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Balow SA, Coyan AG, Smith N, Russell BE, Monteil D, Hopkin RJ, Smolarek TA. Complex genomic rearrangements of the Y chromosome in a premature infant. Mol Cytogenet 2024; 17:19. [PMID: 39183314 PMCID: PMC11346217 DOI: 10.1186/s13039-024-00689-x] [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: 04/25/2024] [Accepted: 08/01/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND Chromoanagenesis is an umbrella term used to describe catastrophic "all at once" cellular events leading to the chaotic reconstruction of chromosomes. It is characterized by numerous rearrangements involving a small number of chromosomes/loci, copy number gains in combination with deletions, reconstruction of chromosomal fragments with improper order/orientation, and preserved heterozygosity in copy number neutral regions. Chromoanagesis is frequently described in association with cancer; however, it has also been described in the germline. The clinical features associated with constitutional chromoanagenesis are typically due to copy number changes and/or disruption of genes or regulatory regions. CASE PRESENTATION We present an 8-year-old male patient with complex rearrangements of the Y chromosome including a ring Y chromosome, a derivative Y;21 chromosome, and a complex rearranged Y chromosome. These chromosomes were characterized by G-banded chromosome analysis, SNP microarray, interphase FISH, and metaphase FISH. The mechanism(s) by which these rearrangements occurred is unclear; however, it is evocative of chromoanagenesis. CONCLUSION This case is a novel example of suspected germline chromoanagenesis leading to large copy number changes that are well-tolerated, possibly because only the sex chromosomes are affected.
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Affiliation(s)
- Stephanie A Balow
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Alyxis G Coyan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nicki Smith
- Seton Center, Good Samaritan Hospital, TriHealth Hospital Systems, Cincinnati, OH, USA
| | - Bianca E Russell
- Department of Human Genetics, Division of Clinical Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Danielle Monteil
- Department of Pediatrics, Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Teresa A Smolarek
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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2
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Teboul L, Amos-Landgraf J, Benavides FJ, Birling MC, Brown SDM, Bryda E, Bunton-Stasyshyn R, Chin HJ, Crispo M, Delerue F, Dobbie M, Franklin CL, Fuchtbauer EM, Gao X, Golzio C, Haffner R, Hérault Y, Hrabe de Angelis M, Lloyd KCK, Magnuson TR, Montoliu L, Murray SA, Nam KH, Nutter LMJ, Pailhoux E, Pardo Manuel de Villena F, Peterson K, Reinholdt L, Sedlacek R, Seong JK, Shiroishi T, Smith C, Takeo T, Tinsley L, Vilotte JL, Warming S, Wells S, Whitelaw CB, Yoshiki A, Pavlovic G. Improving laboratory animal genetic reporting: LAG-R guidelines. Nat Commun 2024; 15:5574. [PMID: 38956430 PMCID: PMC11220107 DOI: 10.1038/s41467-024-49439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024] Open
Abstract
The biomedical research community addresses reproducibility challenges in animal studies through standardized nomenclature, improved experimental design, transparent reporting, data sharing, and centralized repositories. The ARRIVE guidelines outline documentation standards for laboratory animals in experiments, but genetic information is often incomplete. To remedy this, we propose the Laboratory Animal Genetic Reporting (LAG-R) framework. LAG-R aims to document animals' genetic makeup in scientific publications, providing essential details for replication and appropriate model use. While verifying complete genetic compositions may be impractical, better reporting and validation efforts enhance reliability of research. LAG-R standardization will bolster reproducibility, peer review, and overall scientific rigor.
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Affiliation(s)
- Lydia Teboul
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK.
| | - James Amos-Landgraf
- University of Missouri School of Medicine, Columbia, MO, USA
- University of Missouri College of Veterinary Medicine, Columbia, MO, USA
- Rat Resource and Research Center, University of Missouri, Columbia, MO, USA
| | - Fernando J Benavides
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marie-Christine Birling
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France
| | - Steve D M Brown
- Visiting Scientist, Institut Clinique de la Souris, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France
| | - Elizabeth Bryda
- Rat Resource and Research Center, University of Missouri, Columbia, MO, 65201, USA
| | | | - Hsian-Jean Chin
- National Laboratory Animal Center (NLAC), NARLabs, Taipei, Taiwan
| | - Martina Crispo
- Laboratory Animal Biotechnology Unit, Institut Pasteur de Montevideo, Mataojo 2020, CP 1400, Montevideo, Uruguay
| | - Fabien Delerue
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Dobbie
- Phenomics Australia, Australian National University, 131 Garran Road, Canberra, ACT 2601, Australia
| | - Craig L Franklin
- University of Missouri Mutant Mouse Resource and Research Center (MU MMRRC), University of Missouri, Columbia, MO, 65201, USA
| | | | - Xiang Gao
- National Resource Center of Mutant Mice (NRCMM), Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Christelle Golzio
- Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104- UMR-S 1258, F-67400, Illkirch, France
| | - Rebecca Haffner
- Department Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Yann Hérault
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France
- Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104- UMR-S 1258, F-67400, Illkirch, France
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Alte Akademie 8, 85354, Freising, Germany
- German Center for Diabetes Research (DZD), Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
| | | | - Terry R Magnuson
- Department of Genetics, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7264, USA
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), 28029, Madrid, Spain
| | | | - Ki-Hoan Nam
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Lauryl M J Nutter
- Genetics and Genome Biology, The Hospital for Sick Children and The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada
| | - Eric Pailhoux
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | | | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, and Korea Mouse Phenotyping Center, Seoul, 08826, Republic of Korea
| | | | - Cynthia Smith
- Mouse Genome Informatics (MGI), Jackson Laboratory, Bar Harbor, ME, USA
| | - Toru Takeo
- Center for Animal Resources and Development (CARD), Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Louise Tinsley
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK
| | - Jean-Luc Vilotte
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Søren Warming
- Genentech, Inc., a member of the Roche group, South San Francisco, CA, USA
| | - Sara Wells
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK
- Francis Crick Institute, London, NW1 1AT, UK
| | - C Bruce Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Guillaume Pavlovic
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France.
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3
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Hasnain A, Thompson LL, Hoppman NL, Hovanes K, Liu J, Hashemi B. Constitutional Chromothripsis on Chromosome 2: A Rare Case with Severe Presentation. Case Rep Genet 2024; 2024:6319030. [PMID: 38322183 PMCID: PMC10846923 DOI: 10.1155/2024/6319030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/08/2024] Open
Abstract
Chromothripsis is characterized by shattering and subsequent reassembly of chromosomes by DNA repair processes, which can give rise to a variety of congenital abnormalities and cancer. Constitutional chromothripsis is a rare occurrence, reported in children presenting with a wide range of birth defects. We present a case of a female child born with multiple major congenital abnormalities including severe microcephaly, ocular dysgenesis, heart defect, and imperforate anus. Chromosomal microarray and mate pair sequencing identified a complex chromosomal rearrangement involving the terminal end of the long arm of chromosome 2, with two duplications (located at 2p25.3-p25.1 and 2q35-q37.2 regions) and two deletions (located at 2q37.2-q37.3 and 2q37.3 regions) along with structural changes including inverted segments. A review of the literature for complex rearrangements on chromosome 2 revealed overlapping features; however, our patient had a significantly more severe phenotype which resulted in early death at the age of 2 years. Breakpoints analysis did not reveal the involvement of any candidate genes. We concluded that the complexity of the genomic rearrangement and the combined dosage/structural effect of these copy number variants are likely explanations for the severe presentation in our patient.
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Affiliation(s)
- Afia Hasnain
- Genomics Laboratory, Diagnostic Services, Shared Health, Winnipeg, MB, Canada
| | - Laura L. Thompson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L. Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Jing Liu
- Genomics Laboratory, Diagnostic Services, Shared Health, Winnipeg, MB, Canada
| | - Bita Hashemi
- Genetics and Metabolism Program, Shared Health, Winnipeg, MB, Canada
- Department of Pediatrics, Division of Genetics and Metabolism, Saskatchewan Health Authority, Saskatoon, SK, Canada
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4
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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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5
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Guo W, Comai L, Henry IM. Chromoanagenesis in plants: triggers, mechanisms, and potential impact. Trends Genet 2023; 39:34-45. [PMID: 36055901 DOI: 10.1016/j.tig.2022.08.003] [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: 05/11/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022]
Abstract
Chromoanagenesis is a single catastrophic event that involves, in most cases, localized chromosomal shattering and reorganization, resulting in a dramatically restructured chromosome. First discovered in cancer cells, it has since been observed in various other systems, including plants. In this review, we discuss the origin, characteristics, and potential mechanisms underlying chromoanagenesis in plants. We report that multiple processes, including mutagenesis and genetic engineering, can trigger chromoanagenesis via a variety of mechanisms such as micronucleation, breakage-fusion-bridge (BFB) cycles, or chain-like translocations. The resulting rearranged chromosomes can be preserved during subsequent plant growth, and sometimes inherited to the next generation. Because of their high tolerance to genome restructuring, plants offer a unique system for investigating the evolutionary consequences and potential practical applications of chromoanagenesis.
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Affiliation(s)
- Weier Guo
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Luca Comai
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Isabelle M Henry
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA.
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6
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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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7
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Cao Y, Luk HM, Zhang Y, Chau MHK, Xue S, Cheng SSW, Li AM, Chong JSC, Leung TY, Dong Z, Choy KW, Lo IFM. Investigation of Chromosomal Structural Abnormalities in Patients With Undiagnosed Neurodevelopmental Disorders. Front Genet 2022; 13:803088. [PMID: 35495136 PMCID: PMC9046776 DOI: 10.3389/fgene.2022.803088] [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: 10/27/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Structural variations (SVs) are various types of the genomic rearrangements encompassing at least 50 nucleotides. These include unbalanced gains or losses of DNA segments (copy number changes, CNVs), balanced rearrangements (such as inversion or translocations), and complex combinations of several distinct rearrangements. SVs are known to play a significant role in contributing to human genomic disorders by disrupting the protein-coding genes or the interaction(s) with cis-regulatory elements. Recently, different types of genome sequencing-based tests have been introduced in detecting various types of SVs other than CNVs and regions with absence of heterozygosity (AOH) with clinical significance.Method: In this study, we applied the mate-pair low pass (∼4X) genome sequencing with large DNA-insert (∼5 kb) in a cohort of 100 patients with neurodevelopmental disorders who did not receive informative results from a routine CNV investigation. Read-depth-based CNV analysis and chimeric-read-pairs analysis were used for CNV and SV analyses. The region of AOH was indicated by a simultaneous decrease in the rate of heterozygous SNVs and increase in the rate of homozygous SNVs.Results: First, we reexamined the 25 previously reported CNVs among 24 cases in this cohort. The boundaries of these twenty-five CNVs including 15 duplications and 10 deletions detected were consistent with the ones indicated by the chimeric-read-pairs analysis, while the location and orientation were determined in 80% of duplications (12/15). Particularly, one duplication was involved in complex rearrangements. In addition, among all the 100 cases, 10% of them were detected with rare or complex SVs (>10 Kb), and 3% were with multiple AOH (≥5 Mb) locating in imprinting chromosomes identified. In particular, one patient with an overall value of 214.5 Mb of AOH identified on 13 autosomal chromosomes suspected parental consanguinity.Conclusion: In this study, mate-pair low-pass GS resolved a significant proportion of CNVs with inconclusive significance, and detected additional SVs and regions of AOH in patients with undiagnostic neurodevelopmental disorders. This approach complements the first-tier CNV analysis for NDDs, not only by increasing the resolution of CNV detection but also by enhancing the characterization of SVs and the discovery of potential causative regions (or genes) contributory to could be complex in composition NDDs.
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Affiliation(s)
- Ye Cao
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ho Ming Luk
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | - Yanyan Zhang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shuwen Xue
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | | | - Albert Martin Li
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Josephine S. C. Chong
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- *Correspondence: Kwong Wai Choy, ; Ivan Fai Man Lo,
| | - Ivan Fai Man Lo
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
- *Correspondence: Kwong Wai Choy, ; Ivan Fai Man Lo,
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8
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Gauthier BR, Comaills V. Nuclear Envelope Integrity in Health and Disease: Consequences on Genome Instability and Inflammation. Int J Mol Sci 2021; 22:ijms22147281. [PMID: 34298904 PMCID: PMC8307504 DOI: 10.3390/ijms22147281] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 12/11/2022] Open
Abstract
The dynamic nature of the nuclear envelope (NE) is often underestimated. The NE protects, regulates, and organizes the eukaryote genome and adapts to epigenetic changes and to its environment. The NE morphology is characterized by a wide range of diversity and abnormality such as invagination and blebbing, and it is a diagnostic factor for pathologies such as cancer. Recently, the micronuclei, a small nucleus that contains a full chromosome or a fragment thereof, has gained much attention. The NE of micronuclei is prone to collapse, leading to DNA release into the cytoplasm with consequences ranging from the activation of the cGAS/STING pathway, an innate immune response, to the creation of chromosomal instability. The discovery of those mechanisms has revolutionized the understanding of some inflammation-related diseases and the origin of complex chromosomal rearrangements, as observed during the initiation of tumorigenesis. Herein, we will highlight the complexity of the NE biology and discuss the clinical symptoms observed in NE-related diseases. The interplay between innate immunity, genomic instability, and nuclear envelope leakage could be a major focus in future years to explain a wide range of diseases and could lead to new classes of therapeutics.
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Affiliation(s)
- Benoit R. Gauthier
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, 41092 Seville, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), 28029 Madrid, Spain
- Correspondence: (B.R.G.); (V.C.)
| | - Valentine Comaills
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, 41092 Seville, Spain
- Correspondence: (B.R.G.); (V.C.)
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9
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Villela D, Mazzonetto PC, Migliavacca MP, Perrone E, Guida G, Milanezi MFG, Jorge AAL, Ribeiro-Bicudo LA, Kok F, Campagnari F, de Rosso-Giuliani L, da Costa SS, Vianna-Morgante AM, Pearson PL, Krepischi ACV, Rosenberg C. Congenital chromoanagenesis in the routine postnatal chromosomal microarray analyses. Am J Med Genet A 2021; 185:2335-2344. [PMID: 33988290 DOI: 10.1002/ajmg.a.62237] [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: 09/28/2020] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 11/07/2022]
Abstract
Chromosomal microarray analyses (CMA) have greatly increased both the yield and diagnostic accuracy of postnatal analysis; it has been used as a first-tier cytogenetic test in patients with intellectual disability, autism spectrum disorder, and multiple congenital abnormalities. During the last 15 years, we performed CMA in approximately 8,000 patients with neurodevelopmental and/or congenital disorders, of which 13 (0.16%) genetically catastrophic complex chromosomal rearrangements were identified. These ultrarare rearrangements showed clustering of breakpoints, characteristic of chromoanagenesis events. Al1 13 complex events display underlying formation mechanisms, originating either by a synchronization of the shattering of clustered chromosome regions in which regional asynchrony of DNA replication may be one of the main causes of disruption. We provide an overview of the copy number profiling in these patients. Although several previous studies have suggested that chromoanagenesis is often a genetic disease source in postnatal diagnostic screening, due to either the challenge of clinical interpretation of these complex rearrangements or the limitation of microarray resolution relative to the small size and complexity of chromogenic induced chromosome abnormalities, bringing further attention and to study its occurrence in the clinical setting is extremely important.
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Affiliation(s)
- Darine Villela
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,GeneOne, DASA, Brazil
| | | | | | - Eduardo Perrone
- GeneOne, DASA, Brazil.,Department of Clinical Genetics, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | | | | | - Alexander A L Jorge
- Genetic Endocrinology Unit, Laboratory of Cellular and Molecular Endocrinology LIM25, Division of Endocrinology and Metabology, Clinical Hospital of University of São Paulo Medical School (FMUSP), São Paulo, Brazil
| | | | | | | | - Liane de Rosso-Giuliani
- University Hospital Maria Aparecida Pedrossian, Federal University of Mato Grosso Do Sul (HUMAP-UFMS), Campo Grande, Brazil
| | - Silvia Souza da Costa
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Angela M Vianna-Morgante
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Peter L Pearson
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,GeneOne, DASA, Brazil
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10
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Shapiro JA. What can evolutionary biology learn from cancer biology? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 165:19-28. [PMID: 33930405 DOI: 10.1016/j.pbiomolbio.2021.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/15/2022]
Abstract
Detecting and treating cancer effectively involves understanding the disease as one of somatic cell and tumor macroevolution. That understanding is key to avoid triggering an adverse reaction to therapy that generates an untreatable and deadly tumor population. Macroevolution differs from microevolution by karyotype changes rather than isolated localized mutations being the major source of hereditary variation. Cancer cells display major multi-site chromosome rearrangements that appear to have arisen in many different cases abruptly in the history of tumor evolution. These genome restructuring events help explain the punctuated macroevolutionary changes that mark major transitions in cancer progression. At least two different nonrandom patterns of rapid multisite genome restructuring - chromothripsis ("chromosome shattering") and chromoplexy ("chromosome weaving") - are clearly distinct in their distribution within the genome and in the cell biology of the stress-induced processes responsible for their occurrence. These observations tell us that eukaryotic cells have the capacity to reorganize their genomes rapidly in response to calamity. Since chromothripsis and chromoplexy have been identified in the human germline and in other eukaryotes, they provide a model for organismal macroevolution in response to the kinds of stresses that lead to mass extinctions.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, United States.
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11
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Pellestor F, Gaillard JB, Schneider A, Puechberty J, Gatinois V. Chromoanagenesis, the mechanisms of a genomic chaos. Semin Cell Dev Biol 2021; 123:90-99. [PMID: 33608210 DOI: 10.1016/j.semcdb.2021.01.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023]
Abstract
Designated under the name of chromoanagenesis, the phenomena of chromothripsis, chromanasynthesis and chromoplexy constitute new types of complex rearrangements, including many genomic alterations localized on a few chromosomal regions, and whose discovery over the last decade has changed our perception about the formation of chromosomal abnormalities and their etiology. Although exhibiting specific features, these new catastrophic mechanisms generally occur within a single cell cycle and their emergence is closely linked to genomic instability. Various non-exclusive exogenous or cellular mechanisms capable of generating chromoanagenesis have been evoked. However, recent experimental data shed light on 2 major processes, which following a defect in the mitotic segregation of chromosomes, can generate a cascade of cellular events leading to chromoanagenesis. These mechanisms are the formation of micronuclei integrating isolated chromosomal material, and the occurrence of chromatin bridges around chromosomal material resulting from telomeric fusions. In both cases, the cellular and molecular mechanisms of fragmentation, repair and transmission of damaged chromosomal material are consistent with the features of chromoanagenesis-related complex chromosomal rearrangements. In this review, we introduce each type of chromoanagenesis, and describe the experimental models that have allowed to validate the existence of chromoanagenesis events and to better understand their cellular mechanisms of formation and transmission, as well as their impact on the stability and the plasticity of the genome.
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Affiliation(s)
- F Pellestor
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France; INSERM 1183 Unit "Genome and Stem Cell Plasticity in Development and Aging" Institute of Regenerative Medecine and Biotherapies, St Eloi Hospital, Montpellier, France.
| | - J B Gaillard
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - A Schneider
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - J Puechberty
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - V Gatinois
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France; INSERM 1183 Unit "Genome and Stem Cell Plasticity in Development and Aging" Institute of Regenerative Medecine and Biotherapies, St Eloi Hospital, Montpellier, France
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12
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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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13
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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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14
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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: 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: 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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15
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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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16
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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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17
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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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18
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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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19
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Pellestor F, Gatinois V. Chromoanagenesis: a piece of the macroevolution scenario. Mol Cytogenet 2020; 13:3. [PMID: 32010222 PMCID: PMC6988253 DOI: 10.1186/s13039-020-0470-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/05/2020] [Indexed: 01/04/2023] Open
Abstract
Over the last decade, new types of massive and complex chromosomal rearrangements based on the chaotic shattering and restructuring of chromosomes have been identified in cancer cells as well as in patients with congenital diseases and healthy individuals. These unanticipated phenomena are named chromothripsis, chromoanasynthesis and chromoplexy, and are grouped under the term of chromoanagenesis. As mechanisms for rapid and profound genome modifications in germlines and early development, these processes can be regarded as credible pathways for genomic evolution and speciation process. Their discovery confirms the importance of genome-centric investigations to fully understand organismal evolution. Because they oppose the model of progressive acquisition of driver mutations or rearrangements, these phenomena conceptually give support to the concept of macroevolution, known through the models of “Hopeful Monsters” and the “Punctuated Equilibrium”. In this review, we summarize mechanisms underlying chromoanagenesis processes and we show that numerous cases of chromosomal speciation and short-term adaptation could be correlated to chromoanagenesis-related mechanisms. In the frame of a modern and integrative analysis of eukaryote evolutionary processes, it seems important to consider the unexpected chromoanagenesis phenomena.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
| | - Vincent Gatinois
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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20
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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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21
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Pellestor F, Gatinois V. Chromoanasynthesis: another way for the formation of complex chromosomal abnormalities in human reproduction. Hum Reprod 2019; 33:1381-1387. [PMID: 30325427 DOI: 10.1093/humrep/dey231] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Indexed: 12/24/2022] Open
Abstract
Chromoanasynthesis has been described as a novel cause of massive constitutional chromosomal rearrangements. Based on DNA replication machinery defects, chromoanasynthesis is characterized by the presence of chromosomal duplications and triplications locally clustered on one single chromosome, or a few chromosomes, associated with various other types of structural rearrangements. Two distinct mechanisms have been described for the formation of these chaotic genomic disorders, i.e. the fork stalling and template switching and the microhomology-mediated break-induced replication. Micronucleus-based processes have been evidenced as a causative mechanism, thus, highlighting the close connection between segregation errors and structural rearrangements. Accumulating data indicate that chromoanasynthesis is operating in human germline cells and during early embryonic development. The development of new tools for quantifying chromoanasynthesis events should provide further insight into the impact of this catastrophic cellular phenomenon in human reproduction.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, Montpellier, France
| | - Vincent Gatinois
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, Montpellier, France
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22
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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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23
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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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Potential Role of Chromothripsis in the Genesis of Complex Chromosomal Rearrangements in Human Gametes and Preimplantation Embryo. Methods Mol Biol 2019; 1769:35-41. [PMID: 29564816 DOI: 10.1007/978-1-4939-7780-2_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
The discovery of a new class of massive chromosomal rearrangement, baptized chromothripsis, in different cancers and congenital disorders has deeply modified our understanding on the genesis of complex genomic rearrangements. Several mechanisms, involving abortive apoptosis, telomere erosion, mitotic errors, micronuclei formation, and p53 inactivation, might cause chromothripsis. The remarkable point is that all these plausible mechanisms have been identified in the field of human reproduction as causal factors for reproductive failures and chromosomal abnormality genesis. Specific features of gametogenesis and early embryonic development may contribute to the emergence of chromothripsis. Multiple lines of evidence support the assumption that chromothripsis may arise more frequently than previously thought in both gametogenesis and early human embryogenesis.
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Pellestor F. Chromoanagenesis: cataclysms behind complex chromosomal rearrangements. Mol Cytogenet 2019; 12:6. [PMID: 30805029 PMCID: PMC6371609 DOI: 10.1186/s13039-019-0415-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background During the last decade, genome sequencing projects in cancer genomes as well as in patients with congenital diseases and healthy individuals have led to the identification of new types of massive chromosomal rearrangements arising during single chaotic cellular events. These unanticipated catastrophic phenomenon are termed chromothripsis, chromoanasynthesis and chromoplexis., and are grouped under the name of “chromoanagenesis”. Results For each process, several specific features have been described, allowing each phenomenon to be distinguished from each other and to understand its mechanism of formation and to better understand its aetiology. Thus, chromothripsis derives from chromosome shattering followed by the random restitching of chromosomal fragments with low copy-number change whereas chromoanasynthesis results from erroneous DNA replication of a chromosome through serial fork stalling and template switching with variable copy-number gains, and chromoplexy refers to the occurrence of multiple inter-and intra-chromosomal translocations and deletions with little or no copy-number alterations in prostate cancer. Cumulating data and experimental models have shown that chromothripsis and chromoanasynthesis may essentially result from lagging chromosome encapsulated in micronuclei or telomere attrition and end-to-end telomere fusion. Conclusion The concept of chromanagenesis has provided new insight into the aetiology of complex structural rearrangements, the connection between defective cell cycle progression and genomic instability, and the complexity of cancer evolution. Increasing reported chromoanagenesis events suggest that these chaotic mechanisms are probably much more frequent than anticipated.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371, avenue du Doyen Gaston Giraud, 34295 Montpellier cedex 5, France.,INSERM 1183 Unit «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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26
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Kurtas NE, Xumerle L, Giussani U, Pansa A, Cardarelli L, Bertini V, Valetto A, Liehr T, Clara Bonaglia M, Errichiello E, Delledonne M, Zuffardi O. Insertional translocation involving an additional nonchromothriptic chromosome in constitutional chromothripsis: Rule or exception? Mol Genet Genomic Med 2018; 7:e00496. [PMID: 30565424 PMCID: PMC6393660 DOI: 10.1002/mgg3.496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/06/2018] [Accepted: 10/02/2018] [Indexed: 01/17/2023] Open
Abstract
Background Chromothripsis, which is the local massive shattering of one or more chromosomes and their reassembly in a disordered array with frequent loss of some fragments, has been mainly reported in association with abnormal phenotypes. We report three unrelated healthy persons, two of which parenting a child with some degree of intellectual disability, carrying a chromothripsis involving respectively one, two, and three chromosomes, which was detected only after whole‐genome sequencing. Unexpectedly, in all three cases a fragment from one of the chromothripsed chromosomes resulted to be inserted within a nonchromothripsed one. Methods Conventional cytogenetic techniques, paired‐end whole‐genome sequencing, polymerase chain reaction, and Sanger sequencing were used to characterize complex rearrangements, copy‐number variations, and breakpoint sequences in all three families. Results In two families, one parent was carrier of a balanced chromothripsis causing in the index case a deletion and a noncontiguous duplication at 3q in case 1, and a t(6;14) translocation associated with interstitial 14q deletion in case 2. In the third family, an unbalanced chromothripsis involving chromosomes 6, 7, and 15 was inherited to the proband by the mosaic parent. In all three parents, the chromothripsis was concurrent with an insertional translocation of a portion of one of the chromothriptic chromosomes within a further chromosome that was not involved in the chromothripsis event. Conclusion Our findings show that (a) both simple and complex unbalanced rearrangements may result by the recombination of a cryptic parental balanced chromothripsis and that (b) insertional translocations are the spy of more complex rearrangements and not simply a three‐breakpoint event.
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Affiliation(s)
| | - Luciano Xumerle
- Personal Genomics srl, Department of Biotechnologies, University of Verona, Verona, Italy
| | | | | | | | | | | | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Lecco, Italy
| | | | - Massimo Delledonne
- Personal Genomics srl, Department of Biotechnologies, University of Verona, Verona, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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Nazaryan-Petersen L, Eisfeldt J, Pettersson M, Lundin J, Nilsson D, Wincent J, Lieden A, Lovmar L, Ottosson J, Gacic J, Mäkitie O, Nordgren A, Vezzi F, Wirta V, Käller M, Hjortshøj TD, Jespersgaard C, Houssari R, Pignata L, Bak M, Tommerup N, Lundberg ES, Tümer Z, Lindstrand A. Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization. PLoS Genet 2018; 14:e1007780. [PMID: 30419018 PMCID: PMC6258378 DOI: 10.1371/journal.pgen.1007780] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/26/2018] [Accepted: 10/23/2018] [Indexed: 01/25/2023] Open
Abstract
Clustered copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) are often reported as germline chromothripsis. However, such cases might need further investigations by massive parallel whole genome sequencing (WGS) in order to accurately define the underlying complex rearrangement, predict the occurrence mechanisms and identify additional complexities. Here, we utilized WGS to delineate the rearrangement structure of 21 clustered CNV carriers first investigated by CMA and identified a total of 83 breakpoint junctions (BPJs). The rearrangements were further sub-classified depending on the patterns observed: I) Cases with only deletions (n = 8) often had additional structural rearrangements, such as insertions and inversions typical to chromothripsis; II) cases with only duplications (n = 7) or III) combinations of deletions and duplications (n = 6) demonstrated mostly interspersed duplications and BPJs enriched with microhomology. In two cases the rearrangement mutational signatures indicated both a breakage-fusion-bridge cycle process and haltered formation of a ring chromosome. Finally, we observed two cases with Alu- and LINE-mediated rearrangements as well as two unrelated individuals with seemingly identical clustered CNVs on 2p25.3, possibly a rare European founder rearrangement. In conclusion, through detailed characterization of the derivative chromosomes we show that multiple mechanisms are likely involved in the formation of clustered CNVs and add further evidence for chromoanagenesis mechanisms in both “simple” and highly complex chromosomal rearrangements. Finally, WGS characterization adds positional information, important for a correct clinical interpretation and deciphering mechanisms involved in the formation of these rearrangements. Clustered copy number variants (CNVs) as detected by chromosomal microarray are often reported as germline chromoanagenesis. However, such cases might need further investigation by whole genome sequencing (WGS) to accurately resolve the complexity of the structural rearrangement and predict underlying mutational mechanisms. Here, we used WGS to characterize 83 breakpoint-junctions (BPJs) from 21 clustered CNVs, and outlined the rearrangement connectivity pictures. Cases with only deletions often had additional structural rearrangements, such as insertions and inversions, which could be a result of multiple double-strand DNA breaks followed by non-homologous repair, typical to chromothripsis. In contrast, cases with only duplications or combinations of deletions and duplications, demonstrated mostly interspersed duplications and BPJs enriched with microhomology, consistent with serial template switching during DNA replication (chromoanasynthesis). Only two rearrangements were repeat mediated. In aggregate, our results suggest that multiple CNVs clustered on a single chromosome may arise through either chromothripsis or chromoanasynthesis.
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Affiliation(s)
- Lusine Nazaryan-Petersen
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Johanna Lundin
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Agne Lieden
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Lovisa Lovmar
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jesper Ottosson
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jelena Gacic
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Francesco Vezzi
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Valtteri Wirta
- SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Max Käller
- SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Tina Duelund Hjortshøj
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Cathrine Jespersgaard
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Rayan Houssari
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Laura Pignata
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Mads Bak
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Syk Lundberg
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- * E-mail: (AL); (ZT)
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- * E-mail: (AL); (ZT)
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Pettersson M, Eisfeldt J, Syk Lundberg E, Lundin J, Lindstrand A. Flanking complex copy number variants in the same family formed through unequal crossing-over during meiosis. Mutat Res 2018; 812:1-4. [PMID: 30384002 DOI: 10.1016/j.mrfmmm.2018.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/08/2018] [Indexed: 05/22/2023]
Abstract
Two phenomena that have been described in germline complex genomic rearrangements (CGRs) formation are chromothripsis and chromoanasynthesis, characterized by distinct features such as the orientation and copy number of the involved fragments. Herein we present different CGRs on chromosome 5p in a mother and her daughter that through unequal crossing-over during meiosis has evolved from a chromothriptic rearrangement in the mother into another complex rearrangement in her daughter involving both deletions and duplications. Initially, both rearrangements were classified as simple copy number variants, but follow-up studies using whole-genome sequencing revealed a much more complex nature of both rearrangements and enabled us to decipher the biological process involved in the formation of the rearrangement found in the daughter. In conclusion, these two cases highlight the need of analyzing the inheritance patterns of CGRs, and provide an example of a disease-causing CGR formed through multiple genetic events.
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Affiliation(s)
- Maria Pettersson
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm and Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Elisabeth Syk Lundberg
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm and Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Lundin
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm and Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm and Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
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29
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Sabatini PJB, Ejaz R, Stavropoulos DJ, Mendoza-Londono R, Joseph-George AM. Stable transmission of an unbalanced chromosome 21 derived from chromoanasynthesis in a patient with a SYNGAP1 likely pathogenic variant. Mol Cytogenet 2018; 11:50. [PMID: 30181777 PMCID: PMC6114485 DOI: 10.1186/s13039-018-0394-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/06/2018] [Indexed: 11/30/2022] Open
Abstract
Background Complex genomic structural variations, involving chromoanagenesis, have been implicated in multiple congenital anomalies and abnormal neurodevelopment. Familial inheritance of complex chromosomal structural alteration resulting from germline chromoanagenesis-type mechanisms are limited. Case presentation We report a two-year eleven-month old male presenting with epilepsy, ataxia and dysmorphic features of unknown etiology. Chromosomal microarray identified a complex unbalanced rearrangement involving chromosome 21. G-banding and FISH for targeted regions of chromosome 21 revealed that the copy number imbalances were limited to gains dispersed throughout the long arm of chromosome 21, characteristic of a chromosome derived from chromoanagenesis. Family studies showed that the unbalanced chromosome had been stably inherited, as it was present in both his healthy mother and maternal grandfather. Further molecular testing for non-syndromic intellectual disability genes found a likely pathogenic mutation in SYNGAP1 (NM_006772.2:c.3722_3723del). Conclusions This study indicates that complex rearrangements involving an unbalanced chromosome derived from chromoanasynthesis can be familial and should be not be presumed pathogenic.
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Affiliation(s)
- Peter J B Sabatini
- 1Laboratory Medicine Program, Department of Pathology, University Health Network, 200 Elizabeth St, Toronto, ON M5G 2C4 Canada.,2Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Resham Ejaz
- 3Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Dimitri J Stavropoulos
- 2Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada.,4Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Roberto Mendoza-Londono
- 3Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Ann M Joseph-George
- 2Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada.,4Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
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30
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Pellestor F, Gatinois V. Chromothripsis, a credible chromosomal mechanism in evolutionary process. Chromosoma 2018; 128:1-6. [DOI: 10.1007/s00412-018-0679-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 01/17/2023]
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Chromothripsis in acute myeloid leukemia: biological features and impact on survival. Leukemia 2018; 32:1609-1620. [PMID: 29472722 PMCID: PMC6035145 DOI: 10.1038/s41375-018-0035-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/31/2017] [Accepted: 11/21/2017] [Indexed: 12/12/2022]
Abstract
Chromothripsis is a one-step genome-shattering catastrophe resulting from disruption of one or few chromosomes in multiple fragments and consequent random rejoining and repair. This study defines incidence of chromothripsis in 395 newly diagnosed adult acute myeloid leukemia (AML) patients from three institutions, its impact on survival and its genomic background. SNP 6.0 or CytoscanHD Array (Affymetrix®) were performed on all samples. We detected chromothripsis with a custom algorithm in 26/395 patients. Patients harboring chromothripsis had higher age (p = 0.002), ELN high risk (HR) (p < 0.001), lower white blood cell (WBC) count (p = 0.040), TP53 loss, and/or mutations (p < 0.001) while FLT3 (p = 0.025), and NPM1 (p = 0.032) mutations were mutually exclusive with chromothripsis. Chromothripsis-positive patients showed a worse overall survival (OS) (p < 0.001) compared with HR patients (p = 0.011) and a poor prognosis in a COX-HR optimal regression model. Chromothripsis presented the hallmarks of chromosome instability [i.e., TP53 alteration, 5q deletion, higher mean of copy number alteration (CNA), complex karyotype, alterations in DNA repair, and cell cycle] and focal deletions on chromosomes 4, 7, 12, 16, and 17. CBA. FISH showed that chromothripsis is associated with marker, derivative, and ring chromosomes. In conclusion, chromothripsis frequently occurs in AML (6.6%) and influences patient prognosis and disease biology.
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32
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Slamova Z, Nazaryan-Petersen L, Mehrjouy MM, Drabova J, Hancarova M, Marikova T, Novotna D, Vlckova M, Vlckova Z, Bak M, Zemanova Z, Tommerup N, Sedlacek Z. Very short DNA segments can be detected and handled by the repair machinery during germline chromothriptic chromosome reassembly. Hum Mutat 2018; 39:709-716. [DOI: 10.1002/humu.23408] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Zuzana Slamova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Lusine Nazaryan-Petersen
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Mana M. Mehrjouy
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Jana Drabova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Tatana Marikova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Drahuse Novotna
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Marketa Vlckova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | | | - Mads Bak
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Zuzana Zemanova
- Institute of Medical Biochemistry and Laboratory Diagnostics; General University Hospital and Charles University 1st Faculty of Medicine; Prague Czech Republic
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Zdenek Sedlacek
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
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Abstract
The highly complex structural genome variations chromothripsis, chromoanasynthesis, and chromoplexy are subsumed under the term chromoanagenesis, which means chromosome rebirth. Precipitated by numerous DNA double-strand breaks, they differ in number of and distances between breakpoints, associated copy number variations, order and orientation of segments, and flanking sequences at joining points. Results from patients with the autosomal dominant cancer susceptibility disorder Li-Fraumeni syndrome implicated somatic TP53 mutations in chromothripsis. TP53 participates in the G2/M phase checkpoint, halting cell cycling after premature chromosome compaction during the second half of the S phase, thus preventing chromosome shattering. By experimental TP53 ablation and micronucleus induction, one or a few isolated chromosomes underwent desynchronized replication and chromothripsis. Secondly, chromothripsis occurred after experimental induction of telomere crisis after which dicentric chromosomes sustained TREX1-mediated resolution of chromosome bridges and kataegis. Third, DNA polymerase Polθ-dependent chromothripsis has been documented. Finally, a family with chromothripsis after L1 element-dependent retrotransposition and Alu/Alu homologous recombination has been reported. Human chromosomal instability syndromes share defects in responses to DNA double-strand breaks, characteristic cell cycle perturbations, elevated rates of micronucleus formation, premature chromosome compaction, and apoptosis. They are also associated with elevated susceptibility to malignant disease, such as medulloblastomas and gliomas in ataxia-telangiectasia, leukemia and lymphoma in Bloom syndrome, and osteosarcoma and soft tissue sarcoma in Werner syndrome. The latter syndrome is characterized by a premature aging-like progressive decline of mesenchymal tissues. In all thus far studied cases, constitutional chromothripsis occurred in the male germline and male patients with defects in the double-strand break response genes ATM, MRE11, BLM, LIG4, WRN, and Ku70 show impaired fertility. Conceivably, chromothripsis may, in a stochastic rather than deterministic way, be implicated in germline structural variation, malignant disease, premature aging, genome mosaicism in somatic tissues, and male infertility.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany.
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34
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Marcozzi A, Pellestor F, Kloosterman WP. The Genomic Characteristics and Origin of Chromothripsis. Methods Mol Biol 2018; 1769:3-19. [PMID: 29564814 DOI: 10.1007/978-1-4939-7780-2_1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In 2011 a phenomenon involving complex chromosomal rearrangements was discovered in cancer genomes. This phenomenon has been termed chromothripsis, on the basis of its chromosomal hallmarks, which point to an underlying process involving chromosome (chromo) shattering (thripsis). The prevailing hypothesis of cancer genome evolution as a gradual process of mutation and selection was challenged by the discovery of chromothripsis, because its patterns of chromosome rearrangement rather indicated an one-off catastrophic burst of genome rearrangement. The initial discovery of chromothripsis has led to many more examples of chromothripsis both in cancer genomes as well as in patients with congenital diseases and in the genomes of healthy individuals. Since then, a burning topic has been the study of the molecular mechanism that leads to chromothripsis. Cumulating evidence has shown that chromothripsis may result from lagging chromosomes encapsulated in micronuclei, as well as from telomere fusions followed by chromosome bridge formation. In this chapter, we will outline the genomic characteristics of chromothripsis, and we present genomic methodologies that enable the detection of chromothripsis. Furthermore, we will give an overview of recent insights into the mechanisms underlying chromothripsis.
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Affiliation(s)
- Alessio Marcozzi
- Division of Biomedical Genetics, Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Franck Pellestor
- Laboratory of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, Montpellier, France.,INSERM Unit Plasticity of the Genome and Aging, Institute of Functional Genomics, Montpellier, France
| | - Wigard P Kloosterman
- Division of Biomedical Genetics, Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.
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35
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Abstract
Chromothripsis is a mutational event driven by tens to hundreds of double-stranded DNA breaks which occur in a single event between a limited number of chromosomes. Following chromosomal shattering, DNA fragments are stitched together in a seemingly random manner resulting in complex genomic rearrangements including sequence shuffling, deletions, and inversions of varying size. This genomic catastrophe has been observed in cancer genomes and the genomes of patients harboring developmental and congenital defects. The mechanisms catalyzing DNA breakage and coordinating the "random" assembly of genomic fragments are actively being investigated. Recently, retrotransposons-a type of "jumping gene"-have been implicated as one means to generate double-stranded DNA breaks during chromothripsis and as sequences which can contribute to the final configuration of the derived chromosomes. In this methods chapter, I discuss how to apply available bioinformatic tools and the hallmarks of retrotransposon mobilization to breakpoint junctions to assess the role for active and inactive retrotransposon sequences in chromothriptic events.
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Abstract
The recent discovery of a new class of massive chromosomal rearrangements, occurring during one unique cellular event and baptized "chromothripsis," deeply modifies our perception on the genesis of complex genomic rearrangements, but also it raises the question of the potential driving role of chromothripsis in species evolution. The occurrence of chromothripsis appears to be in good agreement with macroevolution models proposed as a complement to phyletic gradualism. The emergence of this unexpected phenomenon may help to demonstrate the contribution of chromosome rearrangements to speciation process.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, Montpellier, France. .,INSERM U1183 Unit "Genome and Stem Cell Plasticity in Development and Ageing", Institute for Regenerative Medicine and Biotherapy, St Eloi Hospital, Montpellier, France.
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Fontana MC, Marconi G, Milosevic Feenstra JD, Fonzi E, Papayannidis C, Ghelli Luserna di Rorá A, Padella A, Solli V, Franchini E, Ottaviani E, Ferrari A, Baldazzi C, Testoni N, Iacobucci I, Soverini S, Haferlach T, Guadagnuolo V, Semerad L, Doubek M, Steurer M, Racil Z, Paolini S, Manfrini M, Cavo M, Simonetti G, Kralovics R, Martinelli G. Chromothripsis in Acute Myeloid Leukemia: biological features and
impact on survival. Leukemia 2017:10.1038/leu.2017.351. [PMCID: PMC5892717 DOI: 10.1038/leu.2017.351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
Chromothripsis is a one-step genome-shattering catastrophe resulting from
disruption of one or few chromosomes in multiple fragments and consequent random
rejoining and repair. This study define incidence of chromothripsis in 395
newly-diagnosed adult acute myeloid leukemia (AML) patients from three
institutions, its impact on survival and its genomic background. SNP 6.0 or
CytoscanHD Array (Affymetrix®) were performed on all samples. We detected
chromothripsis with a custom algorithm in 26/395 patients. Patients harboring
chromothripsis had higher age (p=.002), ELN high risk (HR) (p<.001),
lower white blood cell (WBC) count (p=.040), TP53 loss and/or
mutations (p<.001) while FLT3 (p=.025) and
NPM1 (p=.032) mutations were mutually exclusive with
chromothripsis. Chromothripsis-positive patients showed a worse overall survival
(OS) (p<.001) compared with HR patients (p=.011) and a poor prognosis in
a COX-HR optimal regression model. Chromothripsis presented the hallmarks of
chromosome instability [i.e. TP53 alteration, 5q deletion,
higher mean of copy number alteration (CNA), complex karyotype, alterations in
DNA repair and cell cycle] and focal deletions on chromosomes 4, 7, 12, 16, 17.
CBA. FISH showed that chromothripsis is associated with marker, derivative and
ring chromosomes. In conclusion, chromothripsis frequently occurs in AML (6.6%)
and influences patient prognosis and disease biology.
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Affiliation(s)
| | - Giovanni Marconi
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | | | - Eugenio Fonzi
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | | | | | - Antonella Padella
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Vincenza Solli
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Eugenia Franchini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Emanuela Ottaviani
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Anna Ferrari
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Carmen Baldazzi
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Nicoletta Testoni
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Ilaria Iacobucci
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Simona Soverini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | | | | | - Lukas Semerad
- Department of Internal Medicine - Hematology and Oncology, Masaryk
University and Hospital, Brno, CR
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, Masaryk
University and Hospital, Brno, CR
| | - Michael Steurer
- Division of Hematology and Oncology, Medical University of
Innsbruck, Innsbruck, Austria
| | - Zdenek Racil
- Department of Internal Medicine - Hematology and Oncology, Masaryk
University and Hospital, Brno, CR
| | - Stefania Paolini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Marco Manfrini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Michele Cavo
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Giorgia Simonetti
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy
of Sciences, Wien, Austria
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38
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Chan SH, Ngeow J. Germline mutation contribution to chromosomal instability. Endocr Relat Cancer 2017; 24:T33-T46. [PMID: 28808044 DOI: 10.1530/erc-17-0062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/18/2017] [Indexed: 12/29/2022]
Abstract
Genomic instability is a feature of cancer that fuels oncogenesis through increased frequency of genetic disruption, leading to loss of genomic integrity and promoting clonal evolution as well as tumor transformation. A form of genomic instability prevalent across cancer types is chromosomal instability, which involves karyotypic changes including chromosome copy number alterations as well as gross structural abnormalities such as transversions and translocations. Defects in cellular mechanisms that are in place to govern fidelity of chromosomal segregation, DNA repair and ultimately genomic integrity are known to contribute to chromosomal instability. In this review, we discuss the association of germline mutations in these pathways with chromosomal instability in the background of related cancer predisposition syndromes. We will also reflect on the impact of genetic predisposition to clinical management of patients and how we can exploit this vulnerability to promote catastrophic genomic instability as a therapeutic strategy.
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Affiliation(s)
- Sock Hoai Chan
- Division of Medical OncologyCancer Genetics Service, National Cancer Centre Singapore, Singapore
| | - Joanne Ngeow
- Division of Medical OncologyCancer Genetics Service, National Cancer Centre Singapore, Singapore
- Oncology Academic Clinical ProgramDuke-NUS Medical School Singapore, Singapore
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39
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Collins RL, Brand H, Redin CE, Hanscom C, Antolik C, Stone MR, Glessner JT, Mason T, Pregno G, Dorrani N, Mandrile G, Giachino D, Perrin D, Walsh C, Cipicchio M, Costello M, Stortchevoi A, An JY, Currall BB, Seabra CM, Ragavendran A, Margolin L, Martinez-Agosto JA, Lucente D, Levy B, Sanders SJ, Wapner RJ, Quintero-Rivera F, Kloosterman W, Talkowski ME. Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome. Genome Biol 2017; 18:36. [PMID: 28260531 PMCID: PMC5338099 DOI: 10.1186/s13059-017-1158-6] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/20/2017] [Indexed: 12/13/2022] Open
Abstract
Background Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies. Results We sequenced 689 participants with autism spectrum disorder (ASD) and other developmental abnormalities to construct a genome-wide map of large SV. Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution. Our results encompass 11,735 distinct large SV sites, 38.1% of which are novel and 16.8% of which are balanced or complex. We characterize 16 recurrent subclasses of complex SV (cxSV), revealing that: (1) cxSV are larger and rarer than canonical SV; (2) each genome harbors 14 large cxSV on average; (3) 84.4% of large cxSVs involve inversion; and (4) most large cxSV (93.8%) have not been delineated in previous studies. Rare SVs are more likely to disrupt coding and regulatory non-coding loci, particularly when truncating constrained and disease-associated genes. We also identify multiple cases of catastrophic chromosomal rearrangements known as chromoanagenesis, including somatic chromoanasynthesis, and extreme balanced germline chromothripsis events involving up to 65 breakpoints and 60.6 Mb across four chromosomes, further defining rare categories of extreme cxSV. Conclusions These data provide a foundational map of large SV in the morbid human genome and demonstrate a previously underappreciated abundance and diversity of cxSV that should be considered in genomic studies of human disease. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1158-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryan L Collins
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, 02115, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Harrison Brand
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Claire E Redin
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Carrie Hanscom
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Caroline Antolik
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Matthew R Stone
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Joseph T Glessner
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Tamara Mason
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Giulia Pregno
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Naghmeh Dorrani
- Department of Pathology & Laboratory Medicine and UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, UCLA, Los Angeles, CA, 90095, USA
| | - Giorgia Mandrile
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Danielle Perrin
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Cole Walsh
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Michelle Cipicchio
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Maura Costello
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Alexei Stortchevoi
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Joon-Yong An
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, 94103, USA
| | - Benjamin B Currall
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Catarina M Seabra
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA.,GABBA Program, University of Porto, Porto, 4099-002, Portugal
| | - Ashok Ragavendran
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Lauren Margolin
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Julian A Martinez-Agosto
- Department of Pathology & Laboratory Medicine and UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, UCLA, Los Angeles, CA, 90095, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Brynn Levy
- Department of Pathology, Columbia University, New York, NY, 10032, USA
| | - Stephan J Sanders
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, 94103, USA
| | - Ronald J Wapner
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology & Laboratory Medicine and UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, UCLA, Los Angeles, CA, 90095, USA
| | - Wigard Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, 3584CG, The Netherlands
| | - Michael E Talkowski
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA. .,Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, 02115, USA. .,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA.
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40
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Fukami M, Shima H, Suzuki E, Ogata T, Matsubara K, Kamimaki T. Catastrophic cellular events leading to complex chromosomal rearrangements in the germline. Clin Genet 2017; 91:653-660. [PMID: 27888607 DOI: 10.1111/cge.12928] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 12/28/2022]
Abstract
Although complex chromosomal rearrangements were thought to reflect the accumulation of DNA damage over time, recent studies have shown that such rearrangements frequently arise from 'all-at-once' catastrophic cellular events. These events, designated chromothripsis, chromoanasynthesis, and chromoanagenesis, were first documented in the cancer genome and subsequently observed in the germline. These events likely result from micronucleus-mediated chromosomal shattering and subsequent random reassembly of DNA fragments, although several other mechanisms have also been proposed. Typically, only one or a few chromosomes of paternal origin are affected per event. These events can produce intrachromosomal deletions, duplications, inversions, and translocations, as well as interchromosomal translocations. Germline complex rearrangements of autosomes often result in developmental delay and dysmorphic features, whereas X chromosomal rearrangements are usually associated with relatively mild clinical manifestations. The concept of these catastrophic events provides novel insights into the etiology of human genomic disorders. This review introduces the molecular characteristics and phenotypic outcomes of catastrophic cellular events in the germline.
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Affiliation(s)
- M Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - H Shima
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - E Suzuki
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - T Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - K Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - T Kamimaki
- Department of Pediatrics, Shizuoka City Shimizu Hospital, Shizuoka, Japan
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41
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Poot M. Of Simple and Complex Genome Rearrangements, Chromothripsis, Chromoanasynthesis, and Chromosome Chaos. Mol Syndromol 2017; 8:115-117. [PMID: 28588432 DOI: 10.1159/000454964] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2016] [Indexed: 01/23/2023] Open
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42
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Mapping Breakpoints of Complex Chromosome Rearrangements Involving a Partial Trisomy 15q23.1-q26.2 Revealed by Next Generation Sequencing and Conventional Techniques. PLoS One 2016; 11:e0154574. [PMID: 27218255 PMCID: PMC4878739 DOI: 10.1371/journal.pone.0154574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/16/2016] [Indexed: 11/25/2022] Open
Abstract
Complex chromosome rearrangements (CCRs), which are rather rare in the whole population, may be associated with aberrant phenotypes. Next-generation sequencing (NGS) and conventional techniques, could be used to reveal specific CCRs for better genetic counseling. We report the CCRs of a girl and her mother, which were identified using a combination of NGS and conventional techniques including G-banding, fluorescence in situ hybridization (FISH) and PCR. The girl demonstrated CCRs involving chromosomes 3 and 8, while the CCRs of her mother involved chromosomes 3, 5, 8, 11 and 15. HumanCytoSNP-12 Chip analysis identified a 35.4 Mb duplication on chromosome 15q21.3-q26.2 in the proband and a 1.6 Mb microdeletion at chromosome 15q21.3 in her mother. The proband inherited the rearranged chromosomes 3 and 8 from her mother, and the duplicated region on chromosome 15 of the proband was inherited from the mother. Approximately one hundred genes were identified in the 15q21.3-q26.2 duplicated region of the proband. In particular, TPM1, SMAD6, SMAD3, and HCN4 may be associated with her heart defects, and HEXA, KIF7, and IDH2 are responsible for her developmental and mental retardation. In addition, we suggest that a microdeletion on the 15q21.3 region of the mother, which involved TCF2, TCF12, ADMA10 and AQP9, might be associated with mental retardation. We delineate the precise structures of the derivative chromosomes, chromosome duplication origin and possible molecular mechanisms for aberrant phenotypes by combining NGS data with conventional techniques.
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43
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Nazaryan-Petersen L, Bertelsen B, Bak M, Jønson L, Tommerup N, Hancks DC, Tümer Z. Germline Chromothripsis Driven by L1-Mediated Retrotransposition and Alu/Alu Homologous Recombination. Hum Mutat 2016; 37:385-95. [PMID: 26929209 DOI: 10.1002/humu.22953] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/03/2016] [Indexed: 12/20/2022]
Abstract
Chromothripsis (CTH) is a phenomenon where multiple localized double-stranded DNA breaks result in complex genomic rearrangements. Although the DNA-repair mechanisms involved in CTH have been described, the mechanisms driving the localized "shattering" process remain unclear. High-throughput sequence analysis of a familial germline CTH revealed an inserted SVAE retrotransposon associated with a 110-kb deletion displaying hallmarks of L1-mediated retrotransposition. Our analysis suggests that the SVAE insertion did not occur prior to or after, but concurrent with the CTH event. We also observed L1-endonuclease potential target sites in other breakpoints. In addition, we found four Alu elements flanking the 110-kb deletion and associated with an inversion. We suggest that chromatin looping mediated by homologous Alu elements may have brought distal DNA regions into close proximity facilitating DNA cleavage by catalytically active L1-endonuclease. Our data provide the first evidence that active and inactive human retrotransposons can serve as endogenous mutagens driving CTH in the germline.
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Affiliation(s)
- Lusine Nazaryan-Petersen
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, 2600, Denmark.,Department of Cellular and Molecular Medicine (ICMM), Faculty of Health Science, University of Copenhagen, Copenhagen, N. 2200, Denmark
| | - Birgitte Bertelsen
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, 2600, Denmark
| | - Mads Bak
- Department of Cellular and Molecular Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, N. 2200, Denmark
| | - Lars Jønson
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, O. 2100, Denmark
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, N. 2200, Denmark
| | - Dustin C Hancks
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, 84112
| | - Zeynep Tümer
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, 2600, Denmark
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44
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Itani OA, Flibotte S, Dumas KJ, Moerman DG, Hu PJ. Chromoanasynthetic Genomic Rearrangement Identified in a N-Ethyl-N-Nitrosourea (ENU) Mutagenesis Screen in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2015; 6:351-6. [PMID: 26628482 PMCID: PMC4751554 DOI: 10.1534/g3.115.024257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/28/2015] [Indexed: 12/18/2022]
Abstract
Chromoanasynthesis is a recently discovered phenomenon in humans with congenital diseases that is characterized by complex genomic rearrangements (CGRs) resulting from aberrant repair of catastrophic chromosomal damage. How these CGRs are induced is not known. Here, we describe the structure and function of dpDp667, a causative CGR that emerged from a Caenorhabditis elegans dauer suppressor screen in which animals were treated with the point mutagen N-ethyl-N-nitrosourea (ENU). dpDp667 comprises nearly 3 Mb of sequence on the right arm of the X chromosome, contains three duplications and one triplication, and is devoid of deletions. Sequences from three out of the four breakpoint junctions in dpDp667 reveal microhomologies that are hallmarks of chromoanasynthetic CGRs. Our findings suggest that environmental insults and physiological processes that cause point mutations may give rise to chromoanasynthetic rearrangements associated with congenital disease. The relatively subtle phenotype of animals harboring dpDp667 suggests that the prevalence of CGRs in the genomes of mutant and/or phenotypically unremarkable animals may be grossly underestimated.
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Affiliation(s)
- Omar A Itani
- Institute of Gerontology, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Stephane Flibotte
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kathleen J Dumas
- Institute of Gerontology, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Donald G Moerman
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Patrick J Hu
- Institute of Gerontology, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109
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