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Krupina K, Goginashvili A, Cleveland DW. Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements. Nat Rev Genet 2024; 25:196-210. [PMID: 37938738 PMCID: PMC10922386 DOI: 10.1038/s41576-023-00663-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 11/09/2023]
Abstract
Complex chromosome rearrangements, known as chromoanagenesis, are widespread in cancer. Based on large-scale DNA sequencing of human tumours, the most frequent type of complex chromosome rearrangement is chromothripsis, a massive, localized and clustered rearrangement of one (or a few) chromosomes seemingly acquired in a single event. Chromothripsis can be initiated by mitotic errors that produce a micronucleus encapsulating a single chromosome or chromosomal fragment. Rupture of the unstable micronuclear envelope exposes its chromatin to cytosolic nucleases and induces chromothriptic shattering. Found in up to half of tumours included in pan-cancer genomic analyses, chromothriptic rearrangements can contribute to tumorigenesis through inactivation of tumour suppressor genes, activation of proto-oncogenes, or gene amplification through the production of self-propagating extrachromosomal circular DNAs encoding oncogenes or genes conferring anticancer drug resistance. Here, we discuss what has been learned about the mechanisms that enable these complex genomic rearrangements and their consequences in cancer.
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Affiliation(s)
- Ksenia Krupina
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Alexander Goginashvili
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
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2
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Baker TM, Waise S, Tarabichi M, Van Loo P. Aneuploidy and complex genomic rearrangements in cancer evolution. NATURE CANCER 2024; 5:228-239. [PMID: 38286829 PMCID: PMC7616040 DOI: 10.1038/s43018-023-00711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Mutational processes that alter large genomic regions occur frequently in developing tumors. They range from simple copy number gains and losses to the shattering and reassembly of entire chromosomes. These catastrophic events, such as chromothripsis, chromoplexy and the formation of extrachromosomal DNA, affect the expression of many genes and therefore have a substantial effect on the fitness of the cells in which they arise. In this review, we cover large genomic alterations, the mechanisms that cause them and their effect on tumor development and evolution.
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Affiliation(s)
- Toby M Baker
- The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara Waise
- The Francis Crick Institute, London, UK
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK
- Institute for Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Peter Van Loo
- The Francis Crick Institute, London, UK.
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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3
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Mazzagatti A, Engel JL, Ly P. Boveri and beyond: Chromothripsis and genomic instability from mitotic errors. Mol Cell 2024; 84:55-69. [PMID: 38029753 PMCID: PMC10842135 DOI: 10.1016/j.molcel.2023.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023]
Abstract
Mitotic cell division is tightly monitored by checkpoints that safeguard the genome from instability. Failures in accurate chromosome segregation during mitosis can cause numerical aneuploidy, which was hypothesized by Theodor Boveri over a century ago to promote tumorigenesis. Recent interrogation of pan-cancer genomes has identified unexpected classes of chromosomal abnormalities, including complex rearrangements arising through chromothripsis. This process is driven by mitotic errors that generate abnormal nuclear structures that provoke extensive yet localized shattering of mis-segregated chromosomes. Here, we discuss emerging mechanisms underlying chromothripsis from micronuclei and chromatin bridges, as well as highlight how this mutational cascade converges on the DNA damage response. A fundamental understanding of these catastrophic processes will provide insight into how initial errors in mitosis can precipitate rapid cancer genome evolution.
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Affiliation(s)
- Alice Mazzagatti
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Justin L Engel
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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4
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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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5
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Masson J, Pebrel-Richard C, Egloff M, Frétigny M, Beaumont M, Uguen K, Rollat-Farnier PA, Diguet F, Perthus I, Le Gudayer G, Haye D, Dupeyron MNB, Putoux A, Raskin-Champion F, Till M, Chatron N, Doray B, Bardel C, Vinciguerra C, Sanlaville D, Schluth-Bolard C. Familial transmission of chromoanagenesis leads to unpredictable unbalanced rearrangements through meiotic recombination. Clin Genet 2023; 103:401-412. [PMID: 36576162 DOI: 10.1111/cge.14291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Chromoanagenesis is a cellular mechanism that leads to complex chromosomal rearrangements (CCR) during a single catastrophic event. It may result in loss and/or gain of genetic material and may be responsible for various phenotypes. These rearrangements are usually sporadic. However, some familial cases have been reported. Here, we studied six families in whom an asymptomatic or paucisymptomatic parent transmitted a CCR to its offspring in an unbalanced manner. The rearrangements were characterized by karyotyping, fluorescent in situ hybridization, chromosomal microarray (CMA) and/or whole genome sequencing (WGS) in the carrier parents and offspring. We then hypothesized meiosis-pairing figures between normal and abnormal parental chromosomes that may have led to the formation of new unbalanced rearrangements through meiotic recombination. Our work indicates that chromoanagenesis might be associated with a normal phenotype and normal fertility, even in males, and that WGS may be the only way to identify these events when there is no imbalance. Subsequently, the CCR can be transmitted to the next generation in an unbalanced and unpredictable manner following meiotic recombination. Thereby, prenatal diagnosis using CMA should be proposed to these families to detect any pathogenic imbalances in the offspring.
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Affiliation(s)
- Julie Masson
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | | | | | - Mathilde Frétigny
- Service d'hématologie, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Bron, France
| | - Marion Beaumont
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Genetics and NIPT, Laboratoire Eylau-Unilabs, Neuilly-sur-Seine, France
| | - Kevin Uguen
- UMR 1078, GGB, CHU Brest, Inserm, Univ Brest, EFS, Brest, France
- Service de Génétique Médicale, CHRU de Brest, Brest, France
| | - Pierre-Antoine Rollat-Farnier
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Plateforme NGS, Hospices Civils de Lyon, Bron, France
| | - Flavie Diguet
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Isabelle Perthus
- Service de Génétique Médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | | | - Damien Haye
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Marie-Noëlle Bonnet Dupeyron
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Service de Génétique, CH de Valence, Valence, France
| | - Audrey Putoux
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Fabienne Raskin-Champion
- Service de Gynécologie Médicale et Obstétrique, Groupement Hospitalier Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Marianne Till
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Nicolas Chatron
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | - Bérénice Doray
- Service de Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Service de Génétique, CHU de la Réunion - Hôpital Félix Guyon, Saint-Denis, France
| | - Claire Bardel
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Plateforme NGS, Hospices Civils de Lyon, Bron, France
- ISPB, Université Claude Bernard Lyon 1, Lyon, France
| | - Christine Vinciguerra
- Service d'hématologie, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Bron, France
- ISPB, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Sanlaville
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | - Caroline Schluth-Bolard
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
- Laboratoires de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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6
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Zhang Q, Yang L, Xiao H, Dang Z, Kuang X, Xiong Y, Zhu J, Huang Z, Li M. Pan-cancer analysis of chromothripsis-related gene expression patterns indicates an association with tumor immune and therapeutic agent responses. Front Oncol 2023; 13:1074955. [PMID: 36761982 PMCID: PMC9902954 DOI: 10.3389/fonc.2023.1074955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Chromothripsis is a catastrophic event involving numerous chromosomal rearrangements in confined genomic regions of one or a few chromosomes, causing complex effects on cells via the extensive structural variation. The development of whole-genome sequencing (WGS) has promoted great progress in exploring the mechanism and effect of chromothripsis. However, the gene expression characteristics of tumors undergone chromothripsis have not been well characterized. In this study, we found that the transcriptional profile of five tumor types experiencing chromothripsis is associated with an immune evasion phenotype. A gene set variation analysis (GSVA) was used to develop a CHP score, which is based on differentially expressed gene sets in the TCGA database, revealing that chromothripsis status in multiple cancers is consistent with an abnormal tumor immune microenvironment and immune cell cytotoxicity. Evaluation using four immunotherapy datasets uncovered the ability of the CHP score to predict immunotherapy response in diverse tumor types. In addition, the CHP score was found to be related to resistance against a variety of anti-tumor drugs, including anti-angiogenesis inhibitors and platinum genotoxins, while EGFR pathway inhibitors were found to possibly be sensitizers for high CHP score tumors. Univariate COX regression analysis indicated that the CHP score can be prognostic for several types of tumors. Our study has defined gene expression characteristics of tumors with chromothripsis, supporting the controversial link between chromothripsis and tumor immunity. We also describe the potential value of the CHP score in predicting the efficacy of immunotherapy and other treatments, elevating chromothripsis as a tool in clinical practice.
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Affiliation(s)
| | | | | | | | | | | | | | - Zhou Huang
- *Correspondence: Zhou Huang, ; Mengxia Li,
| | - Mengxia Li
- *Correspondence: Zhou Huang, ; Mengxia Li,
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7
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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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8
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Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes. Nat Commun 2022; 13:6470. [PMID: 36309531 PMCID: PMC9617858 DOI: 10.1038/s41467-022-34053-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
Structural variants are a common cause of disease and contribute to a large extent to inter-individual variability, but their detection and interpretation remain a challenge. Here, we investigate 11 individuals with complex genomic rearrangements including germline chromothripsis by combining short- and long-read genome sequencing (GS) with Hi-C. Large-scale genomic rearrangements are identified in Hi-C interaction maps, allowing for an independent assessment of breakpoint calls derived from the GS methods, resulting in >300 genomic junctions. Based on a comprehensive breakpoint detection and Hi-C, we achieve a reconstruction of whole rearranged chromosomes. Integrating information on the three-dimensional organization of chromatin, we observe that breakpoints occur more frequently than expected in lamina-associated domains (LADs) and that a majority reshuffle topologically associating domains (TADs). By applying phased RNA-seq, we observe an enrichment of genes showing allelic imbalanced expression (AIG) within 100 kb around the breakpoints. Interestingly, the AIGs hit by a breakpoint (19/22) display both up- and downregulation, thereby suggesting different mechanisms at play, such as gene disruption and rearrangements of regulatory information. However, the majority of interpretable genes located 200 kb around a breakpoint do not show significant expression changes. Thus, there is an overall robustness in the genome towards large-scale chromosome rearrangements.
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A Maternally Inherited Rare Case with Chromoanagenesis-Related Complex Chromosomal Rearrangements and De Novo Microdeletions. Diagnostics (Basel) 2022; 12:diagnostics12081900. [PMID: 36010250 PMCID: PMC9406357 DOI: 10.3390/diagnostics12081900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/22/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Chromoanagenesis is a phenomenon of highly complex rearrangements involving the massive genomic shattering and reconstitution of chromosomes that has had a great impact on cancer biology and congenital anomalies. Complex chromosomal rearrangements (CCRs) are structural alterations involving three or more chromosomal breakpoints between at least two chromosomes. Here, we present a 3-year-old boy exhibiting multiple congenital malformations and developmental delay. The cytogenetic analysis found a highly complex CCR inherited from the mother involving four chromosomes and five breakpoints due to forming four derivative chromosomes (2, 3, 6 and 11). FISH analysis identified an ultrarare derivative chromosome 11 containing three parts that connected the 11q telomere to partial 6q and 3q fragments. We postulate that this derivative chromosome 11 is associated with chromoanagenesis-like phenomena by which DNA repair can result in a cooccurrence of inter-chromosomal translocations. Additionally, chromosome microarray studies revealed that the child has one subtle maternal-inherited deletion at 6p12.1 and two de novo deletions at 6q14.1 and 6q16.1~6q16.3. Here, we present a familial CCR case with rare rearranged chromosomal structures and the use of multiple molecular techniques to delineate these genomic alterations. We suggest that chromoanagenesis may be a possible mechanism involved in the repair and reconstitution of these rearrangements with evidence for increasing genomic imbalances such as additional deletions in this case.
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10
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Córdova-Fletes C, Rivera H, Aguayo-Orozco TA, Martínez-Jacobo LA, Garza-González E, Robles-Espinoza CD, Basurto-Lozada P, Avalos-Gómez HG, Esparza-García E, Domínguez-Quezada MG. A chromoanagenesis-driven ultra-complex t(5;7;21)dn truncates neurodevelopmental genes in a disabled boy as revealed by whole-genome sequencing. Eur J Med Genet 2022; 65:104579. [PMID: 35933106 DOI: 10.1016/j.ejmg.2022.104579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 05/30/2022] [Accepted: 07/22/2022] [Indexed: 11/03/2022]
Abstract
Germline or constitutional chromoanagenesis-related complex chromosomal rearrangements (CCRs) are rare, apparently "all-at-once", catastrophic events that occur in a single cell cycle, exhibit an unexpected complexity, and sometimes correlate with a severe abnormal phenotype. The term chromoanagenesis encompasses three distinct phenomena, namely chromothripsis, chromoanasynthesis, and chromoplexy. Herein, we found hallmarks of chromothripsis and chromoplexy in an ultra-complex t(5; 7;21)dn involving several disordered breakpoint junctions (BPJs) accompanied by some microdeletions and the disruption of neurodevelopmental genes in a patient with a phenotype resembling autosomal dominant MRD44 (OMIM 617061). G-banded chromosomes and FISH showed that the CCR implied the translocation of the 5p15.2→pter segment onto 7q11.23; in turn, the fragment 7q11.23→qter of der(7) separated into two pieces: the segment q11.23→q32 translocated onto 5p15.2 and fused to 21q22.1→ter in the der(5) while the distal 7q32→qter segment translocated onto der(21) at q22.1. Subsequent whole-genome sequencing unveiled that CCT5, CMBL, RETREG1, MYO10, and TRIO from der(5), IMMP2L, TES, VPS37D, DUS4L, TYW1B, and FEZF1-AS1 from der(7), and TIAM1 and SOD1 from der(21), were disrupted by BPJs, whereas some other genes (predicted to be haplosufficient or inconsequential) were completely deleted. Although remarkably CCT5, TRIO, TES, MYO10, and TIAM1 (and even VPS37D) cooperate in key biological processes for normal neuronal development such as cell adhesion, migration, growth, and/or cytoskeleton formation, the disruption of TRIO most likely caused the patient's MRD44-like phenotype, including intellectual disability, microcephaly, finger anomalies, and facial dysmorphia. Our observation represents the first truncation of TRIO related to a chromoanagenesis event and therefore expands the mutational spectrum of this crucial gene. Moreover, our findings indicate that more than one mechanism is involved in modeling the architecture of ultra-complex rearrangements.
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Affiliation(s)
- Carlos Córdova-Fletes
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico.
| | - Horacio Rivera
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Thania Alejandra Aguayo-Orozco
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico; División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | - Lizeth Alejandra Martínez-Jacobo
- Departamento de Ciencias Básicas, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Mexico
| | - Elvira Garza-González
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Santiago de Querétaro, Mexico; Wellcome Sanger Institute, Hinxton, UK
| | - Patricia Basurto-Lozada
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Santiago de Querétaro, Mexico
| | | | - Eduardo Esparza-García
- Hospital de Pediatría, UMAE-CMNO, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | - Ma Guadalupe Domínguez-Quezada
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico.
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11
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Pfaff AL, Singleton LM, Kõks S. Mechanisms of disease-associated SINE-VNTR-Alus. Exp Biol Med (Maywood) 2022; 247:756-764. [PMID: 35387528 DOI: 10.1177/15353702221082612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
SINE-VNTR-Alus (SVAs) are the youngest retrotransposon family in the human genome. Their ongoing mobilization has generated genetic variation within the human population. At least 24 insertions to date, detailed in this review, have been associated with disease. The predominant mechanisms through which this occurs are alterations to normal splicing patterns, exonic insertions causing loss-of-function mutations, and large genomic deletions. Dissecting the functional impact of these SVAs and the mechanism through which they cause disease provides insight into the consequences of their presence in the genome and how these elements could influence phenotypes. Many of these disease-associated SVAs have been difficult to characterize and would not have been identified through routine analyses. However, the number identified has increased in recent years as DNA and RNA sequencing data became more widely available. Therefore, as the search for complex structural variation in disease continues, it is likely to yield further disease-causing SVA insertions.
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Affiliation(s)
- Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Lewis M Singleton
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
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12
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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: 6] [Impact Index Per Article: 3.0] [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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13
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Dahiya R, Hu Q, Ly P. Mechanistic origins of diverse genome rearrangements in cancer. Semin Cell Dev Biol 2022; 123:100-109. [PMID: 33824062 PMCID: PMC8487437 DOI: 10.1016/j.semcdb.2021.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/08/2021] [Indexed: 12/14/2022]
Abstract
Cancer genomes frequently harbor structural chromosomal rearrangements that disrupt the linear DNA sequence order and copy number. To date, diverse classes of structural variants have been identified across multiple cancer types. These aberrations span a wide spectrum of complexity, ranging from simple translocations to intricate patterns of rearrangements involving multiple chromosomes. Although most somatic rearrangements are acquired gradually throughout tumorigenesis, recent interrogation of cancer genomes have uncovered novel categories of complex rearrangements that arises rapidly through a one-off catastrophic event, including chromothripsis and chromoplexy. Here we review the cellular and molecular mechanisms contributing to the formation of diverse structural rearrangement classes during cancer development. Genotoxic stress from a myriad of extrinsic and intrinsic sources can trigger DNA double-strand breaks that are subjected to DNA repair with potentially mutagenic outcomes. We also highlight how aberrant nuclear structures generated through mitotic cell division errors, such as rupture-prone micronuclei and chromosome bridges, can instigate massive DNA damage and the formation of complex rearrangements in cancer genomes.
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Affiliation(s)
- Rashmi Dahiya
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Qing Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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14
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Liang Y, Xie Y, Kong S, Pan Q, Qiu W, Wang D, Li M, Lin S, Liu Z, Sun X. Complex Chromosomal Rearrangement Causes Male Azoospermia: A Case Report and Literature Review. Front Genet 2022; 13:792539. [PMID: 35281846 PMCID: PMC8907855 DOI: 10.3389/fgene.2022.792539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Male carriers of complex chromosomal rearrangements (CCRs) may have decreased fertility and usually present with azoospermia, oligospermia or teratospermia.Methods: High-resolution karyotype analysis using G-banding on peripheral blood lymphocytes was performed in an azoospermic male. Copy number variations (CNVs) were detected by chromosomal microarray analysis, and genetic variations were determined by long-read nanopore sequencing with Sanger sequencing for breakpoint confirmation.Results: The karyotype of the patient was 46,XY,t(4;21)(p11;p11),t(5;6;14)(p13q22;p22q22;q22), which did not involve CNVs with clinical significance. Twelve breakpoints in chromosomes 5, 6, and 14 were found by long-read nanopore sequencing. Reports on 17 males carrying CCRs with azoospermia were also reviewed.Conclusion: The extent of asynaptic regions in synaptonemal complexes during pachytene and the disruption of genes involved in male gametogenesis may cause azoospermia in CCR carriers.
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Affiliation(s)
- Yi Liang
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shu Kong
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qianying Pan
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenjun Qiu
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ding Wang
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mengting Li
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Sisi Lin
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Zihang Liu
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Xiaofang Sun
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Xiaofang Sun,
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15
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Scharf F, Leal Silva RM, Morak M, Hastie A, Pickl JMA, Sendelbach K, Gebhard C, Locher M, Laner A, Steinke-Lange V, Koehler U, Holinski-Feder E, Wolf DA. Constitutional chromothripsis of the APC locus as a cause of genetic predisposition to colon cancer. J Med Genet 2021; 59:976-983. [PMID: 34911816 PMCID: PMC9554066 DOI: 10.1136/jmedgenet-2021-108147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/11/2021] [Indexed: 11/21/2022]
Abstract
Purpose Approximately 20% of patients with clinical familial adenomatous polyposis (FAP) remain unsolved after molecular genetic analysis of the APC and other polyposis genes, suggesting additional pathomechanisms. Methods We applied multidimensional genomic analysis employing chromosomal microarray profiling, optical mapping, long-read genome and RNA sequencing combined with FISH and standard PCR of genomic and complementary DNA to decode a patient with an attenuated FAP that had remained unsolved by Sanger sequencing and multigene panel next-generation sequencing for years. Results We identified a complex 3.9 Mb rearrangement involving 14 fragments from chromosome 5q22.1q22.3 of which three were lost, 1 reinserted into chromosome 5 and 10 inserted into chromosome 10q21.3 in a seemingly random order and orientation thus fulfilling the major criteria of chromothripsis. The rearrangement separates APC promoter 1B from the coding ORF (open reading frame) thus leading to allele-specific downregulation of APC mRNA. The rearrangement also involves three additional genes implicated in the APC–Axin–GSK3B–β-catenin signalling pathway. Conclusions Based on comprehensive genomic analysis, we propose that constitutional chromothripsis dampening APC expression, possibly modified by additional APC–Axin–GSK3B–β-catenin pathway disruptions, underlies the patient’s clinical phenotype. The combinatorial approach we deployed provides a powerful tool set for deciphering unsolved familial polyposis and potentially other tumour syndromes and monogenic diseases.
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Affiliation(s)
| | | | - Monika Morak
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Alex Hastie
- BioNano Genomics Inc, San Diego, California, USA
| | | | | | | | | | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | | | - Udo Koehler
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany .,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Dieter A Wolf
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany .,Department of Medicine II, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
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16
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Poot M. Balanced at First Sight, but in Reality out of Balance. Mol Syndromol 2021; 12:333-334. [PMID: 34899141 DOI: 10.1159/000519174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 08/22/2021] [Indexed: 11/19/2022] Open
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17
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Crasta K. Chromothripsis: A shattered chromosome in the spotlight. Semin Cell Dev Biol 2021; 123:88-89. [PMID: 34840079 DOI: 10.1016/j.semcdb.2021.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Karen Crasta
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; A(⁎)STAR Institute of Molecular and Cell Biology, Singapore.
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18
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Grochowski CM, Krepischi ACV, Eisfeldt J, Du H, Bertola DR, Oliveira D, Costa SS, Lupski JR, Lindstrand A, Carvalho CMB. Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome. Front Genet 2021; 12:708348. [PMID: 34512724 PMCID: PMC8427664 DOI: 10.3389/fgene.2021.708348] [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: 05/11/2021] [Accepted: 07/23/2021] [Indexed: 02/02/2023] Open
Abstract
Chromoanagenesis is a descriptive term that encompasses classes of catastrophic mutagenic processes that generate localized and complex chromosome rearrangements in both somatic and germline genomes. Herein, we describe a 5-year-old female presenting with a constellation of clinical features consistent with a clinical diagnosis of Coffin–Siris syndrome 1 (CSS1). Initial G-banded karyotyping detected a 90-Mb pericentric and a 47-Mb paracentric inversion on a single chromosome. Subsequent analysis of short-read whole-genome sequencing data and genomic optical mapping revealed additional inversions, all clustered on chromosome 6, one of them disrupting ARID1B for which haploinsufficiency leads to the CSS1 disease trait (MIM:135900). The aggregate structural variant data show that the resolved, the resolved derivative chromosome architecture presents four de novo inversions, one pericentric and three paracentric, involving six breakpoint junctions in what appears to be a shuffling of genomic material on this chromosome. Each junction was resolved to nucleotide-level resolution with mutational signatures suggestive of non-homologous end joining. The disruption of the gene ARID1B is shown to occur between the fourth and fifth exon of the canonical transcript with subsequent qPCR studies confirming a decrease in ARID1B expression in the patient versus healthy controls. Deciphering the underlying genomic architecture of chromosomal rearrangements and complex structural variants may require multiple technologies and can be critical to elucidating the molecular etiology of a patient’s clinical phenotype or resolving unsolved Mendelian disease cases.
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Affiliation(s)
- Christopher M Grochowski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Ana C V Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Debora R Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,Clinical Genetics Unit, Instituto da Criança do Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - Danyllo Oliveira
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia S Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States.,Texas Children's Hospital, Houston, TX, United States
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Pacific Northwest Research Institute, Seattle, WA, United States
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19
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Osia B, Alsulaiman T, Jackson T, Kramara J, Oliveira S, Malkova A. Cancer cells are highly susceptible to accumulation of templated insertions linked to MMBIR. Nucleic Acids Res 2021; 49:8714-8731. [PMID: 34379776 PMCID: PMC8421209 DOI: 10.1093/nar/gkab685] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 07/25/2021] [Accepted: 07/29/2021] [Indexed: 01/23/2023] Open
Abstract
Microhomology-mediated break-induced replication (MMBIR) is a DNA repair pathway initiated by polymerase template switching at microhomology, which can produce templated insertions that initiate chromosomal rearrangements leading to neurological and metabolic diseases, and promote complex genomic rearrangements (CGRs) found in cancer. Yet, how often templated insertions accumulate from processes like MMBIR in genomes is poorly understood due to difficulty in directly identifying these events by whole genome sequencing (WGS). Here, by using our newly developed MMBSearch software, we directly detect such templated insertions (MMB-TIs) in human genomes and report substantial differences in frequency and complexity of MMB-TI events between normal and cancer cells. Through analysis of 71 cancer genomes from The Cancer Genome Atlas (TCGA), we observed that MMB-TIs readily accumulate de novo across several cancer types, with particularly high accumulation in some breast and lung cancers. By contrast, MMB-TIs appear only as germline variants in normal human fibroblast cells, and do not accumulate as de novo somatic mutations. Finally, we performed WGS on a lung adenocarcinoma patient case and confirmed MMB-TI-initiated chromosome fusions that disrupted potential tumor suppressors and induced chromothripsis-like CGRs. Based on our findings we propose that MMB-TIs represent a trigger for widespread genomic instability and tumor evolution.
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Affiliation(s)
- Beth Osia
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Thamer Alsulaiman
- Department of Computer Science, University of Iowa, Iowa City, IA 52245, USA
| | - Tyler Jackson
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Juraj Kramara
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Suely Oliveira
- Department of Computer Science, University of Iowa, Iowa City, IA 52245, USA
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
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20
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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: 23] [Impact Index Per Article: 7.7] [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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21
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Abstract
Our understanding of genetic disease(s) has increased exponentially since the completion of human genome sequencing and the development of numerous techniques to detect genetic variants. These techniques have not only allowed us to diagnose genetic disease, but in so doing, also provide increased understanding of the pathogenesis of these diseases to aid in developing appropriate therapeutic options. Additionally, the advent of next-generation or massively parallel sequencing (NGS/MPS) is increasingly being used in the clinical setting, as it can detect a number of abnormalities from point mutations to chromosomal rearrangements as well as aberrations within the transcriptome. In this article, we will discuss the use of multiple techniques that are used in genetic diagnosis. © 2020 by John Wiley & Sons, Inc.
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Affiliation(s)
- Rashmi S Goswami
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.,Sunnybrook Research Institute, Biological Sciences, Odette Cancer Research Program, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shuko Harada
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
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22
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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: 3] [Impact Index Per Article: 1.0] [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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23
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Arya P, Hodge JC, Matlock PA, Vance GH, Breman AM. Two Patients with Complex Rearrangements Suggestive of Germline Chromoanagenesis. Cytogenet Genome Res 2021; 160:671-679. [PMID: 33535208 DOI: 10.1159/000512898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/09/2020] [Indexed: 11/19/2022] Open
Abstract
Chromoanagenesis, a phenomenon characterized by complex chromosomal rearrangement and reorganization events localized to a limited number of genomic regions, includes the subcategories chromothripsis, chromoanasynthesis, and chromoplexy. Although definitions of these terms are evolving, constitutional chromoanagenesis events have been reported in a limited number of patients with variable phenotypes. We report on 2 cases with complex genomic events characterized by multiple copy number gains and losses confined to a single chromosome region, which are suggestive of constitutional chromoanagenesis. Case 1 is a 43-year-old male with intellectual disability and recently developed generalized tonic-clonic seizures. Chromosomal microarray analysis identified a complex rearrangement involving chromosome region 14q31.1q32.2, consisting of 16 breakpoints ranging in size from 0.2 to 6.2 Mb, with 5 segments of normal copy number present between these alterations. Interestingly, this case represents the oldest known patient with a complex rearrangement indicative of constitutional chromoanagenesis. Case 2 is a 2-year-old female with developmental delay, speech delay, low muscle tone, and seizures. Chromosomal microarray analysis identified a complex rearrangement consisting of 28 breakpoints localized to 18q21.32q23. The size of the copy number alterations ranged from 0.042 to 5.1 Mb, flanked by 12 small segments of normal copy number. These cases add to a growing body of literature demonstrating complex chromosomal rearrangements as a disease mechanism for congenital anomalies.
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Affiliation(s)
- Priyanka Arya
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jennelle C Hodge
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Peggy A Matlock
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Gail H Vance
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Amy M Breman
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA,
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24
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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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25
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Mastio J, Saeed MB, Wurzer H, Krecke M, Westerberg LS, Thomas C. Higher Incidence of B Cell Malignancies in Primary Immunodeficiencies: A Combination of Intrinsic Genomic Instability and Exocytosis Defects at the Immunological Synapse. Front Immunol 2020; 11:581119. [PMID: 33240268 PMCID: PMC7680899 DOI: 10.3389/fimmu.2020.581119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022] Open
Abstract
Congenital defects of the immune system called primary immunodeficiency disorders (PID) describe a group of diseases characterized by a decrease, an absence, or a malfunction of at least one part of the immune system. As a result, PID patients are more prone to develop life-threatening complications, including cancer. PID currently include over 400 different disorders, however, the variety of PID-related cancers is narrow. We discuss here reasons for this clinical phenotype. Namely, PID can lead to cell intrinsic failure to control cell transformation, failure to activate tumor surveillance by cytotoxic cells or both. As the most frequent tumors seen among PID patients stem from faulty lymphocyte development leading to leukemia and lymphoma, we focus on the extensive genomic alterations needed to create the vast diversity of B and T lymphocytes with potential to recognize any pathogen and why defects in these processes lead to malignancies in the immunodeficient environment of PID patients. In the second part of the review, we discuss PID affecting tumor surveillance and especially membrane trafficking defects caused by altered exocytosis and regulation of the actin cytoskeleton. As an impairment of these membrane trafficking pathways often results in dysfunctional effector immune cells, tumor cell immune evasion is elevated in PID. By considering new anti-cancer treatment concepts, such as transfer of genetically engineered immune cells, restoration of anti-tumor immunity in PID patients could be an approach to complement standard therapies.
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Affiliation(s)
- Jérôme Mastio
- Department of Oncology, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Mezida B Saeed
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hannah Wurzer
- Department of Oncology, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Max Krecke
- Department of Oncology, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Lisa S Westerberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Clément Thomas
- Department of Oncology, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg City, Luxembourg
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26
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Anzick S, Thurm A, Burkett S, Velez D, Cho E, Chlebowski C, Virtaneva K, Bruno D, Martin CB, Lang DM, Brooks B, Martens C, McDermott DH, Murphy PM. Chromoanasynthesis as a cause of Jacobsen syndrome. Am J Med Genet A 2020; 182:2533-2539. [PMID: 32841469 PMCID: PMC11007684 DOI: 10.1002/ajmg.a.61824] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/21/2020] [Accepted: 07/25/2020] [Indexed: 01/02/2023]
Abstract
Jacobsen syndrome (MIM #147791) is a rare multisystem genomic disorder involving craniofacial abnormalities, intellectual disability, other neurodevelopmental defects, and terminal truncation of chromosome 11q, typically deleting ~170 to >340 genes. We describe the first case of Jacobsen syndrome caused by congenital chromoanasynthesis, an extreme form of complex chromosomal rearrangement. Six duplications and five deletions occurred on one copy of chromosome 11q with microhomology signatures in the breakpoint junctions, indicating an all-at-once replication-based rearrangement mechanism in a gametocyte or early post-zygotic cell. Eighteen genes were deleted from the Jacobsen region, including KIRREL3, which is associated with intellectual disability.
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Affiliation(s)
- Sarah Anzick
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Audrey Thurm
- National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | | | - Daniel Velez
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Elena Cho
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Colby Chlebowski
- National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - Kimmo Virtaneva
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Daniel Bruno
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Clare B. Martin
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - David M. Lang
- Warren Grant Magnuson Clinical Center, NIH, Bethesda, MD 20892, USA
| | - Brian Brooks
- National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Craig Martens
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - David H. McDermott
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Philip M. Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
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27
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Yin Y, He Q, Li Y, Long J, Lei X, Li Z, Zhu W. Emerging functions of PRKDC in the initiation and progression of cancer. TUMORI JOURNAL 2020; 107:483-488. [PMID: 32867618 DOI: 10.1177/0300891620950472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is encoded by the protein kinase, DNA-activated, catalytic polypeptide (PRKDC) gene. DNA-PKcs plays a major role in nonhomologous end joining DNA repair, and it has been identified to be an important factor in tumor progression and metastasis. DNA-PKcs may have opposite effects in diseases, depending on the cell and tissue types. In this review, we discuss its role in various tumors. High levels of DNA-PKcs are directly associated with prognosis, neoplasm recurrence rates, and overall survival. Our results suggest that DNA-PKcs may serve as a therapeutic target for advanced malignancies.
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Affiliation(s)
- Yuting Yin
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
| | - Qinglian He
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
| | - Yuling Li
- Department of Pathology, Dongguan Hospital of Southern Medical University, Dongguan, Guangdong Province, China
| | - Jiali Long
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
| | - Xue Lei
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
| | - Ziqi Li
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
| | - Wei Zhu
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
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28
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Prenatal Diagnosis of a De Novo Partial Trisomy 6q and Partial Monosomy 18p Associated with Cephalocele: A Case Report. Balkan J Med Genet 2020; 23:99-102. [PMID: 32953417 PMCID: PMC7474219 DOI: 10.2478/bjmg-2020-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 28-year-old woman underwent amniocentesis at 18 weeks’ gestation upon detection of increased fetal nuchal fold and parietal cephalocele on the second trimester ultrasound examination. Prenatal microarray showed a de novo unbalanced translocation resulting in a gain in 6q and loss in 18p. A female infant was delivered at 38 weeks’ gestation. At birth, cephalocele and webbed neck were noted as major dysmorphic features. The case presented here shows how a combination of different genetic studies is used to accurately elucidate a chromosomal anomaly in a prenatal setting.
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29
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Interphase Cytogenetic Analysis of G0 Lymphocytes Exposed to α-Particles, C-Ions, and Protons Reveals their Enhanced Effectiveness for Localized Chromosome Shattering-A Critical Risk for Chromothripsis. Cancers (Basel) 2020; 12:cancers12092336. [PMID: 32825012 PMCID: PMC7563219 DOI: 10.3390/cancers12092336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/08/2020] [Accepted: 08/15/2020] [Indexed: 01/21/2023] Open
Abstract
For precision cancer radiotherapy, high linear energy transfer (LET) particle irradiation offers a substantial advantage over photon-based irradiation. In contrast to the sparse deposition of low-density energy by χ- or γ-rays, particle irradiation causes focal DNA damage through high-density energy deposition along the particle tracks. This is characterized by the formation of multiple damage sites, comprising localized clustered patterns of DNA single- and double-strand breaks as well as base damage. These clustered DNA lesions are key determinants of the enhanced relative biological effectiveness (RBE) of energetic nuclei. However, the search for a fingerprint of particle exposure remains open, while the mechanisms underlying the induction of chromothripsis-like chromosomal rearrangements by high-LET radiation (resembling chromothripsis in tumors) await to be elucidated. In this work, we investigate the transformation of clustered DNA lesions into chromosome fragmentation, as indicated by the induction and post-irradiation repair of chromosomal damage under the dynamics of premature chromosome condensation in G0 human lymphocytes. Specifically, this study provides, for the first time, experimental evidence that particle irradiation induces localized shattering of targeted chromosome domains. Yields of chromosome fragments and shattered domains are compared with those generated by γ-rays; and the RBE values obtained are up to 28.6 for α-particles (92 keV/μm), 10.5 for C-ions (295 keV/μm), and 4.9 for protons (28.5 keV/μm). Furthermore, we test the hypothesis that particle radiation-induced persistent clustered DNA lesions and chromatin decompaction at damage sites evolve into localized chromosome shattering by subsequent chromatin condensation in a single catastrophic event—posing a critical risk for random rejoining, chromothripsis, and carcinogenesis. Consistent with this hypothesis, our results highlight the potential use of shattered chromosome domains as a fingerprint of high-LET exposure, while conforming to the new model we propose for the mechanistic origin of chromothripsis-like rearrangements.
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30
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Mitsuhashi S, Ohori S, Katoh K, Frith MC, Matsumoto N. A pipeline for complete characterization of complex germline rearrangements from long DNA reads. Genome Med 2020; 12:67. [PMID: 32731881 PMCID: PMC7393826 DOI: 10.1186/s13073-020-00762-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/10/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Many genetic/genomic disorders are caused by genomic rearrangements. Standard methods can often characterize these variations only partly, e.g., copy number changes or breakpoints. It is important to fully understand the order and orientation of rearranged fragments, with precise breakpoints, to know the pathogenicity of the rearrangements. METHODS We performed whole-genome-coverage nanopore sequencing of long DNA reads from four patients with chromosomal translocations. We identified rearrangements relative to a reference human genome, subtracted rearrangements shared by any of 33 control individuals, and determined the order and orientation of rearranged fragments, with our newly developed analysis pipeline. RESULTS We describe the full characterization of complex chromosomal rearrangements, by filtering out genomic rearrangements seen in controls without the same disease, reducing the number of loci per patient from a few thousand to a few dozen. Breakpoint detection was very accurate; we usually see ~ 0 ± 1 base difference from Sanger sequencing-confirmed breakpoints. For one patient with two reciprocal chromosomal translocations, we find that the translocation points have complex rearrangements of multiple DNA fragments involving 5 chromosomes, which we could order and orient by an automatic algorithm, thereby fully reconstructing the rearrangement. A rearrangement is more than the sum of its parts: some properties, such as sequence loss, can be inferred only after reconstructing the whole rearrangement. In this patient, the rearrangements were evidently caused by shattering of the chromosomes into multiple fragments, which rejoined in a different order and orientation with loss of some fragments. CONCLUSIONS We developed an effective analytic pipeline to find chromosomal aberration in congenital diseases by filtering benign changes, only from long read sequencing. Our algorithm for reconstruction of complex rearrangements is useful to interpret rearrangements with many breakpoints, e.g., chromothripsis. Our approach promises to fully characterize many congenital germline rearrangements, provided they do not involve poorly understood loci such as centromeric repeats.
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Affiliation(s)
- Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Sachiko Ohori
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Kazutaka Katoh
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Martin C Frith
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo, Japan.
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan.
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31
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Hanscom T, McVey M. Regulation of Error-Prone DNA Double-Strand Break Repair and Its Impact on Genome Evolution. Cells 2020; 9:E1657. [PMID: 32660124 PMCID: PMC7407515 DOI: 10.3390/cells9071657] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
Abstract
Double-strand breaks are one of the most deleterious DNA lesions. Their repair via error-prone mechanisms can promote mutagenesis, loss of genetic information, and deregulation of the genome. These detrimental outcomes are significant drivers of human diseases, including many cancers. Mutagenic double-strand break repair also facilitates heritable genetic changes that drive organismal adaptation and evolution. In this review, we discuss the mechanisms of various error-prone DNA double-strand break repair processes and the cellular conditions that regulate them, with a focus on alternative end joining. We provide examples that illustrate how mutagenic double-strand break repair drives genome diversity and evolution. Finally, we discuss how error-prone break repair can be crucial to the induction and progression of diseases such as cancer.
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Affiliation(s)
| | - Mitch McVey
- Department. of Biology, Tufts University, Medford, MA 02155, USA;
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32
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Brás A, Rodrigues AS, Rueff J. Copy number variations and constitutional chromothripsis (Review). Biomed Rep 2020; 13:11. [PMID: 32765850 PMCID: PMC7391299 DOI: 10.3892/br.2020.1318] [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: 11/04/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
Both copy number variations (CNVs) and chromothripsis are phenomena that involve complex genomic rearrangements. Chromothripsis results in CNVs and other structural changes. CNVs are frequently observed in the human genome. Studies on CNVs have been increasing exponentially; the Database of Genomic Variants shows an increase in the number of data published on structural variations added to the database in the last 15 years. CNVs may be a result of replicative and non-replicative mechanisms, and are hypothesized to serve important roles in human health and disease. Chromothripsis is a phenomena of chromosomal rearrangement following chromosomal breaks at multiple locations and involves impaired DNA repair. In 2011, Stephens et al coined the term chromothripsis for this type of fragmenting event. Several proposed mechanisms have been suggested to underlie chromothripsis, such as p53 inactivation, micronuclei formation, abortive apoptosis and telomere fusions in telomere crisis. Chromothripsis gives rise to normal or abnormal phenotypes. In this review, constitutional chromothripsis, which may coexist with multiple de novo CNVs are described and discussed. This reviews aims to summarize recent advances in our understanding of CNVs and chromothripsis, and describe the effects of these phenomena on human health and birth defects.
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Affiliation(s)
- Aldina Brás
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
| | - António Sebastião Rodrigues
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
| | - José Rueff
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
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33
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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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34
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Yang J, Chen Y, Luo H, Cai H. The Landscape of Somatic Copy Number Alterations in Head and Neck Squamous Cell Carcinoma. Front Oncol 2020; 10:321. [PMID: 32226775 PMCID: PMC7080958 DOI: 10.3389/fonc.2020.00321] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 02/24/2020] [Indexed: 02/05/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. Somatic copy number alterations (CNAs) play a significant role in the development of this lethal cancer. In this study, we present a meta-analysis of CNAs for a total of 1,395 HNSCC samples. Publicly available R packages and in-house scripts were used for genomic array data processing, including normalization, segmentation and CNA calling. We detected 125 regions of significant gains or losses using GISTIC algorithm and found several potential driver genes in these regions. The incidence of chromothripsis in HNSCC was estimated to be 6%, and the chromosome pulverization hotspot regions were detected. We determined 323 genomic locations significantly enriched for breakpoints, which indicate HNSCC-specific genomic instability regions. Unsupervised clustering of genome-wide CNA data revealed a sub-cluster predominantly composed of nasopharynx tumors and presented a large proportion of HPV-positive samples. These results will facilitate the discovery of therapeutic candidates and extend our molecular understanding of HNSCC.
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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, China
| | - Yi Chen
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Luo
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Haoyang Cai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
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35
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Plesser Duvdevani M, Pettersson M, Eisfeldt J, Avraham O, Dagan J, Frumkin A, Lupski JR, Lindstrand A, Harel T. Whole-genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome. Am J Med Genet A 2020; 182:1143-1151. [PMID: 32125084 DOI: 10.1002/ajmg.a.61539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 02/05/2023]
Abstract
Clinical laboratory diagnostic evaluation of the genomes of children with suspected genetic disorders, including chromosomal microarray and exome sequencing, cannot detect copy number neutral genomic rearrangements such as inversions, balanced translocations, and complex chromosomal rearrangements (CCRs). We describe an infant with a clinical diagnosis of Cornelia de Lange syndrome (CdLS) in whom chromosome analysis revealed a de novo complex balanced translocation, 46,XY,t(5;7;6)(q11.2;q32;q13)dn. Subsequent molecular characterization by whole-genome sequencing (WGS) identified 23 breakpoints, delineating segments derived from four chromosomes (5;6;7;21) in ancestral or inverted orientation. One of the breakpoints disrupted a known CdLS gene, NIPBL. Further investigation revealed paternal origin of the CCR allele, clustering of the breakpoint junctions, and molecular repair signatures suggestive of a single catastrophic event. Notably, very short DNA segments (25 and 41 bp) were included in the reassembled chromosomes, lending additional support that the DNA repair machinery can detect and repair such segments. Interestingly, there was an independent paternally derived miniscule complex rearrangement, possibly predisposing to subsequent genomic instability. In conclusion, we report a CCR causing a monogenic Mendelian disorder, urging WGS analysis of similar unsolved cases with suspected Mendelian disorders. Breakpoint analysis allowed for identification of the underlying molecular diagnosis and implicated chromoanagenesis in CCR formation.
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Affiliation(s)
- Morasha Plesser Duvdevani
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - 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
| | - Ortal Avraham
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Judith Dagan
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ayala Frumkin
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - 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
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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36
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Cortés-Ciriano I, Lee JJK, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Park PJ. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet 2020; 52:331-341. [PMID: 32025003 PMCID: PMC7058534 DOI: 10.1038/s41588-019-0576-7] [Citation(s) in RCA: 353] [Impact Index Per Article: 88.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 12/20/2019] [Indexed: 01/12/2023]
Abstract
Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer.
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Affiliation(s)
- Isidro Cortés-Ciriano
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China
| | - Dhawal Jain
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Youngsook L Jung
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Dmitry Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC, USA
| | - Cheng-Zhong Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - David S Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Boston, MA, USA.
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37
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Balachandran P, Beck CR. Structural variant identification and characterization. Chromosome Res 2020; 28:31-47. [PMID: 31907725 PMCID: PMC7131885 DOI: 10.1007/s10577-019-09623-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 10/15/2019] [Accepted: 11/24/2019] [Indexed: 01/06/2023]
Abstract
Structural variant (SV) differences between human genomes can cause germline and mosaic disease as well as inter-individual variation. De-regulation of accurate DNA repair and genomic surveillance mechanisms results in a large number of SVs in cancer. Analysis of the DNA sequences at SV breakpoints can help identify pathways of mutagenesis and regions of the genome that are more susceptible to rearrangement. Large-scale SV analyses have been enabled by high-throughput genome-level sequencing on humans in the past decade. These studies have shed light on the mechanisms and prevalence of complex genomic rearrangements. Recent advancements in both sequencing and other mapping technologies as well as calling algorithms for detection of genomic rearrangements have helped propel SV detection into population-scale studies, and have begun to elucidate previously inaccessible regions of the genome. Here, we discuss the genomic organization of simple and complex SVs, the molecular mechanisms of their formation, and various ways to detect them. We also introduce methods for characterizing SVs and their consequences on human genomes.
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Affiliation(s)
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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38
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Nazaryan-Petersen L, Bjerregaard VA, Nielsen FC, Tommerup N, Tümer Z. Chromothripsis and DNA Repair Disorders. J Clin Med 2020; 9:jcm9030613. [PMID: 32106411 PMCID: PMC7141117 DOI: 10.3390/jcm9030613] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/15/2020] [Accepted: 02/19/2020] [Indexed: 12/18/2022] Open
Abstract
Chromothripsis is a mutational mechanism leading to complex and relatively clustered chromosomal rearrangements, resulting in diverse phenotypic outcomes depending on the involved genomic landscapes. It may occur both in the germ and the somatic cells, resulting in congenital and developmental disorders and cancer, respectively. Asymptomatic individuals may be carriers of chromotriptic rearrangements and experience recurrent reproductive failures when two or more chromosomes are involved. Several mechanisms are postulated to underlie chromothripsis. The most attractive hypothesis involves chromosome pulverization in micronuclei, followed by the incorrect reassembly of fragments through DNA repair to explain the clustered nature of the observed complex rearrangements. Moreover, exogenous or endogenous DNA damage induction and dicentric bridge formation may be involved. Chromosome instability is commonly observed in the cells of patients with DNA repair disorders, such as ataxia telangiectasia, Nijmegen breakage syndrome, and Bloom syndrome. In addition, germline variations of TP53 have been associated with chromothripsis in sonic hedgehog medulloblastoma and acute myeloid leukemia. In the present review, we focus on the underlying mechanisms of chromothripsis and the involvement of defective DNA repair genes, resulting in chromosome instability and chromothripsis-like rearrangements.
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Affiliation(s)
- Lusine Nazaryan-Petersen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (L.N.-P.); (N.T.)
- Center for Genomic Medicine, Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Victoria Alexandra Bjerregaard
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark;
| | | | - Niels Tommerup
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (L.N.-P.); (N.T.)
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark;
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Correspondence: ; Tel.: +45-292-048-55
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39
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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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40
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Brambati A, Barry RM, Sfeir A. DNA polymerase theta (Polθ) - an error-prone polymerase necessary for genome stability. Curr Opin Genet Dev 2020; 60:119-126. [PMID: 32302896 PMCID: PMC7230004 DOI: 10.1016/j.gde.2020.02.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/21/2022]
Abstract
Mammalian cells have evolved multiple pathways to repair DNA double strand breaks (DSBs) and ensure genome stability. In addition to non-homologous end-joining (NHEJ) and homologous recombination (HR), cells evolved an error-prone repair pathway termed microhomology-mediated end joining (MMEJ). The mutagenic outcome of MMEJ derives from the activity of DNA polymerase theta (Polθ) - a multidomain enzyme that is minimally expressed in normal tissue but overexpressed in tumors. Polθ expression is particularly crucial for the proliferation of HR deficient cancer cells. As a result, this mutagenic repair emerged as an attractive target for cancer therapy, and inhibitors are currently in pre-clinical development. Here, we review the multifunctionality of this enigmatic polymerase, focusing on its role during DSB repair in mammalian cells and its impact on cancer genomes.
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Affiliation(s)
- Alessandra Brambati
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Raymond Mario Barry
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA.
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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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42
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Li Z, Zhang X, Hou C, Zhou Y, Chen J, Cai H, Ye Y, Liu J, Huang N. Comprehensive identification and characterization of somatic copy number alterations in triple‑negative breast cancer. Int J Oncol 2019; 56:522-530. [PMID: 31894314 PMCID: PMC6959384 DOI: 10.3892/ijo.2019.4950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/30/2019] [Indexed: 12/27/2022] Open
Abstract
Triple‑negative breast cancer (TNBC) accounts for ~15% of all breast cancer diagnoses each year. Patients with TNBC tend to have a higher risk for early relapse and a worse prognosis. TNBC is characterized by extensive somatic copy number alterations (CNAs). However, the DNA CNA profile of TNBC remains to be extensively investigated. The present study assessed the genomic profile of CNAs in 201 TNBC samples, aiming to identify recurrent CNAs that may drive the pathogenesis of TNBC. In total, 123 regions of significant amplification and deletion were detected using the Genomic Identification of Significant Targets in Cancer algorithm, and potential driver genes for TNBC were identified. A total of 31 samples exhibited signs of chromothripsis and revealed chromosome pulverization hotspot regions. The present study further determined 199 genomic locations that were significantly enriched for breakpoints, which indicated TNBC‑specific genomic instability regions. Unsupervised hierarchical clustering of tumors resulted in three main subgroups that exhibited distinct CNA profiles, which may reveal the heterogeneity of molecular mechanisms in TNBC subgroups. These results will extend the molecular understanding of TNBC and will facilitate the discovery of therapeutic and diagnostic target candidates.
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Affiliation(s)
- Zaibing Li
- Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiao Zhang
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Chenxin Hou
- West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yuqing Zhou
- West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Junli Chen
- Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Haoyang Cai
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio‑Resources and Eco‑Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Yifeng Ye
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Jinping Liu
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Ning Huang
- Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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43
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Lambo S, Gröbner SN, Rausch T, Waszak SM, Schmidt C, Gorthi A, Romero JC, Mauermann M, Brabetz S, Krausert S, Buchhalter I, Koster J, Zwijnenburg DA, Sill M, Hübner JM, Mack N, Schwalm B, Ryzhova M, Hovestadt V, Papillon-Cavanagh S, Chan JA, Landgraf P, Ho B, Milde T, Witt O, Ecker J, Sahm F, Sumerauer D, Ellison DW, Orr BA, Darabi A, Haberler C, Figarella-Branger D, Wesseling P, Schittenhelm J, Remke M, Taylor MD, Gil-da-Costa MJ, Łastowska M, Grajkowska W, Hasselblatt M, Hauser P, Pietsch T, Uro-Coste E, Bourdeaut F, Masliah-Planchon J, Rigau V, Alexandrescu S, Wolf S, Li XN, Schüller U, Snuderl M, Karajannis MA, Giangaspero F, Jabado N, von Deimling A, Jones DTW, Korbel JO, von Hoff K, Lichter P, Huang A, Bishop AJR, Pfister SM, Korshunov A, Kool M. The molecular landscape of ETMR at diagnosis and relapse. Nature 2019; 576:274-280. [PMID: 31802000 PMCID: PMC6908757 DOI: 10.1038/s41586-019-1815-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 10/16/2019] [Indexed: 12/18/2022]
Abstract
Embryonal tumours with multilayered rosettes (ETMRs) are aggressive paediatric embryonal brain tumours with a universally poor prognosis1. Here we collected 193 primary ETMRs and 23 matched relapse samples to investigate the genomic landscape of this distinct tumour type. We found that patients with tumours in which the proposed driver C19MC2-4 was not amplified frequently had germline mutations in DICER1 or other microRNA-related aberrations such as somatic amplification of miR-17-92 (also known as MIR17HG). Whole-genome sequencing revealed that tumours had an overall low recurrence of single-nucleotide variants (SNVs), but showed prevalent genomic instability caused by widespread occurrence of R-loop structures. We show that R-loop-associated chromosomal instability can be induced by the loss of DICER1 function. Comparison of primary tumours and matched relapse samples showed a strong conservation of structural variants, but low conservation of SNVs. Moreover, many newly acquired SNVs are associated with a mutational signature related to cisplatin treatment. Finally, we show that targeting R-loops with topoisomerase and PARP inhibitors might be an effective treatment strategy for this deadly disease.
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Affiliation(s)
- Sander Lambo
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Susanne N Gröbner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Sebastian M Waszak
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Christin Schmidt
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aparna Gorthi
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, TX, USA
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX, USA
| | - July Carolina Romero
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, TX, USA
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX, USA
| | - Monika Mauermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Brabetz
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sonja Krausert
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ivo Buchhalter
- Omics IT and Data Management Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, Amsterdam, The Netherlands
| | - Danny A Zwijnenburg
- Department of Oncogenomics, Academic Medical Center, Amsterdam, The Netherlands
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jens-Martin Hübner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Norman Mack
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Schwalm
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon Papillon-Cavanagh
- Department of Pediatrics, McGill University Health Center, McGill University, Montreal, Quebec, Canada
| | - Jennifer A Chan
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Pablo Landgraf
- Department of Pediatrics, Pediatric Oncology and Hematology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Ben Ho
- Division of Hematology/Oncology Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Sumerauer
- Department of Pediatric Hematology and Oncology, University Hospital Motol, Prague, Czech Republic
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Anna Darabi
- Department of Clinical Sciences Lund, Section of Neurosurgery, Faculty of Medicine, Lund University, Lund, Sweden
| | | | - Dominique Figarella-Branger
- Aix-Marseille University, Neurophysiopathology Institute (INP), CNRS, Marseille, France
- Department of Pathology, APHM, Marseille, France
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, Amsterdam University Medical Centers/location VUmc, Amsterdam, The Netherlands
| | - Jens Schittenhelm
- Department of Neuropathology, Institute of Pathology and Neuropathology, University Hospital of Tübingen, Tübingen, Germany
- Center for CNS Tumors, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital of Tübingen, Tübingen, Germany
| | - Marc Remke
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Maria J Gil-da-Costa
- Pediatric Hematology and Oncology Division, University Hospital São João Alameda Hernani Monteiro, Porto, Portugal
| | - Maria Łastowska
- Department of Pathology, Children's Memorial Health Institute, Warsaw, Poland
| | - Wiesława Grajkowska
- Department of Pathology, Children's Memorial Health Institute, Warsaw, Poland
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Peter Hauser
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Torsten Pietsch
- Institute of Neuropathology, Brain Tumor Reference Center of the German Society of Neuropathology and Neuroanatomy, University of Bonn Medical Center, Bonn, Germany
| | - Emmanuelle Uro-Coste
- Department of Pathology, Toulouse University Hospital, Toulouse, France
- INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France
| | - Franck Bourdeaut
- INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Paris Sciences Lettres Research University, Curie Institute, Paris, France
| | - Julien Masliah-Planchon
- Pediatric Oncology Department, SIREDO Pediatric Oncology Centre, Curie Institute, Paris, France
- Paris Sciences et Lettres Research University, Institut Curie Hospital, Laboratory of Somatic Genetics, Paris, France
| | - Valérie Rigau
- Department of Pathology, Montpellier University Medical Center, Montpellier, France
- Institute for Neuroscience of Montpellier (INM), INSERM U1051, Montpellier University Hospital, Montpellier, France
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, High Throughput Sequencing Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xiao-Nan Li
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Matthias A Karajannis
- Division of Pediatric Hematology/Oncology, NYU Langone Medical Center, The Stephen D. Hassenfeld Children's Center for Cancer and Blood Disorders, New York, NY, USA
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomopathological Sciences, Sapienza University of Rome, Rome, Italy
- IRCCS Neuromed-Mediterranean Neurological Institute, Pozzilli, Italy
| | - Nada Jabado
- Department of Pediatrics, McGill University Health Center, McGill University, Montreal, Quebec, Canada
| | - Andreas von Deimling
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Katja von Hoff
- Department of Pediatric Oncology/Hematology, Charité University Medicine, Berlin, Germany
- Department for Pediatric Hematology and Oncology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Lichter
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annie Huang
- Division of Hematology/Oncology Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, Medical Biophysics, Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Alexander J R Bishop
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, TX, USA
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health at San Antonio, San Antonio, TX, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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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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45
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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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Gudipati MA, Waters E, Greene C, Goel N, Hoppman NL, Pitel BA, Webley MR, Zou Y. Stable transmission of complex chromosomal rearrangements involving chromosome 1q derived from constitutional chromoanagenesis. Mol Cytogenet 2019; 12:43. [PMID: 31695749 PMCID: PMC6822454 DOI: 10.1186/s13039-019-0455-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/16/2019] [Indexed: 01/10/2023] Open
Abstract
Background Chromoanagenesis events encompassing chromoanasynthesis, chromoplexy, and chromothripsis are described in cancers and can result in highly complex chromosomal rearrangements derived from ‘all-at-once’ catastrophic cellular events. The complexity of these rearrangements and the original descriptions in cancer cells initially led to the assumption that it was an acquired anomaly. While rare, these phenomena involving chromosome 1 have been reported a few individuals in a constitutional setting. Case presentation Here, we describe a newborn baby who was initially referred for cytogenetic testing for multiple congenital anomalies including cystic encephalomalacia, patent ductus arteriosus, inguinal hernia, and bilateral undescended testicles. Chromosome analysis was performed and revealed a derivative chromosome 1 with an 1q24-q31 segment inserted into 1q42.13 resulting in gain of 1q24-q31. Whole genome SNP microarray analysis showed a complex pattern of copy number variants with four gains and one loss involving 1q24-q31. Mate pair next-generation sequencing analysis revealed 18 chromosome breakpoints, six gains along an 1q24-q31 segment, one deletion of 1q31.3 segment and one deletion of 1q42.13 segment, which is strongly evocative of a chromoanasynthesis event for developing this complex rearrangement. Parental chromosome analyses were performed and showed the same derivative chromosome 1 in the mother. Conclusions To our knowledge, our case is the first case with familial constitutional chromoanagenesis involving chromosome 1q24-q42. This report emphasizes the value of performing microarray and mate pair next-generation sequencing analysis for individuals with germline abnormal or complex chromosome rearrangements.
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Affiliation(s)
- Mary A Gudipati
- 1Department of Pathology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Elizabeth Waters
- 1Department of Pathology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Carol Greene
- 2Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD USA
| | - Nidhi Goel
- 3Department of Internal Medicine, University of Maryland School of Medicine, Baltimore, MD USA
| | - Nicole L Hoppman
- 4Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Beth A Pitel
- 4Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Matthew R Webley
- 4Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Ying Zou
- 1Department of Pathology, University of Maryland School of Medicine, Baltimore, MD USA.,5Department of Pathology, Johns Hopkins University, 1812 Ashland Ave., Suite 200, Room 221, Baltimore, MD 2120 USA
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Ader F, Heide S, Marzin P, Afenjar A, Diguet F, Chantot Bastaraud S, Rollat-Farnier PA, Sanlaville D, Portnoï MF, Siffroi JP, Schluth-Bolard C. A 14q distal chromoanagenesis elucidated by whole genome sequencing. Eur J Med Genet 2019; 63:103776. [PMID: 31562959 DOI: 10.1016/j.ejmg.2019.103776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 02/07/2019] [Accepted: 09/22/2019] [Indexed: 11/19/2022]
Abstract
Chromoanagenesis represents an extreme form of genomic rearrangements involving multiple breaks occurring on a single or multiple chromosomes. It has been recently described in both acquired and rare constitutional genetic disorders. Constitutional chromoanagenesis events could lead to abnormal phenotypes including developmental delay and congenital anomalies, and have also been implicated in some specific syndromic disorders. We report the case of a girl presenting with growth retardation, hypotonia, microcephaly, dysmorphic features, coloboma, and hypoplastic corpus callosum. Karyotype showed a de novo structurally abnormal chromosome 14q31qter region. Molecular characterization using SNP-array revealed a complex unbalanced rearrangement in 14q31.1-q32.2, on the paternal chromosome 14, including thirteen interstitial deletions ranging from 33 kb to 1.56 Mb in size, with a total of 4.1 Mb in size, thus suggesting that a single event like chromoanagenesis occurred. To our knowledge, this is one of the first case of 14q distal deletion due to a germline chromoanagenesis. Genome sequencing allowed the characterization of 50 breakpoints, leading to interruption of 10 genes including YY1 which fit with the patient's phenotype. This precise genotyping of breaking junction allowed better definition of genotype-phenotype correlations.
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Affiliation(s)
- Flavie Ader
- Sorbonne Université, Physiopathologie des Maladies Génétiques d'Expression Pédiatrique, F-75012, Paris, France.
| | - Solveig Heide
- Sorbonne Université, Physiopathologie des Maladies Génétiques d'Expression Pédiatrique, F-75012, Paris, France
| | - Pauline Marzin
- Sorbonne Université, Physiopathologie des Maladies Génétiques d'Expression Pédiatrique, F-75012, Paris, France
| | - Alexandra Afenjar
- Unité de neuropédiatrie et pathologie du développement, GHU Paris Est - Hôpital d'Enfants Armand-Trousseau, France
| | - Flavie Diguet
- Service de Génétique, Laboratoire de Cytogénétique Constitutionnelle, Hospices Civils de Lyon, Bron, France; GENDEV Team, Neurosciences Research Center of Lyon, INSERM U1028, CNRS UMR5292, UCBL1, 69677, Bron, France
| | - Sandra Chantot Bastaraud
- Sorbonne Université, Physiopathologie des Maladies Génétiques d'Expression Pédiatrique, F-75012, Paris, France
| | - Pierre-Antoine Rollat-Farnier
- Service de Génétique, Laboratoire de Cytogénétique Constitutionnelle, Hospices Civils de Lyon, Bron, France; Cellule bioinformatique de la plateforme NGS, Hospices Civils de Lyon, Bron, France
| | - Damien Sanlaville
- Service de Génétique, Laboratoire de Cytogénétique Constitutionnelle, Hospices Civils de Lyon, Bron, France; GENDEV Team, Neurosciences Research Center of Lyon, INSERM U1028, CNRS UMR5292, UCBL1, 69677, Bron, France
| | - Marie-France Portnoï
- Sorbonne Université, Physiopathologie des Maladies Génétiques d'Expression Pédiatrique, F-75012, Paris, France
| | - Jean-Pierre Siffroi
- Sorbonne Université, Physiopathologie des Maladies Génétiques d'Expression Pédiatrique, F-75012, Paris, France
| | - Caroline Schluth-Bolard
- Service de Génétique, Laboratoire de Cytogénétique Constitutionnelle, Hospices Civils de Lyon, Bron, France; GENDEV Team, Neurosciences Research Center of Lyon, INSERM U1028, CNRS UMR5292, UCBL1, 69677, Bron, France
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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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49
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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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50
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Zepeda-Mendoza CJ, Morton CC. The Iceberg under Water: Unexplored Complexity of Chromoanagenesis in Congenital Disorders. Am J Hum Genet 2019; 104:565-577. [PMID: 30951674 DOI: 10.1016/j.ajhg.2019.02.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/25/2019] [Indexed: 01/16/2023] Open
Abstract
Structural variation, composed of balanced and unbalanced genomic rearrangements, is an important contributor to human genetic diversity with prominent roles in somatic and congenital disease. At the nucleotide level, structural variants (SVs) have been shown to frequently harbor additional breakpoints and copy-number imbalances, a complexity predicted to emerge wholly as a single-cell division event. Chromothripsis, chromoplexy, and chromoanasynthesis, collectively referred to as chromoanagenesis, are three major mechanisms that explain the occurrence of complex germline and somatic SVs. While chromothripsis and chromoplexy have been shown to be key signatures of cancer, chromoanagenesis has been detected in numerous cases of developmental disease and phenotypically normal individuals. Such observations advocate for a deeper study of the polymorphic and pathogenic properties of complex germline SVs, many of which go undetected by traditional clinical molecular and cytogenetic methods. This review focuses on congenital chromoanagenesis, mechanisms leading to occurrence of these complex rearrangements, and their impact on chromosome organization and genome function. We highlight future applications of routine screening of complex and balanced SVs in the clinic, as these represent a potential and often neglected genetic disease source, a true "iceberg under water."
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Affiliation(s)
- Cinthya J Zepeda-Mendoza
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Cynthia C Morton
- Departments of Obstetrics and Gynecology and of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Manchester Center for Audiology and Deafness, School of Health Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9NT, UK.
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