XB-ART-55895
Nat Genet
2019 Apr 01;514:705-715. doi: 10.1038/s41588-019-0360-8.
Show Gene links
Show Anatomy links
Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements.
Ly P
,
Brunner SF
,
Shoshani O
,
Kim DH
,
Lan W
,
Pyntikova T
,
Flanagan AM
,
Behjati S
,
Page DC
,
Campbell PJ
,
Cleveland DW
.
???displayArticle.abstract???
Cancer genomes are frequently characterized by numerical and structural chromosomal abnormalities. Here we integrated a centromere-specific inactivation approach with selection for a conditionally essential gene, a strategy termed CEN-SELECT, to systematically interrogate the structural landscape of mis-segregated chromosomes. We show that single-chromosome mis-segregation into a micronucleus can directly trigger a broad spectrum of genomic rearrangement types. Cytogenetic profiling revealed that mis-segregated chromosomes exhibit 120-fold-higher susceptibility to developing seven major categories of structural aberrations, including translocations, insertions, deletions, and complex reassembly through chromothripsis coupled to classical non-homologous end joining. Whole-genome sequencing of clonally propagated rearrangements identified random patterns of clustered breakpoints with copy-number alterations resulting in interspersed gene deletions and extrachromosomal DNA amplification events. We conclude that individual chromosome segregation errors during mitotic cell division are sufficient to drive extensive structural variations that recapitulate genomic features commonly associated with human disease.
???displayArticle.pubmedLink??? 30833795
???displayArticle.pmcLink??? PMC6441390
???displayArticle.link??? Nat Genet
???displayArticle.grants??? [+]
Wellcome Trust , K99 CA218871 NCI NIH HHS , P30 NS047101 NINDS NIH HHS , R35 GM122476 NIGMS NIH HHS , R00 CA218871 NCI NIH HHS
Species referenced: Xenopus laevis
Genes referenced: dld
GO keywords: chromosome segregation
???attribute.lit??? ???displayArticles.show???
Figure 2 |. Missegregated chromosomes acquire a broad spectrum of structural genomic rearrangement types.a) Measurements of Y chromosome rearrangement frequencies in parental cells and 3 independent clonal lines following 0d or 3d DOX/IAA treatment and G418 selection. Metaphase spreads were subjected to DNA fluorescence in situ hybridization (FISH) using Y chromosome-specific paint probes. n = number of metaphase spreads examined. Parental CENP-AC–H3 frequencies were pooled from 3 independent experiments. RA, rearrangement. b) Schematic of multi-colored DNA FISH probes used to characterize structural anomolies of the Y chromosome. c-d) Representative FISH images of c) a normal Y chromosome without visible defects from control metaphases (scale bar, 5 μm) and d) examples of derivative Y chromosomes from 3d DOX/IAA-treated, G418-resistant metaphases. See Supplementary Note for a description of each rearrangement type. | |
Figure 3 |. Systematic classification of the structural rearrangement landscape.a-b) The distribution of structural rearrangement types quantified from metaphase spreads using MSY/YqH FISH probes following a) transient centromere inactivation induced by 3d DOX/IAA treatment, washout, and G418 selection, or b) prolonged centromere inactivation induced by continuous passage in DOX/IAA and G418 (detailed in Supplementary Fig. 6). The number of each case detected is depicted on the right of each graph. | |
Figure 4 |. Chromosome rearrangements develop with high frequency and specificity through classical non-homologous end joining repair.a) DLD-1 cells carrying a CENP-AC–H3 rescue gene were treated as indicated in Supplementary Fig. 7e, followed by metaphase spread preparation and hybridization to the indicated chromosome paint probes. Metaphases were examined for structural rearrangements affecting each chromosome. Bar graph represents n = 42–65 metaphases scored per chromosome per condition, analysing a total of 1,968 metaphase spreads (exact sample sizes provided in Supplementary Fig. 7g). b) Schematic of experimental hypothesis tested in panels c and d. NHEJ, non-homologous end joining; alt-EJ, alternative end joining. c-d) DLD-1 CENP-AC–H3 rescue cells were treated with or without 3d DOX/IAA and transfected with the indicated siRNAs simultaneous with DOX/IAA washout for an additional 3d. Cells were then re-plated into G418 medium for c) 10d selection followed by metaphase FISH using MSY/YqH probes (102–159 metaphase spreads per condition) or d) 14d at single-cell density for colony formation assays. Data in c and d represent the mean ± SEM of n = 3 independent experiments; P-values were derived from two-tailed Student’s t-test comparing groups as indicated. | |
Figure 5 |. Isolation and propagation of single cell-derived clones with genetically stable derivative chromosomes.a) Schematic of approach used to generate clonally propagated Y chromosome rearrangements from a bulk cell population. b) Frequency of Y chromosome rearrangement types obtained from single cell-derived clones. The boxed section indicates clonal rearrangements, and the number of clones subjected to whole-genome sequencing is shown on the right. c-d) Experimental schematic and representative metaphase FISH images from the indicated clones, which were passaged in parallel cultures with (ON) or without (OFF) G418 selection for c) 0 weeks, d) 2 weeks, and e) 4 weeks. Scale bar, 2 μm. Values below the image represent the number of metaphases positive for the depicted derivative chromosome over the total number of metaphases examined. RA, rearrangements. | |
Figure 6 |. Whole-genome sequencing reveals complex rearrangements that include the hallmark signatures of chromothripsis.a-b) DNA copy-number profiles from WGS (top) and representative metaphase FISH images hybridized to the indicated probes captured by super-resolution microscopy (bottom) from a) clone PD37303a with a normal Y chromosome and b) clone PD37307a with 83 breakpoints detected across the mappable Y chromosome region. 3D-SIM, 3D structured illumination microscopy. c-f) DNA copy-number profiles of additional clones carrying a chromothriptic Y chromosome coupled to c,d) translocations, e) a simple insertion into chromosome 1p, or f) a complex insertion at a duplicated region on chromosome 1q. X-axes of Y chromosome plots are clipped at 30 Mb to exclude the Yq heterochromatic region. g-h) Metaphase FISH images using MSY and chromosome 1 painting probes on clones g) PD37306a and h) PD37313a. Scale bar, 5 μm. | |
Figure 7 |. Gene disruption and extrachromosomal DNA amplification from chromosome missegregation-induced rearrangements.a) Each grey vertical line represents an individual gene or pseudogene depicted at its chromosomal start position, and red lines represent a copy-number of zero. Clones are ranked from fewest to most gene deletions. b) Magnification of clone PD37307a (boxed region in a) exhibiting oscillating patterns of gene retention and deletion within an 8 Mb segment. c) Schematic of chromosome shattering and reassembly events resulting in a derivative chromosome harboring rearrangements with interspersed deletions. d) DNA copy-number profile of clone PD37310a showing extensive Y chromosome loss except for the region harboring the selection marker accompanied by two inversions. e) Images of metaphase spreads prepared from the parental or PD37310a clone and hybridized to MSY (green) and RP11–113K10 BAC (red) probes recognizing the region shown in d. Arrows denote extrachromosomal DNA fragments hybridizing to the RP11–113K10 probe, and regions of the X chromosome partially hybridize to MSY probes due to X-Y sequence homology. Scale bar, 5 μm. f) Quantification of e. Each data point represents an individual metaphase spread derived from the parental clone (n = 48) or PD37310a clone (n = 56). CN, copy-number. g) Schematic depicting the predicted steps leading to the generation of the extrachromosomal DNA (ecDNA) element through the circular reassembly of two broken DNA fragments. h) Reconstructed ecDNA sequence from WGS. Genes and pseudogenes in the corresponding region are shown, and red arrows depict 5’ to 3’ orientation. |
References [+] :
Anderson,
Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors.
2018, Pubmed
Anderson, Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors. 2018, Pubmed
Anderson, Phosphorylation and rapid relocalization of 53BP1 to nuclear foci upon DNA damage. 2001, Pubmed , Xenbase
Baca, Punctuated evolution of prostate cancer genomes. 2013, Pubmed
Bass, Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. 2011, Pubmed
Behjati, Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma. 2017, Pubmed
Burma, ATM phosphorylates histone H2AX in response to DNA double-strand breaks. 2001, Pubmed
Campbell, Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. 2008, Pubmed
Carvalho, Mechanisms underlying structural variant formation in genomic disorders. 2016, Pubmed
Chiang, Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. 2012, Pubmed
Cogen, Deletion mapping of the medulloblastoma locus on chromosome 17p. 1990, Pubmed
Cortés-Ciriano, Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. 2020, Pubmed
Crasta, DNA breaks and chromosome pulverization from errors in mitosis. 2012, Pubmed
Cretu Stancu, Mapping and phasing of structural variation in patient genomes using nanopore sequencing. 2017, Pubmed
Dixon, Integrative detection and analysis of structural variation in cancer genomes. 2018, Pubmed
Gao, Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. 2018, Pubmed
Garaycoechea, Alcohol and endogenous aldehydes damage chromosomes and mutate stem cells. 2018, Pubmed
Garsed, The architecture and evolution of cancer neochromosomes. 2014, Pubmed
Hatch, Catastrophic nuclear envelope collapse in cancer cell micronuclei. 2013, Pubmed
Henssen, PGBD5 promotes site-specific oncogenic mutations in human tumors. 2017, Pubmed
Hnisz, Activation of proto-oncogenes by disruption of chromosome neighborhoods. 2016, Pubmed
Holland, Inducible, reversible system for the rapid and complete degradation of proteins in mammalian cells. 2012, Pubmed
Janssen, Chromosome segregation errors as a cause of DNA damage and structural chromosome aberrations. 2011, Pubmed
Kato, Chromosome pulverization in human cells with micronuclei. 1968, Pubmed
Kloosterman, Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. 2011, Pubmed
Kloosterman, Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms. 2012, Pubmed
Leibowitz, Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. 2015, Pubmed
Li, Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia. 2014, Pubmed
Li, Fast and accurate long-read alignment with Burrows-Wheeler transform. 2010, Pubmed
Lin, Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer. 2009, Pubmed
Liu, An Organismal CNV Mutator Phenotype Restricted to Early Human Development. 2017, Pubmed
Liu, Nuclear envelope assembly defects link mitotic errors to chromothripsis. 2018, Pubmed
Lombard, DNA repair, genome stability, and aging. 2005, Pubmed
Ly, Rebuilding Chromosomes After Catastrophe: Emerging Mechanisms of Chromothripsis. 2017, Pubmed
Ly, Selective Y centromere inactivation triggers chromosome shattering in micronuclei and repair by non-homologous end joining. 2017, Pubmed
Ly, Interrogating cell division errors using random and chromosome-specific missegregation approaches. 2017, Pubmed
Maciejowski, Chromothripsis and Kataegis Induced by Telomere Crisis. 2015, Pubmed
Mardin, A cell-based model system links chromothripsis with hyperploidy. 2015, Pubmed
Masumoto, A human centromere antigen (CENP-B) interacts with a short specific sequence in alphoid DNA, a human centromeric satellite. 1989, Pubmed
Miake-Lye, Induction of early mitotic events in a cell-free system. 1985, Pubmed , Xenbase
Mitchell, Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal. 2018, Pubmed
Murray, Cell cycle extracts. 1991, Pubmed
Mühlhäusser, An in vitro nuclear disassembly system reveals a role for the RanGTPase system and microtubule-dependent steps in nuclear envelope breakdown. 2007, Pubmed , Xenbase
NOWELL, The minute chromosome (Phl) in chronic granulocytic leukemia. 1962, Pubmed
Nik-Zainal, Mutational processes molding the genomes of 21 breast cancers. 2012, Pubmed
Nik-Zainal, Landscape of somatic mutations in 560 breast cancer whole-genome sequences. 2016, Pubmed
Nishimura, An auxin-based degron system for the rapid depletion of proteins in nonplant cells. 2009, Pubmed
Northcott, Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. 2014, Pubmed
Notta, A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns. 2016, Pubmed
Raine, ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data. 2016, Pubmed
Rausch, Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. 2012, Pubmed
Redin, The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. 2017, Pubmed
Rowley, Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. 1973, Pubmed
Santaguida, Chromosome Mis-segregation Generates Cell-Cycle-Arrested Cells with Complex Karyotypes that Are Eliminated by the Immune System. 2017, Pubmed
Santaguida, Dissecting the role of MPS1 in chromosome biorientation and the spindle checkpoint through the small molecule inhibitor reversine. 2010, Pubmed
Schultz, p53 binding protein 1 (53BP1) is an early participant in the cellular response to DNA double-strand breaks. 2000, Pubmed
Shankaran, A time-lapse imaging assay to study nuclear envelope breakdown. 2013, Pubmed , Xenbase
Skaletsky, The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. 2003, Pubmed
Soto, p53 Prohibits Propagation of Chromosome Segregation Errors that Produce Structural Aneuploidies. 2017, Pubmed
Soto, Chromosomes trapped in micronuclei are liable to segregation errors. 2018, Pubmed
Stephens, Complex landscapes of somatic rearrangement in human breast cancer genomes. 2009, Pubmed
Stephens, Massive genomic rearrangement acquired in a single catastrophic event during cancer development. 2011, Pubmed
Sun, An azoospermic man with a de novo point mutation in the Y-chromosomal gene USP9Y. 1999, Pubmed
Taylor, DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis. 2013, Pubmed
Terradas, DNA lesions sequestered in micronuclei induce a local defective-damage response. 2009, Pubmed
Truong, Microhomology-mediated End Joining and Homologous Recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells. 2013, Pubmed
Turner, Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. 2017, Pubmed
Weckselblatt, Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis. 2015, Pubmed
Weischenfeldt, Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking. 2017, Pubmed
Willis, Mechanism of tandem duplication formation in BRCA1-mutant cells. 2017, Pubmed
Wu, ATM phosphorylation of Nijmegen breakage syndrome protein is required in a DNA damage response. 2000, Pubmed
Yang, Diverse mechanisms of somatic structural variations in human cancer genomes. 2013, Pubmed
Zhang, Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers. 2016, Pubmed
Zhang, Chromothripsis from DNA damage in micronuclei. 2015, Pubmed
Zhao, Functional link between ataxia-telangiectasia and Nijmegen breakage syndrome gene products. 2000, Pubmed
de Klein, A cellular oncogene is translocated to the Philadelphia chromosome in chronic myelocytic leukaemia. 1982, Pubmed
deCarvalho, Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma. 2018, Pubmed