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Meier B, Volkova NV, Hong Y, Bertolini S, González-Huici V, Petrova T, Boulton S, Campbell PJ, Gerstung M, Gartner A. Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation. PLoS One 2021; 16:e0250291. [PMID: 33905417 PMCID: PMC8078821 DOI: 10.1371/journal.pone.0250291] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
Maintaining genome integrity is particularly important in germ cells to ensure faithful transmission of genetic information across generations. Here we systematically describe germ cell mutagenesis in wild-type and 61 DNA repair mutants cultivated over multiple generations. ~44% of the DNA repair mutants analysed showed a >2-fold increased mutagenesis with a broad spectrum of mutational outcomes. Nucleotide excision repair deficiency led to higher base substitution rates, whereas polh-1(Polη) and rev-3(Polζ) translesion synthesis polymerase mutants resulted in 50-400 bp deletions. Signatures associated with defective homologous recombination fall into two classes: 1) brc-1/BRCA1 and rad-51/RAD51 paralog mutants showed increased mutations across all mutation classes, 2) mus-81/MUS81 and slx-1/SLX1 nuclease, and him-6/BLM, helq-1/HELQ or rtel-1/RTEL1 helicase mutants primarily accumulated structural variants. Repetitive and G-quadruplex sequence-containing loci were more frequently mutated in specific DNA repair backgrounds. Tandem duplications embedded in inverted repeats were observed in helq-1 helicase mutants, and a unique pattern of 'translocations' involving homeologous sequences occurred in rip-1 recombination mutants. atm-1/ATM checkpoint mutants harboured structural variants specifically enriched in subtelomeric regions. Interestingly, locally clustered mutagenesis was only observed for combined brc-1 and cep-1/p53 deficiency. Our study provides a global view of how different DNA repair pathways contribute to prevent germ cell mutagenesis.
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Affiliation(s)
- Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | - Nadezda V. Volkova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Ye Hong
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | - Simone Bertolini
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | | | - Tsvetana Petrova
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | | | - Peter J. Campbell
- Cancer, Ageing and Somatic Mutation Program, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
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2
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Singh SM, Castellani CA, Hill KA. Postzygotic Somatic Mutations in the Human Brain Expand the Threshold-Liability Model of Schizophrenia. Front Psychiatry 2020; 11:587162. [PMID: 33192734 PMCID: PMC7642466 DOI: 10.3389/fpsyt.2020.587162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022] Open
Abstract
The search for what causes schizophrenia has been onerous. This research has included extensive assessment of a variety of genetic and environmental factors using ever emerging high-resolution technologies and traditional understanding of the biology of the brain. These efforts have identified a large number of schizophrenia-associated genes, some of which are altered by mutational and epi-mutational mechanisms in a threshold liability model of schizophrenia development. The results, however, have limited predictability and the actual cause of the disease remains unknown. This current state asks for conceptualizing the problem differently in light of novel insights into the nature of mutations, the biology of the brain and the fine precision and resolution of emerging technologies. There is mounting evidence that mutations acquired during postzygotic development are more common than germline mutations. Also, the postzygotic somatic mutations including epimutations (PZMs), which often lead to somatic mosaicism, are relatively common in the mammalian brain in comparison to most other tissues and PZMs are more common in patients with neurodevelopmental mental disorders, including schizophrenia. Further, previously inaccessible, detection of PZMs is becoming feasible with the advent of novel technologies that include single-cell genomics and epigenomics and the use of exquisite experimental designs including use of monozygotic twins discordant for the disease. These developments allow us to propose a working hypothesis and expand the threshold liability model of schizophrenia that already encompasses familial genetic, epigenetic and environmental factors to include somatic de novo PZMs. Further, we offer a test for this expanded model using currently available genome sequences and methylome data on monozygotic twins discordant for schizophrenia (MZD) and their parents. The results of this analysis argue that PZMs play a significant role in the development of schizophrenia and explain extensive heterogeneity seen across patients. It also offers the potential to convincingly link PZMs to both nervous system health and disease, an area that has remained challenging to study and relatively under explored.
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Affiliation(s)
- Shiva M. Singh
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, Canada
| | | | - Kathleen A. Hill
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, Canada
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3
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Hancks DC, Kazazian HH. Roles for retrotransposon insertions in human disease. Mob DNA 2016; 7:9. [PMID: 27158268 PMCID: PMC4859970 DOI: 10.1186/s13100-016-0065-9] [Citation(s) in RCA: 421] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022] Open
Abstract
Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a "copy-and-paste" mechanism, LINE-1 is able to retrotranspose other RNAs including Alu, SVA, and occasionally cellular RNAs. To date in humans, 124 LINE-1-mediated insertions which result in genetic diseases have been reported. Disease causing LINE-1 insertions have provided a wealth of insight and the foundation for valuable tools to study these genomic parasites. In this review, we provide an overview of LINE-1 biology followed by highlights from new reports of LINE-1-mediated genetic disease in humans.
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Affiliation(s)
- Dustin C. Hancks
- />Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Haig H. Kazazian
- />McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins School of Medicine, Baltimore, MD USA
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4
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Bozkaya OG, Ataman E, Randa C, Cura DO, Gürsoy S, Aksel O, Ulgenalp A. Three novel mutations of CHD7 gene in two turkish patients with charge syndrome; A double point mutation and an insertion. Balkan J Med Genet 2016; 18:65-70. [PMID: 26929907 PMCID: PMC4768827 DOI: 10.1515/bjmg-2015-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The CHARGE (coloboma, heart defects, atresia, retardation, genital, ear) syndrome is a genetic disease characterized by ocular coloboma, choanal atresia or stenosis and semicircular canal abnormalities. Most of the patients clinically diagnosed with CHARGE syndrome have mutations in chromodomain helicase DNA-binding protein 7 (CHD7) gene. The CHD7 gene is located on chromosome 8q12.1, and up to now, there are more than 500 pathogenic mutations identified in the literature. We report two patients diagnosed with CHARGE syndrome with two novel mutations in the CHD7 gene: the first patient has double consecutive novel mutations in three adjacent codons, and the other has a novel insertion.
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Affiliation(s)
- O Giray Bozkaya
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - E Ataman
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - C Randa
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - D Onur Cura
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - S Gürsoy
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - O Aksel
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - A Ulgenalp
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
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5
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Gamba BF, Richieri-Costa A, Costa S, Rosenberg C, Ribeiro-Bicudo LA. Chromothripsis with at least 12 breaks at 1p36.33-p35.3 in a boy with multiple congenital anomalies. Mol Genet Genomics 2015; 290:2213-6. [DOI: 10.1007/s00438-015-1072-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/20/2015] [Indexed: 12/20/2022]
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6
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Plaisancié J, Kleinfinger P, Cances C, Bazin A, Julia S, Trost D, Lohmann L, Vigouroux A. Constitutional chromoanasynthesis: description of a rare chromosomal event in a patient. Eur J Med Genet 2014; 57:567-70. [PMID: 25128687 DOI: 10.1016/j.ejmg.2014.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/30/2014] [Indexed: 11/24/2022]
Abstract
Structural alterations in chromosomes are a frequent cause of cancers and congenital diseases. Recently, the phenomenon of chromosome crisis, consisting of a set of tens to hundreds of clustered genomic rearrangements, localized in one or a few chromosomes, was described in cancer cells under the term chromothripsis. Better knowledge and recognition of this catastrophic chromosome event has brought to light two distinct entities, chromothripsis and chromoanasynthesis. The complexity of these rearrangements and the original descriptions in tumor cells initially led to the thought that it was an acquired anomaly. In fact, a few patients have been reported with constitutional chromothripsis or chromoanasynthesis. Using microarray we identified a very complex chromosomal rearrangement in a patient who had a cytogenetically visible rearrangement of chromosome 18. The rearrangement contained more than 15 breakpoints localized on a single chromosome. Our patient displayed intellectual disability, behavioral troubles and craniofacial dysmorphism. Interestingly, the succession of duplications and triplications identified in our patient was not clustered on a single chromosomal region but spread over the entire chromosome 18. In the light of this new spectrum of chromosomal rearrangements, this report outlines the main features of these catastrophic events and discusses the underlying mechanism of the complex chromosomal rearrangement identified in our patient, which is strongly evocative of a chromoanasynthesis.
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Affiliation(s)
- Julie Plaisancié
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, France.
| | - Pascale Kleinfinger
- Laboratoire Cerba, Département de Génétique Humaine, Saint-Ouen l'Aumône, France
| | - Claude Cances
- Service de Neuropédiatrie, Hôpital des Enfants, CHU Toulouse, France
| | - Anne Bazin
- Laboratoire Cerba, Département de Génétique Humaine, Saint-Ouen l'Aumône, France
| | - Sophie Julia
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, France
| | - Detlef Trost
- Laboratoire Cerba, Département de Génétique Humaine, Saint-Ouen l'Aumône, France
| | - Laurence Lohmann
- Laboratoire Cerba, Département de Génétique Humaine, Saint-Ouen l'Aumône, France
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7
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Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SRF, Wilkie AOM, McVean G, Lunter G. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nat Genet 2014; 46:912-918. [PMID: 25017105 PMCID: PMC4753679 DOI: 10.1038/ng.3036] [Citation(s) in RCA: 709] [Impact Index Per Article: 70.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 06/23/2014] [Indexed: 12/19/2022]
Abstract
High-throughput DNA sequencing technology has transformed genetic research and is starting to make an impact on clinical practice. However, analyzing high-throughput sequencing data remains challenging, particularly in clinical settings where accuracy and turnaround times are critical. We present a new approach to this problem, implemented in a software package called Platypus. Platypus achieves high sensitivity and specificity for SNPs, indels and complex polymorphisms by using local de novo assembly to generate candidate variants, followed by local realignment and probabilistic haplotype estimation. It is an order of magnitude faster than existing tools and generates calls from raw aligned read data without preprocessing. We demonstrate the performance of Platypus in clinically relevant experimental designs by comparing with SAMtools and GATK on whole-genome and exome-capture data, by identifying de novo variation in 15 parent-offspring trios with high sensitivity and specificity, and by estimating human leukocyte antigen genotypes directly from variant calls.
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Affiliation(s)
- Andy Rimmer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hang Phan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Iain Mathieson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen R F Twigg
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | - Andrew O M Wilkie
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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8
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Abstract
Discoveries in cytogenetics, molecular biology, and genomics have revealed that genome change is an active cell-mediated physiological process. This is distinctly at variance with the pre-DNA assumption that genetic changes arise accidentally and sporadically. The discovery that DNA changes arise as the result of regulated cell biochemistry means that the genome is best modelled as a read-write (RW) data storage system rather than a read-only memory (ROM). The evidence behind this change in thinking and a consideration of some of its implications are the subjects of this article. Specific points include the following: cells protect themselves from accidental genome change with proofreading and DNA damage repair systems; localized point mutations result from the action of specialized trans-lesion mutator DNA polymerases; cells can join broken chromosomes and generate genome rearrangements by non-homologous end-joining (NHEJ) processes in specialized subnuclear repair centres; cells have a broad variety of natural genetic engineering (NGE) functions for transporting, diversifying and reorganizing DNA sequences in ways that generate many classes of genomic novelties; natural genetic engineering functions are regulated and subject to activation by a range of challenging life history events; cells can target the action of natural genetic engineering functions to particular genome locations by a range of well-established molecular interactions, including protein binding with regulatory factors and linkage to transcription; and genome changes in cancer can usefully be considered as consequences of the loss of homeostatic control over natural genetic engineering functions.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCISW123B, 979 E. 57th Street, Chicago, IL 60637, USA
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9
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Chen JM, Cooper DN, Férec C. A new and more accurate estimate of the rate of concurrent tandem-base substitution mutations in the human germline: ∼0.4% of the single-nucleotide substitution mutation rate. Hum Mutat 2014; 35:392-4. [PMID: 24375656 DOI: 10.1002/humu.22501] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/19/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Jian-Min Chen
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France; Etablissement Français du Sang (EFS) - Bretagne, Brest, France; Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France; Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Universitaire (CHU) Brest, Hôpital Morvan, Brest, France
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10
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Mackinnon RN, Campbell LJ. Chromothripsis under the microscope: a cytogenetic perspective of two cases of AML with catastrophic chromosome rearrangement. Cancer Genet 2013; 206:238-51. [PMID: 23911237 DOI: 10.1016/j.cancergen.2013.05.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/16/2013] [Accepted: 05/28/2013] [Indexed: 12/21/2022]
Abstract
Chromothripsis is a recently described phenomenon identified in cancer cells that produces catastrophic chromosome reorganization of one or a small number of chromosomes. It has been proposed that the multiple breakage events occur at a single point in time. Here we introduce the term anachromosome to describe an abnormal chromosome produced by chromothripsis. We report two cases of acute myeloid leukemia matching the description of chromothripsis that illustrate different aspects of this phenomenon from a cytogenetic perspective. Fluorescence in situ hybridization (FISH) analyses, including multicolor FISH and FISH for repeat elements that are not present on microarrays and that are resistant to sequencing, helped interpret the rearrangements but did not reveal their level of complexity. The anachromosomes conformed to the normal constraints of chromosome structure by including segments that provide two telomeres and a centromere. In patient samples, there are mixtures of cells with and without deletions. The deletion B allele frequencies for heterozygous loci in a mixture of cells with and without the deletions create a distinctive array pattern that is consistent with all the deletions in the anachromosomes having occurred concurrently. This evidence supporting the single-event hypothesis for chromothripsis has not previously been highlighted, to our knowledge. In the context of exploring mechanisms for chromosome shattering, we discuss a possible connection between chromosome pulverization and fragile sites. Understanding chromothripsis in the context of chromosome biology will help us identify its causes and consequences.
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Affiliation(s)
- Ruth N Mackinnon
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital Melbourne, Fitzroy, Australia.
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11
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Chen JM, Férec C, Cooper DN. Patterns and mutational signatures of tandem base substitutions causing human inherited disease. Hum Mutat 2013; 34:1119-30. [PMID: 23606422 DOI: 10.1002/humu.22341] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/09/2013] [Indexed: 12/31/2022]
Abstract
Tandem base substitutions (TBSs) are multiple mutations that comprise two or more contiguous nucleotide substitutions without any net gain or loss of bases. They have recently become recognized as a distinct category of human genomic variant. However, their role in causing human inherited disease so far has not been studied methodically. Here, using data from the Human Gene Mutation Database (http://www.hgmd.org), we identified 477 events to be TBSs (doublets, 448; triplets, 16; and quadruplets to octuplets, 13). A comprehensive sequence pattern and context analysis implied the likely fundamental importance of translesion synthesis (TLS) DNA polymerases in generating these diverse TBSs but revealed that TLS polymerases may operate differently in generating TBSs of ≤ 3 bases (bypass of endogenous DNA lesions) than those of ≥ 4 bases (serial replication slippage). Moreover, GC was found to be the most frequently affected dinucleotide with GC/GC>AA/TT being the most frequent double TBS. Comparison with cancer genome mutational spectra allowed us to conclude that human germline TBSs arise predominantly through the action of endogenous mechanisms of mutagenesis rather than through exposure to exogenous mutagens. Finally, the rates of double and triple TBSs were estimated to be 0.2-1.2 × 10(-10) and 0.8-4.8 × 10(-12) per base per generation, respectively.
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Affiliation(s)
- Jian-Min Chen
- Institut National de la Santé et de la Recherche Médicale, Brest, France.
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12
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Chia NL, Bryce M, Hickman PE, Potter JM, Glasgow N, Koerbin G, Danoy P, Brown MA, Cavanaugh J. High-resolution SNP microarray investigation of copy number variations on chromosome 18 in a control cohort. Cytogenet Genome Res 2013; 141:16-25. [PMID: 23635498 DOI: 10.1159/000350767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2013] [Indexed: 11/19/2022] Open
Abstract
Copy number variations (CNVs) as described in the healthy population are purported to contribute significantly to genetic heterogeneity. Recent studies have described CNVs using lymphoblastoid cell lines or by application of specifically developed algorithms to interrogate previously described data. However, the full extent of CNVs remains unclear. Using high-density SNP array, we have undertaken a comprehensive investigation of chromosome 18 for CNV discovery and characterisation of distribution and association with chromosome architecture. We identified 399 CNVs, of which loss represents 98%, 58% are less than 2.5 kb in size and 71% are intergenic. Intronic deletions account for the majority of copy number changes with gene involvement. Furthermore, one-third of CNVs do not have putative breakpoints within repetitive sequences. We conclude that replicative processes, mediated either by repetitive elements or microhomology, account for the majority of CNVs in the healthy population. Genomic instability involving the formation of a non-B structure is demonstrated in one region.
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Affiliation(s)
- N L Chia
- ANU Medical School, Australian National University, Canberra, A.C.T., Australia.
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13
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Abstract
During oncogenesis, cells acquire multiple genetic alterations that confer essential tumor-specific traits, including immortalization, escape from antimitogenic signaling, neovascularization, invasiveness, and metastatic potential. In most instances, these alterations are thought to arise incrementally over years, if not decades. However, recent progress in sequencing cancer genomes has begun to challenge this paradigm, because a radically different phenomenon, termed chromothripsis, has been suggested to cause complex intra- and interchromosomal rearrangements on short timescales. In this Review, we review established pathways crucial for genome integrity and discuss how their dysfunction could precipitate widespread chromosome breakage and rearrangement in the course of malignancy.
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Affiliation(s)
- Mathew J K Jones
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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14
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Sharma S, Helchowski CM, Canman CE. The roles of DNA polymerase ζ and the Y family DNA polymerases in promoting or preventing genome instability. Mutat Res 2012. [PMID: 23195997 DOI: 10.1016/j.mrfmmm.2012.11.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer cells display numerous abnormal characteristics which are initiated and maintained by elevated mutation rates and genome instability. Chromosomal DNA is continuously surveyed for the presence of damage or blocked replication forks by the DNA Damage Response (DDR) network. The DDR is complex and includes activation of cell cycle checkpoints, DNA repair, gene transcription, and induction of apoptosis. Duplicating a damaged genome is associated with elevated risks to fork collapse and genome instability. Therefore, the DNA damage tolerance (DDT) pathway is also employed to enhance survival and involves the recruitment of translesion DNA synthesis (TLS) polymerases to sites of replication fork blockade or single stranded DNA gaps left after the completion of replication in order to restore DNA to its double stranded form before mitosis. TLS polymerases are specialized for inserting nucleotides opposite DNA adducts, abasic sites, or DNA crosslinks. By definition, the DDT pathway is not involved in the actual repair of damaged DNA, but provides a mechanism to tolerate DNA lesions during replication thereby increasing survival and lessening the chance for genome instability. However this may be associated with increased mutagenesis. In this review, we will describe the specialized functions of Y family polymerases (Rev1, Polη, Polι and Polκ) and DNA polymerase ζ in lesion bypass, mutagenesis, and prevention of genome instability, the latter due to newly appreciated roles in DNA repair. The recently described role of the Fanconi anemia pathway in regulating Rev1 and Polζ-dependent TLS is also discussed in terms of their involvement in TLS, interstrand crosslink repair, and homologous recombination.
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Affiliation(s)
- Shilpy Sharma
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Corey M Helchowski
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Christine E Canman
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States.
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15
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Holland AJ, Cleveland DW. Chromoanagenesis and cancer: mechanisms and consequences of localized, complex chromosomal rearrangements. Nat Med 2012; 18:1630-8. [PMID: 23135524 DOI: 10.1038/nm.2988] [Citation(s) in RCA: 193] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 10/01/2012] [Indexed: 02/08/2023]
Abstract
Next-generation sequencing of DNA from human tumors or individuals with developmental abnormalities has led to the discovery of a process we term chromoanagenesis, in which large numbers of complex rearrangements occur at one or a few chromosomal loci in a single catastrophic event. Two mechanisms underlie these rearrangements, both of which can be facilitated by a mitotic chromosome segregation error to produce a micronucleus containing the chromosome to undergo rearrangement. In the first, chromosome shattering (chromothripsis) is produced by mitotic entry before completion of DNA replication within the micronucleus, with a failure to disassemble the micronuclear envelope encapsulating the chromosomal fragments for random reassembly in the subsequent interphase. Alternatively, locally defective DNA replication initiates serial, microhomology-mediated template switching (chromoanasynthesis) that produces local rearrangements with altered gene copy numbers. Complex rearrangements are present in a broad spectrum of tumors and in individuals with congenital or developmental defects, highlighting the impact of chromoanagenesis on human disease.
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Affiliation(s)
- Andrew J Holland
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
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16
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Hashimoto K, Rogozin IB, Panchenko AR. Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases. Hum Mutat 2012; 33:1566-75. [PMID: 22753356 PMCID: PMC3465464 DOI: 10.1002/humu.22145] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/29/2012] [Indexed: 01/16/2023]
Abstract
Aberrant activation of receptor tyrosine kinases (RTKs) is a common feature of many cancer cells. It was previously suggested that the mechanisms of kinase activation in cancer might be linked to transitions between active and inactive states. Here, we estimate the effects of single and double cancer mutations on the stability of active and inactive states of the kinase domains from different RTKs. We show that singleton cancer mutations destabilize active and inactive states; however, inactive states are destabilized more than the active ones, leading to kinase activation. We show that there exists a relationship between the estimate of oncogenic potential of cancer mutation and kinase activation. Namely, more frequent mutations have a higher activating effect, which might allow us to predict the activating effect of the mutations from the mutation spectra. Independent evolutionary analysis of mutation spectra complements this observation and finds the same frequency threshold defining mutation hotspots. We analyze double mutations and report a positive epistasis and additional advantage of doublets with respect to cancer cell fitness. The activation mechanisms of double mutations differ from those of single mutations and double mutation spectrum is found to be dissimilar to the mutation spectrum of singletons.
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Affiliation(s)
| | - Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna R. Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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17
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Lane AB, Clarke DJ. Genome instability: does genetic diversity amplification drive tumorigenesis? Bioessays 2012; 34:963-72. [PMID: 22948965 DOI: 10.1002/bies.201200082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Recent data show that catastrophic events during one cell cycle can cause massive genome damage producing viable clones with unstable genomes. This is in contrast with the traditional view that tumorigenesis requires a long-term process in which mutations gradually accumulate over decades. These sudden events are likely to result in a large increase in genomic diversity within a relatively short time, providing the opportunity for selective advantages to be gained by a subset of cells within a population. This genetic diversity amplification, arising from a single aberrant cell cycle, may drive a population conversion from benign to malignant. However, there is likely a period of relative genome stability during the clonal expansion of tumors - this may provide an opportunity for therapeutic intervention, especially if mechanisms that limit tolerance of aneuploidy are exploited.
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Affiliation(s)
- Andrew B Lane
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN, USA
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18
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Righolt C, Mai S. Shattered and stitched chromosomes-chromothripsis and chromoanasynthesis-manifestations of a new chromosome crisis? Genes Chromosomes Cancer 2012; 51:975-81. [PMID: 22811041 DOI: 10.1002/gcc.21981] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 06/13/2012] [Indexed: 12/16/2022] Open
Abstract
Chromothripsis (chromosome shattering) has been described as complex rearrangements affecting single chromosome(s) in one catastrophic event. The chromosomes would be "shattered" and "stitched together" during this event. This phenomenon is proposed to constitute the basis for complex chromosomal rearrangements seen in 2-3% of all cancers and in ∼ 25% of bone cancers. Here we discuss chromothripsis, the use of this term and the evidence presented to support a single catastrophic event that remodels the genome in one step. We discuss why care should be taken in using the term chromothripsis and what evidence is lacking to support its use while describing complex rearrangements.
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Affiliation(s)
- Christiaan Righolt
- Manitoba Institute of Cell Biology, CancerCare Manitoba, Department of Physiology, the University of Manitoba, Winnipeg, Canada
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19
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Kloosterman WP, Tavakoli-Yaraki M, van Roosmalen MJ, van Binsbergen E, Renkens I, Duran K, Ballarati L, Vergult S, Giardino D, Hansson K, Ruivenkamp CAL, Jager M, van Haeringen A, Ippel EF, Haaf T, Passarge E, Hochstenbach R, Menten B, Larizza L, Guryev V, Poot M, Cuppen E. Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms. Cell Rep 2012; 1:648-55. [PMID: 22813740 DOI: 10.1016/j.celrep.2012.05.009] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 02/09/2012] [Accepted: 05/14/2012] [Indexed: 12/20/2022] Open
Abstract
Chromothripsis represents a novel phenomenon in the structural variation landscape of cancer genomes. Here, we analyze the genomes of ten patients with congenital disease who were preselected to carry complex chromosomal rearrangements with more than two breakpoints. The rearrangements displayed unanticipated complexity resembling chromothripsis. We find that eight of them contain hallmarks of multiple clustered double-stranded DNA breaks (DSBs) on one or more chromosomes. In addition, nucleotide resolution analysis of 98 breakpoint junctions indicates that break repair involves nonhomologous or microhomology-mediated end joining. We observed that these eight rearrangements are balanced or contain sporadic deletions ranging in size between a few hundred base pairs and several megabases. The two remaining complex rearrangements did not display signs of DSBs and contain duplications, indicative of rearrangement processes involving template switching. Our work provides detailed insight into the characteristics of chromothripsis and supports a role for clustered DSBs driving some constitutional chromothripsis rearrangements.
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Affiliation(s)
- Wigard P Kloosterman
- Department of Medical Genetics, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands.
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20
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Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, Greenman CD, Raine K, Jones D, Hinton J, Marshall J, Stebbings LA, Menzies A, Martin S, Leung K, Chen L, Leroy C, Ramakrishna M, Rance R, Lau KW, Mudie LJ, Varela I, McBride DJ, Bignell GR, Cooke SL, Shlien A, Gamble J, Whitmore I, Maddison M, Tarpey PS, Davies HR, Papaemmanuil E, Stephens PJ, McLaren S, Butler AP, Teague JW, Jönsson G, Garber JE, Silver D, Miron P, Fatima A, Boyault S, Langerød A, Tutt A, Martens JWM, Aparicio SAJR, Borg Å, Salomon AV, Thomas G, Børresen-Dale AL, Richardson AL, Neuberger MS, Futreal PA, Campbell PJ, Stratton MR. Mutational processes molding the genomes of 21 breast cancers. Cell 2012; 149:979-93. [PMID: 22608084 PMCID: PMC3414841 DOI: 10.1016/j.cell.2012.04.024] [Citation(s) in RCA: 1404] [Impact Index Per Article: 117.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 03/12/2012] [Accepted: 04/30/2012] [Indexed: 12/14/2022]
Abstract
All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed “kataegis,” was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed. PaperClip
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Affiliation(s)
- Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
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21
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De Caris L, Cecceroni L, Tummala H. On a Break with the X: The Role of Repair of Double-Stranded DNA Breaks in X-Linked Disease. BIOTECHNOL BIOTEC EQ 2012. [DOI: 10.5504/bbeq.2012.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Laura De Caris
- University of Abertay Dundee, School of Contemporary Sciences, Scotland, UK
| | - Lucia Cecceroni
- University of Abertay Dundee, School of Contemporary Sciences, Scotland, UK
| | - Hemanth Tummala
- University of Abertay Dundee, School of Contemporary Sciences, Scotland, UK
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