with only duplications or combinations of deletions and duplications, demonstrated mostly interspersed duplications and BPJs enriched with microhomology, consistent with serial template switching during DNA replication (chromoanasynthesis). Only two rearrangements were repeat mediated. In aggregate, our results suggest that multiple CNVs clustered on a single chromosome may arise through either chromothripsis or chromoanasynthesis.
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Affiliation(s)
- Lusine Nazaryan-Petersen
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Johanna Lundin
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Agne Lieden
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Lovisa Lovmar
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jesper Ottosson
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jelena Gacic
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Francesco Vezzi
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Valtteri Wirta
- SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Max Käller
- SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Tina Duelund Hjortshøj
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Cathrine Jespersgaard
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Rayan Houssari
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Laura Pignata
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Mads Bak
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Syk Lundberg
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- * E-mail: (AL); (ZT)
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- * E-mail: (AL); (ZT)
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