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Mishra S, Srivastava AK, Khan AW, Tran LSP, Nguyen HT. The era of panomics-driven gene discovery in plants. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00063-3. [PMID: 38658292 DOI: 10.1016/j.tplants.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 04/26/2024]
Abstract
Panomics is an approach to integrate multiple 'omics' datasets, generated using different individuals or natural variations. Considering their diverse phenotypic spectrum, the phenome is inherently associated with panomics-based science, which is further combined with genomics, transcriptomics, metabolomics, and other omics techniques, either independently or collectively. Panomics has been accelerated through recent technological advancements in the field of genomics that enable the detection of population-wide structural variations (SVs) and hence offer unprecedented insights into the genetic variations contributing to important agronomic traits. The present review provides the recent trends of panomics-driven gene discovery toward various traits related to plant development, stress tolerance, accumulation of specialized metabolites, and domestication/dedomestication. In addition, the success stories are highlighted in the broader context of enhancing crop productivity.
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Affiliation(s)
- Shefali Mishra
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra 400085, India
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra 400085, India; Homi Bhabha National Institute, Mumbai 400094, India.
| | - Aamir W Khan
- Division of Plant Science and Technology and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Henry T Nguyen
- Division of Plant Science and Technology and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211, USA.
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2
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Yu Y, Wang X, Fox J, Li Q, Yu Y, Hastings PJ, Chen K, Ira G. RPA and Rad27 limit templated and inverted insertions at DNA breaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583931. [PMID: 38496432 PMCID: PMC10942419 DOI: 10.1101/2024.03.07.583931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Formation of templated insertions at DNA double-strand breaks (DSBs) is very common in cancer cells. The mechanisms and enzymes regulating these events are largely unknown. Here, we investigated templated insertions in yeast at DSBs using amplicon sequencing across a repaired locus. We document very short (most ∼5-34 bp), templated inverted duplications at DSBs. They are generated through a foldback mechanism that utilizes microhomologies adjacent to the DSB. Enzymatic requirements suggest a hybrid mechanism wherein one end requires Polδ-mediated synthesis while the other end is captured by nonhomologous end joining (NHEJ). This process is exacerbated in mutants with low levels or mutated RPA ( rtt105 Δ; rfa1 -t33) or extensive resection mutant ( sgs1 Δ exo1 Δ). Templated insertions from various distant genomic locations also increase in these mutants as well as in rad27 Δ and originate from fragile regions of the genome. Among complex insertions, common events are insertions of two sequences, originating from the same locus and with inverted orientation. We propose that these inversions are also formed by microhomology-mediated template switching. Taken together, we propose that a shortage of RPA typical in cancer cells is one possible factor stimulating the formation of templated insertions.
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3
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Muyas F, Rodriguez MJG, Cascão R, Afonso A, Sauer CM, Faria CC, Cortés-Ciriano I, Flores I. The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients. Nat Commun 2024; 15:82. [PMID: 38167290 PMCID: PMC10762111 DOI: 10.1038/s41467-023-44287-8] [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: 01/28/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Telomere fusions (TFs) can trigger the accumulation of oncogenic alterations leading to malignant transformation and drug resistance. Despite their relevance in tumour evolution, our understanding of the patterns and consequences of TFs in human cancers remains limited. Here, we characterize the rates and spectrum of somatic TFs across >30 cancer types using whole-genome sequencing data. TFs are pervasive in human tumours with rates varying markedly across and within cancer types. In addition to end-to-end fusions, we find patterns of TFs that we mechanistically link to the activity of the alternative lengthening of telomeres (ALT) pathway. We show that TFs can be detected in the blood of cancer patients, which enables cancer detection with high specificity and sensitivity even for early-stage tumours and cancers of high unmet clinical need. Overall, we report a genomic footprint that enables characterization of the telomere maintenance mechanism of tumours and liquid biopsy analysis.
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Affiliation(s)
- Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Rita Cascão
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Angela Afonso
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Carolin M Sauer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Claudia C Faria
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Department of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisboa, Portugal
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
| | - Ignacio Flores
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, 28029, Spain.
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, 28049, Spain.
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4
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Ling C, Dai Y, Geng C, Pan S, Quan W, Ding Q, Yang X, Shen D, Tao Q, Li J, Li J, Wang Y, Jiang S, Wang Y, Chen L, Cui L, Wang D. Uncovering the true features of dystrophin gene rearrangement and improving the molecular diagnosis of Duchenne and Becker muscular dystrophies. iScience 2023; 26:108365. [PMID: 38047063 PMCID: PMC10690541 DOI: 10.1016/j.isci.2023.108365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/19/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023] Open
Abstract
Duchenne and Becker muscular dystrophies (DMD/BMD) are caused by complex mutations in the dystrophin gene (DMD). Currently, there is no integrative method for the precise detection of all potential DMD variants, a gap which we aimed to address using long-read sequencing. The captured long-read sequencing panel developed in this study was applied to 129 subjects, including 11 who had previously unsolved cases. The results showed that this method accurately detected DMD mutations, ranging from single-nucleotide variations to structural variations. Furthermore, our findings revealed that continuous exon duplication/deletion in the DMD/BMD cohort may be attributed to complex segmental rearrangements and that noncontiguous duplication/deletion is generally attributed to intragenic inversion or interchromosome translocation. Mutations in the deep introns were confirmed to produce a pseudoexon. Moreover, variations in female carriers were precisely identified. The integrated and precise DMD gene screening method proposed in this study could improve the molecular diagnosis of DMD/BMD.
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Affiliation(s)
- Chao Ling
- The Laboratory of Clinical Genetics, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Chang Geng
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Shirang Pan
- Grandomics Biosciences, Beijing 102200, China
| | | | - Qingyun Ding
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Xunzhe Yang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Dongchao Shen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Qing Tao
- Grandomics Biosciences, Beijing 102200, China
| | - Jingjing Li
- Grandomics Biosciences, Beijing 102200, China
| | - Jia Li
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yinbing Wang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Shan Jiang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yang Wang
- Grandomics Biosciences, Beijing 102200, China
| | - Lin Chen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102200, China
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5
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Riviello FN, Daponte A, Ponzi E, Ficarella R, Orsini P, Bucci R, Ventura M, Antonacci F, Catacchio CR, Gentile M. A Rare Case of Concurrent 2q34q36 Duplication and 2q37 Deletion in a Neonate with Syndromic Features. Genes (Basel) 2023; 14:2194. [PMID: 38137016 PMCID: PMC10742419 DOI: 10.3390/genes14122194] [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: 11/09/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Large-scale genomic structural variations can have significant clinical implications, depending on the specific altered genomic region. Briefly, 2q37 microdeletion syndrome is a prevalent subtelomeric deletion disorder characterized by variable-sized deletions. Affected patients exhibit a wide range of clinical manifestations, including short stature, facial dysmorphism, and features of autism spectrum disorder, among others. Conversely, isolated duplications of proximal chromosome 2q are rare and lack a distinct phenotype. In this report, we provide an extensive molecular analysis of a 15-day-old newborn referred for syndromic features. Our analysis reveals an 8.5 Mb microdeletion at 2q37.1, which extends to the telomere, in conjunction with an 8.6 Mb interstitial microduplication at 2q34q36.1. Our findings underscore the prominence of 2q37 terminal deletions as commonly reported genomic anomalies. We compare our patient's phenotype with previously reported cases in the literature to contribute to a more refined classification of 2q37 microdeletion syndrome and assess the potential impact of 2q34q36.1 microduplication. We also investigate multiple hypotheses to clarify the genetic mechanisms responsible for the observed genomic rearrangement.
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Affiliation(s)
- Francesco Nicola Riviello
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Alessia Daponte
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Emanuela Ponzi
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Romina Ficarella
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Paola Orsini
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Roberta Bucci
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Mario Ventura
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Francesca Antonacci
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Claudia Rita Catacchio
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Mattia Gentile
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
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6
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Shimojima Yamamoto K, Tamura T, Okamoto N, Nishi E, Noguchi A, Takahashi I, Sawaishi Y, Shimizu M, Kanno H, Minakuchi Y, Toyoda A, Yamamoto T. Identification of small-sized intrachromosomal segments at the ends of INV-DUP-DEL patterns. J Hum Genet 2023; 68:751-757. [PMID: 37423943 DOI: 10.1038/s10038-023-01181-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/14/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023]
Abstract
The mechanism of chromosomal rearrangement associated with inverted-duplication-deletion (INV-DUP-DEL) pattern formation has been investigated by many researchers, and several possible mechanisms have been proposed. Currently, fold-back and subsequent dicentric chromosome formation has been established as non-recurrent INV-DUP-DEL pattern formation mechanisms. In the present study, we analyzed the breakpoint junctions of INV-DUP-DEL patterns in five patients using long-read whole-genome sequencing and detected 2.2-6.1 kb copy-neutral regions in all five patients. At the end of the INV-DUP-DEL, two patients exhibited chromosomal translocations, which are recognized as telomere capture, and one patient showed direct telomere healing. The remaining two patients had additional small-sized intrachromosomal segments at the end of the derivative chromosomes. These findings have not been previously reported but they may only be explained by the presence of telomere capture breakage. Further investigations are required to better understand the mechanisms underlying this finding.
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Affiliation(s)
- Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
- Division of Gene Medicine, Graduate Scholl of Medical Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, 594-1101, Japan
| | - Eriko Nishi
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, 594-1101, Japan
| | - Atsuko Noguchi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, 010-8543, Japan
| | - Ikuko Takahashi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, 010-8543, Japan
| | - Yukio Sawaishi
- Department of Pediatrics, Akita Prefectural Center on Development and Disability, Akita, 010-0000, Japan
| | - Masaki Shimizu
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Yohei Minakuchi
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-0801, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-0801, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
- Division of Gene Medicine, Graduate Scholl of Medical Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
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7
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Page-McCaw PS, Pokidysheva EN, Darris CE, Chetyrkin S, Fidler AL, Murawala P, Gallup J, Hudson JK, Hudson BG. Collagen IV of basement membranes: I. Origin and diversification of COL4 genes enabling animal evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.563013. [PMID: 37905027 PMCID: PMC10614949 DOI: 10.1101/2023.10.18.563013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Collagen IV is a primordial component of basement membranes, a specialized form of extracellular matrix that enabled multi-cellular epithelial tissues. In mammals, collagen IV assembles from a family of six α-chains (α1 to α6), encoded by six genes (COL4A1 to COL4A6), into three distinct scaffolds: the α121, the α345 and a mixed scaffold containing both α121 and α565. The six mammalian COL4A genes occur in pairs that occur in a head-to-head arrangement on three distinct chromosomes. In Alport syndrome, variants in the COL4A3, 4 or 5 genes cause either loss or defective assembly of the collagen IV α345 scaffold which results in a dysfunctional glomerular basement membrane, proteinuria and progression to renal failure in millions of people worldwide. Here, we determine the evolutionary emergence and diversification of the COL4A genes using comparative genomics and biochemical analyses. Using syntenic relationships to genes closely linked to the COL4A genes, we determine that the COL4A3 and COL4A4 gene pair appeared in cyclostomes (hagfish and lampreys) while the COL4A5 and COL4A6 gene pair emerged in gnathostomes, jawed vertebrates. The more basal chordate species, lancelets and tunicates, do not have discrete kidneys and have a single COL4A gene pair, though often with single isolated COL4 genes similar to those found in C elegans . Remarkably, while the six COL4A genes are conserved in vertebrates, amphibians have lost the COL4A3 and COL4A4 genes. Our findings of the evolutionary emergence of these genes, together with the amphibian double-knockout, opens an experimental window to gain insights into functionality of the Col IV α345 scaffold.
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8
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Mason FM, Kounlavong ES, Tebeje AT, Dahiya R, Guess T, Khan A, Vlach L, Norris SR, Lovejoy CA, Dere R, Strahl BD, Ohi R, Ly P, Walker CL, Rathmell WK. SETD2 safeguards the genome against isochromosome formation. Proc Natl Acad Sci U S A 2023; 120:e2303752120. [PMID: 37722039 PMCID: PMC10523680 DOI: 10.1073/pnas.2303752120] [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: 03/06/2023] [Accepted: 08/11/2023] [Indexed: 09/20/2023] Open
Abstract
Isochromosomes are mirror-imaged chromosomes with simultaneous duplication and deletion of genetic material which may contain two centromeres to create isodicentric chromosomes. Although isochromosomes commonly occur in cancer and developmental disorders and promote genome instability, mechanisms that prevent isochromosomes are not well understood. We show here that the tumor suppressor and methyltransferase SETD2 is essential to prevent these errors. Using cellular and cytogenetic approaches, we demonstrate that loss of SETD2 or its epigenetic mark, histone H3 lysine 36 trimethylation (H3K36me3), results in the formation of isochromosomes as well as isodicentric and acentric chromosomes. These defects arise during DNA replication and are likely due to faulty homologous recombination by RAD52. These data provide a mechanism for isochromosome generation and demonstrate that SETD2 and H3K36me3 are essential to prevent the formation of this common mutable chromatin structure known to initiate a cascade of genomic instability in cancer.
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Affiliation(s)
- Frank M. Mason
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | - Emily S. Kounlavong
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | - Anteneh T. Tebeje
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | - Rashmi Dahiya
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Tiffany Guess
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
| | - Abid Khan
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Logan Vlach
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | - Stephen R. Norris
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | | | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX77030
| | - Brian D. Strahl
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI48109
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Cheryl Lyn Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX77030
| | - W. Kimryn Rathmell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
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9
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Cullot G, Boutin J, Fayet S, Prat F, Rosier J, Cappellen D, Lamrissi I, Pennamen P, Bouron J, Amintas S, Thibault C, Moranvillier I, Laharanne E, Merlio JP, Guyonnet-Duperat V, Blouin JM, Richard E, Dabernat S, Moreau-Gaudry F, Bedel A. Cell cycle arrest and p53 prevent ON-target megabase-scale rearrangements induced by CRISPR-Cas9. Nat Commun 2023; 14:4072. [PMID: 37429857 DOI: 10.1038/s41467-023-39632-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/22/2023] [Indexed: 07/12/2023] Open
Abstract
The CRISPR-Cas9 system has revolutionized our ability to precisely modify the genome and has led to gene editing in clinical applications. Comprehensive analysis of gene editing products at the targeted cut-site has revealed a complex spectrum of outcomes. ON-target genotoxicity is underestimated with standard PCR-based methods and necessitates appropriate and more sensitive detection methods. Here, we present two complementary Fluorescence-Assisted Megabase-scale Rearrangements Detection (FAMReD) systems that enable the detection, quantification, and cell sorting of edited cells with megabase-scale loss of heterozygosity (LOH). These tools reveal rare complex chromosomal rearrangements caused by Cas9-nuclease and show that LOH frequency depends on cell division rate during editing and p53 status. Cell cycle arrest during editing suppresses the occurrence of LOH without compromising editing. These data are confirmed in human stem/progenitor cells, suggesting that clinical trials should consider p53 status and cell proliferation rate during editing to limit this risk by designing safer protocols.
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Affiliation(s)
- G Cullot
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
| | - J Boutin
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
- CHU de Bordeaux, Biochemistry Laboratory, F-33000, Bordeaux, France
| | - S Fayet
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
| | - F Prat
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
| | - J Rosier
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
| | - D Cappellen
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
- CHU de Bordeaux, Tumor Biology and Tumor Bank Laboratory, F-33000, Bordeaux, France
| | - I Lamrissi
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
| | - P Pennamen
- CHU de Bordeaux, department of medical genetics, F-33000, Bordeaux, France
| | - J Bouron
- CHU de Bordeaux, department of medical genetics, F-33000, Bordeaux, France
| | - S Amintas
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
- CHU de Bordeaux, Tumor Biology and Tumor Bank Laboratory, F-33000, Bordeaux, France
| | - C Thibault
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
| | - I Moranvillier
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
| | - E Laharanne
- CHU de Bordeaux, Tumor Biology and Tumor Bank Laboratory, F-33000, Bordeaux, France
| | - J P Merlio
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
- CHU de Bordeaux, Tumor Biology and Tumor Bank Laboratory, F-33000, Bordeaux, France
| | - V Guyonnet-Duperat
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
- Vect'UB, vectorology platform, INSERM US 005-CNRS UAR 3427-TBM-Core, Bordeaux university, Bordeaux, France
| | - J M Blouin
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
- CHU de Bordeaux, Biochemistry Laboratory, F-33000, Bordeaux, France
| | - E Richard
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
- CHU de Bordeaux, Biochemistry Laboratory, F-33000, Bordeaux, France
| | - S Dabernat
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France
- CHU de Bordeaux, Biochemistry Laboratory, F-33000, Bordeaux, France
| | - F Moreau-Gaudry
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France.
- CHU de Bordeaux, Biochemistry Laboratory, F-33000, Bordeaux, France.
| | - A Bedel
- Bordeaux University, INSERM, BRIC, U1312, F-33000, Bordeaux, France.
- CHU de Bordeaux, Biochemistry Laboratory, F-33000, Bordeaux, France.
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10
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Fu M, Chen M, Guo N, Lin M, Li Y, Huang H, Cai M, Xu L. Molecular genetic analysis of 1,980 cases of male infertility. Exp Ther Med 2023; 26:345. [PMID: 37383371 PMCID: PMC10294593 DOI: 10.3892/etm.2023.12044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/17/2023] [Indexed: 06/30/2023] Open
Abstract
The present study aimed to investigate the occurrence of chromosomal karyotype abnormalities and azoospermia factor (AZF) microdeletion on the long arm of the Y chromosome (Yq) in infertile men, and to determine their association with infertility to ultimately improve clinical outcomes in these patients. A total of 1,980 azoospermic and oligospermic men from the outpatient department of the Fujian Maternity and Child Health Hospital (Fuzhou, China) were recruited between January 2016 and December 2019. Peripheral blood was used for karyotype analysis; AZF microdeletion analysis of the Yq was performed using capillary electrophoresis. Among the 1,980 patients, 178 had chromosomal abnormalities (9.0%; 178/1,980), of whom 98 had an abnormal number of chromosomes. Among the abnormal karyotypes, the most common was 47, XXY (80/178; 44.9%). AZF microdeletion on the Yq occurred at a rate of 10.66% (211/1,980); the most common type was the AZFb/c deletion (sY1192; 140/211; 66.4%). The present findings showed that karyotype abnormalities and AZF gene microdeletion are important drivers of male infertility. Specifically, men with Yqh- and del(Y)(q11) had a higher risk of AZF microdeletion. These results suggested that patient treatment could be personalized based on routine molecular genetic analysis, which could further alleviate the economic and emotional burden of undergoing redundant or ineffective treatments.
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Affiliation(s)
- Meimei Fu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou, Fujian 350001, P.R. China
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou, Fujian 350001, P.R. China
| | - Nan Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou, Fujian 350001, P.R. China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou, Fujian 350001, P.R. China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou, Fujian 350001, P.R. China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou, Fujian 350001, P.R. China
| | - Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou, Fujian 350001, P.R. China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou, Fujian 350001, P.R. China
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11
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Cui X, Li Y, Xu H, Sun Y, Jiang S, Li W. Characteristics of Hepatitis B virus integration and mechanism of inducing chromosome translocation. NPJ Genom Med 2023; 8:11. [PMID: 37268616 DOI: 10.1038/s41525-023-00355-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/23/2023] [Indexed: 06/04/2023] Open
Abstract
Hepatitis B virus (HBV) integration is closely associated with the onset and progression of tumors. This study utilized the DNA of 27 liver cancer samples for high-throughput Viral Integration Detection (HIVID), with the overarching goal of detecting HBV integration. KEGG pathway analysis of breakpoints was performed using the ClusterProfiler software. The breakpoints were annotated using the latest ANNOVAR software. We identified 775 integration sites and detected two new hotspot genes for virus integration, N4BP1 and WASHP, along with 331 new genes. Furthermore, we conducted a comprehensive analysis to determine the critical impact pathways of virus integration by combining our findings with the results of three major global studies on HBV integration. Meanwhile, we found common characteristics of virus integration hotspots among different ethnic groups. To specify the direct impact of virus integration on genomic instability, we explained the causes of inversion and the frequent occurrence of translocation due to HBV integration. This study detected a series of hotspot integration genes and specified common characteristics of critical hotspot integration genes. These hotspot genes are universal across different ethnic groups, providing an effective target for better research on the pathogenic mechanism. We also demonstrated more comprehensive key pathways affected by HBV integration and elucidated the mechanism for inversion and frequent translocation events due to virus integration. Apart from the great significance of the rule of HBV integration, the current study also provides valuable insights into the mechanism of virus integration.
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Affiliation(s)
- Xiaofang Cui
- Jining Medical University, Jining, Shandong, China
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Yiyan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hanshi Xu
- Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yuhui Sun
- BGI-Shenzhen, 518083, Shenzhen, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Shandong First Medical University, Jining, China.
| | - Weiyang Li
- Jining Medical University, Jining, Shandong, China.
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China.
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12
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Ait Saada A, Guo W, Costa AB, Yang J, Wang J, Lobachev K. Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions. Nucleic Acids Res 2023; 51:3722-3734. [PMID: 36919609 PMCID: PMC10164571 DOI: 10.1093/nar/gkad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
DNA inverted repeats (IRs) are widespread across many eukaryotic genomes. Their ability to form stable hairpin/cruciform secondary structures is causative in triggering chromosome instability leading to several human diseases. Distance and sequence divergence between IRs are inversely correlated with their ability to induce gross chromosomal rearrangements (GCRs) because of a lesser probability of secondary structure formation and chromosomal breakage. In this study, we demonstrate that structural parameters that normally constrain the instability of IRs are overcome when the repeats interact in single-stranded DNA (ssDNA). We established a system in budding yeast whereby >73 kb of ssDNA can be formed in cdc13-707fs mutants. We found that in ssDNA, 12 bp or 30 kb spaced Alu-IRs show similarly high levels of GCRs, while heterology only beyond 25% suppresses IR-induced instability. Mechanistically, rearrangements arise after cis-interaction of IRs leading to a DNA fold-back and the formation of a dicentric chromosome, which requires Rad52/Rad59 for IR annealing as well as Rad1-Rad10, Slx4, Msh2/Msh3 and Saw1 proteins for nonhomologous tail removal. Importantly, using structural characteristics rendering IRs permissive to DNA fold-back in yeast, we found that ssDNA regions mapped in cancer genomes contain a substantial number of potentially interacting and unstable IRs.
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Affiliation(s)
- Anissia Ait Saada
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Wenying Guo
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alex B Costa
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jiaxin Yang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Kirill S Lobachev
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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13
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Pai CC, Durley SC, Cheng WC, Chiang NY, Peters J, Kasparek T, Blaikley E, Wee BY, Walker C, Kearsey SE, Buffa F, Murray JM, Humphrey TC. Homologous recombination suppresses transgenerational DNA end resection and chromosomal instability in fission yeast. Nucleic Acids Res 2023; 51:3205-3222. [PMID: 36951111 PMCID: PMC10123110 DOI: 10.1093/nar/gkad160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/13/2023] [Accepted: 02/23/2023] [Indexed: 03/24/2023] Open
Abstract
Chromosomal instability (CIN) drives cell-to-cell heterogeneity, and the development of genetic diseases, including cancer. Impaired homologous recombination (HR) has been implicated as a major driver of CIN, however, the underlying mechanism remains unclear. Using a fission yeast model system, we establish a common role for HR genes in suppressing DNA double-strand break (DSB)-induced CIN. Further, we show that an unrepaired single-ended DSB arising from failed HR repair or telomere loss is a potent driver of widespread CIN. Inherited chromosomes carrying a single-ended DSB are subject to cycles of DNA replication and extensive end-processing across successive cell divisions. These cycles are enabled by Cullin 3-mediated Chk1 loss and checkpoint adaptation. Subsequent propagation of unstable chromosomes carrying a single-ended DSB continues until transgenerational end-resection leads to fold-back inversion of single-stranded centromeric repeats and to stable chromosomal rearrangements, typically isochromosomes, or to chromosomal loss. These findings reveal a mechanism by which HR genes suppress CIN and how DNA breaks that persist through mitotic divisions propagate cell-to-cell heterogeneity in the resultant progeny.
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Affiliation(s)
- Chen-Chun Pai
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Samuel C Durley
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Wei-Chen Cheng
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Nien-Yi Chiang
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Jennifer Peters
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Torben Kasparek
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Elizabeth Blaikley
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Boon-Yu Wee
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Carol Walker
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Stephen E Kearsey
- Department of Biology, University of Oxford, Zoology Research and Administration Building, Mansfield Road, Oxford OX1 3SZ, UK
| | - Francesca Buffa
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Johanne M Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, SussexBN1 9RQ, UK
| | - Timothy C Humphrey
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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14
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Burssed B, Zamariolli M, Favilla BP, Meloni VA, Goloni-Bertollo EM, Bellucco FT, Melaragno MI. Fold-back mechanism originating inv-dup-del rearrangements in chromosomes 13 and 15. Chromosome Res 2023; 31:10. [PMID: 36826604 DOI: 10.1007/s10577-023-09720-0] [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: 12/21/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/25/2023]
Abstract
Intrachromosomal rearrangements involve a single chromosome and can be formed by several proposed mechanisms. We reported two patients with intrachromosomal duplications and deletions, whose rearrangements and breakpoints were characterized through karyotyping, chromosomal microarray, fluorescence in situ hybridization, whole-genome sequencing, and Sanger sequencing. Inverted duplications associated with terminal deletions, known as inv-dup-del rearrangements, were found in 13q and 15q in these patients. The presence of microhomology at the junction points led to the proposal of the Fold-back mechanism for their formation. The use of different high-resolution techniques allowed for a better characterization of the rearrangements, with Sanger sequencing of the junction points being essential to infer the mechanisms of formation as it revealed microhomologies that were missed by the previous techniques. A karyotype-phenotype correlation was also performed for the characterized rearrangements.
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Affiliation(s)
- Bruna Burssed
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Bianca Pereira Favilla
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vera Ayres Meloni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Eny Maria Goloni-Bertollo
- Genetics and Molecular Biology Research Unit, Department of Molecular Biology, São José Do Rio Preto Medical School, São José Do Rio Preto, Brazil
| | - Fernanda Teixeira Bellucco
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil.
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15
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Schuy J, Grochowski CM, Carvalho CMB, Lindstrand A. Complex genomic rearrangements: an underestimated cause of rare diseases. Trends Genet 2022; 38:1134-1146. [PMID: 35820967 PMCID: PMC9851044 DOI: 10.1016/j.tig.2022.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/12/2022] [Accepted: 06/06/2022] [Indexed: 01/24/2023]
Abstract
Complex genomic rearrangements (CGRs) are known contributors to disease but are often missed during routine genetic screening. Identifying CGRs requires (i) identifying copy number variants (CNVs) concurrently with inversions, (ii) phasing multiple breakpoint junctions incis, as well as (iii) detecting and resolving structural variants (SVs) within repeats. We demonstrate how combining cytogenetics and new sequencing methodologies is being successfully applied to gain insights into the genomic architecture of CGRs. In addition, we review CGR patterns and molecular features revealed by studying constitutional genomic disorders. These data offer invaluable lessons to individuals interested in investigating CGRs, evaluating their clinical relevance and frequency, as well as assessing their impact(s) on rare genetic diseases.
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Affiliation(s)
- Jakob Schuy
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Pacific Northwest Research Institute, Seattle, WA, USA
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
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16
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Bonaglia MC, Fichera M, Marelli S, Romaniello R, Zuffardi O. Low-level complex mosaic with multiple cell lines affecting the 18q21.31q21.32 region in a patient with de novo 18q terminal deletion. Eur J Med Genet 2022; 65:104596. [PMID: 36064004 DOI: 10.1016/j.ejmg.2022.104596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/31/2022] [Accepted: 08/17/2022] [Indexed: 11/15/2022]
Abstract
We describe a 5-year-old girl who was diagnosed at birth with 18q de novo homogeneous deletion at G-banding karyotype. Her clinical condition, characterized by hypotonia, psychomotor retardation, short stature, deafness secondary to bilateral atresia of the external auditory canals, was in agreement with the 18q deletion syndrome though presence of coloboma of a single eye only suggested a mosaic condition as an unusual sign. By combining multiple technologies including array-CGH, FISH, and WGS, we found that the terminal deletion 18q21.32q23 (21 Mb) was in segmental mosaicism of the proximal region 18q21.31q21.32 (2.7 Mb), which showed a variable number of copies: one, two, or three, in 7, 41 and 55% of the cells respectively. Breakpoint junction analysis demonstrated the presence of an inv-dup del (18q) with a disomic segment of 4.7 kb between the inverted and non-inverted copies of the duplicated region 18q21.31q21.32. From these results, we propose that all three types of abnormal chr18 (the inv-dup del and the two 18q terminal deletions of different sizes) arisen from breaks in a dicentric mirror chromosome 18q, either in more than one embryo cell or from subsequent breaking-fusion-bridge cycles. The duplication region was with identical polymorphisms as in all non-recurrent inv-dup del rearrangements though, in contrast with most of them, the 18q abnormality was of maternal origin. Taking into account that distal 18q deletions are not rarely associated with inv-dup del(18q) cell lines, and that the non-disjunction of chromosome 18 takes place especially at maternal meiosis II rather than meiosis I, multiple rescue events starting from trisomic zygotes could be considered alternative to the postmitotic ones. From the clinical point of view, our case, as well as those of del(18q) in mosaic with the dic(18q), shows that the final phenotype is the sum of the different cell lines that acted on embryonic development with signs typical of both the 18q deletion syndrome and trisomy 18. Asymmetrical malformations, such as coloboma of the iris only in the right eye, confirm the underlying mosaicism regardless of whether it is still detectable in the blood.
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Affiliation(s)
- Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy.
| | - Marco Fichera
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy; Oasi Research Institute-IRCCS, Troina, Italy.
| | - Susan Marelli
- Medical Genetics Service, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy.
| | - Romina Romaniello
- Neuropsychiatry and Neurorehabilitation Unit, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy.
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
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17
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Zuffardi O, Fichera M, Bonaglia MC. The embryo battle against adverse genomes: Are de novo terminal deletions the rescue of unfavorable zygotic imbalances? Eur J Med Genet 2022; 65:104532. [PMID: 35724817 DOI: 10.1016/j.ejmg.2022.104532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 04/02/2022] [Accepted: 05/21/2022] [Indexed: 11/03/2022]
Abstract
De novo distal deletions are structural variants considered to be already present in the zygote. However, investigations especially in the prenatal setting have documented that they are often in mosaic with cell lines in which the same deleted chromosome shows different types of aberrations such as: 1) neutral copy variants with loss of heterozygosity that replace the deleted region with equivalent portions of the homologous chromosome and create distal uniparental disomy (UPD); 2) derivative chromosomes where the deleted one ends with the distal region of another chromosome or has the shape of a ring; 3) U-type mirror dicentric or inv-dup del rearrangements. Unstable dicentrics had already been entailed as causative of terminal deletions even when no trace of the reciprocal inv-dup del had been detected. To clarify the mechanism of origin of distal deletions, we examined PubMed using as keywords: complex/mosaic chromosomal deletions, distal UPD, U-type dicentrics, inv-dup del chromosomes, excluding the recurrent inv-dup del(8p)s which are known to originate by NAHR at the maternal meiosis. The literature has shown that U-type dicentrics leading to nearly complete trisomy and therefore incompatible with zygotic survival underlie many types of de novo unbalanced rearrangements, including terminal deletions. In the early embryo, the position of the postzygotic breaks of the dicentric, the different ways of acquiring telomeres by the broken portions and the selection of the most favorable cell lines in the different tissues determine the prevalence of one or the other rearrangement. Multiple lines with simple terminal deletions, inv-dup dels, unbalanced translocations and segmental UPDs can coexist in various mosaic combinations although it is rare to identify them all in the blood. Regarding the origin of the dicentric, among the 30 cases of non-recurrent inv-dup del with sufficient genotyping information, paternal origin was markedly prevalent with consistently identical polymorphisms within the duplication region, regardless of parental origin. The non-random parental origin made any postzygotic origin unlikely and suggested the occurrence of these dicentrics mainly in spermatogenesis. This study strengthens the evidence that non-recurrent de novo structural rearrangements are often secondary to the rescue of a zygotic genome incompatible with embryo survival.
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Affiliation(s)
- Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
| | - Marco Fichera
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy; Oasi Research Institute-IRCCS, Troina, Italy.
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy.
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18
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Burssed B, Zamariolli M, Bellucco FT, Melaragno MI. Mechanisms of structural chromosomal rearrangement formation. Mol Cytogenet 2022; 15:23. [PMID: 35701783 PMCID: PMC9199198 DOI: 10.1186/s13039-022-00600-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/31/2022] [Indexed: 12/31/2022] Open
Abstract
Structural chromosomal rearrangements result from different mechanisms of formation, usually related to certain genomic architectural features that may lead to genetic instability. Most of these rearrangements arise from recombination, repair, or replication mechanisms that occur after a double-strand break or the stalling/breakage of a replication fork. Here, we review the mechanisms of formation of structural rearrangements, highlighting their main features and differences. The most important mechanisms of constitutional chromosomal alterations are discussed, including Non-Allelic Homologous Recombination (NAHR), Non-Homologous End-Joining (NHEJ), Fork Stalling and Template Switching (FoSTeS), and Microhomology-Mediated Break-Induced Replication (MMBIR). Their involvement in chromoanagenesis and in the formation of complex chromosomal rearrangements, inverted duplications associated with terminal deletions, and ring chromosomes is also outlined. We reinforce the importance of high-resolution analysis to determine the DNA sequence at, and near, their breakpoints in order to infer the mechanisms of formation of structural rearrangements and to reveal how cells respond to DNA damage and repair broken ends.
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Affiliation(s)
- Bruna Burssed
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernanda Teixeira Bellucco
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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19
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Cosenza MR, Rodriguez-Martin B, Korbel JO. Structural Variation in Cancer: Role, Prevalence, and Mechanisms. Annu Rev Genomics Hum Genet 2022; 23:123-152. [DOI: 10.1146/annurev-genom-120121-101149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Somatic rearrangements resulting in genomic structural variation drive malignant phenotypes by altering the expression or function of cancer genes. Pan-cancer studies have revealed that structural variants (SVs) are the predominant class of driver mutation in most cancer types, but because they are difficult to discover, they remain understudied when compared with point mutations. This review provides an overview of the current knowledge of somatic SVs, discussing their primary roles, prevalence in different contexts, and mutational mechanisms. SVs arise throughout the life history of cancer, and 55% of driver mutations uncovered by the Pan-Cancer Analysis of Whole Genomes project represent SVs. Leveraging the convergence of cell biology and genomics, we propose a mechanistic classification of somatic SVs, from simple to highly complex DNA rearrangement classes. The actions of DNA repair and DNA replication processes together with mitotic errors result in a rich spectrum of SV formation processes, with cascading effects mediating extensive structural diversity after an initiating DNA lesion has formed. Thanks to new sequencing technologies, including the sequencing of single-cell genomes, open questions about the molecular triggers and the biomolecules involved in SV formation as well as their mutational rates can now be addressed. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | | | - Jan O. Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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20
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Porubsky D, Höps W, Ashraf H, Hsieh P, Rodriguez-Martin B, Yilmaz F, Ebler J, Hallast P, Maria Maggiolini FA, Harvey WT, Henning B, Audano PA, Gordon DS, Ebert P, Hasenfeld P, Benito E, Zhu Q, Lee C, Antonacci F, Steinrücken M, Beck CR, Sanders AD, Marschall T, Eichler EE, Korbel JO. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 2022; 185:1986-2005.e26. [PMID: 35525246 PMCID: PMC9563103 DOI: 10.1016/j.cell.2022.04.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/14/2022] [Accepted: 04/08/2022] [Indexed: 12/13/2022]
Abstract
Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversions <2 kbp form by twin-priming during L1 retrotransposition; 80% of the larger inversions are balanced and affect twice as many nucleotides as CNVs. Balanced inversions show an excess of common variants, and 72% are flanked by segmental duplications (SDs) or retrotransposons. Since flanking repeats promote non-allelic homologous recombination, we developed complementary approaches to identify recurrent inversion formation. We describe 40 recurrent inversions encompassing 0.6% of the genome, showing inversion rates up to 2.7 × 10-4 per locus per generation. Recurrent inversions exhibit a sex-chromosomal bias and co-localize with genomic disorder critical regions. We propose that inversion recurrence results in an elevated number of heterozygous carriers and structural SD diversity, which increases mutability in the population and predisposes specific haplotypes to disease-causing CNVs.
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21
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Target enrichment long-read sequencing with adaptive sampling can determine the structure of the small supernumerary marker chromosomes. J Hum Genet 2022; 67:363-368. [PMID: 35027654 DOI: 10.1038/s10038-021-01004-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/05/2021] [Accepted: 12/04/2021] [Indexed: 12/23/2022]
Abstract
Structural analysis of small supernumerary marker chromosomes (sSMCs) has revealed that many have complex structures. Structural analysis of sSMCs by whole genome sequencing using short-read sequencers is challenging however because most present with a low level of mosaicism and consist of a small region of the involved chromosome. In this present study, we applied adaptive sampling using nanopore long-read sequencing technology to enrich the target region and thereby attempted to determine the structure of two sSMCs with complex structural rearrangements previously revealed by cytogenetic microarray. In adaptive sampling, simple specification of the target region in the FASTA file enables to identify whether or not the sequencing DNA is included in the target, thus promoting efficient long-read sequencing. To evaluate the target enrichment efficiency, we performed conventional pair-end short-read sequencing in parallel. Sequencing with adaptive sampling achieved a target enrichment at about a 11.0- to 11.5-fold higher coverage rate than conventional pair-end sequencing. This enabled us to quickly identify all breakpoint junctions and determine the exact sSMC structure as a ring chromosome. In addition to the microhomology and microinsertion at the junctions, we identified inverted repeat structure in both sSMCs, suggesting the common generation mechanism involving replication impairment. Adaptive sampling is thus an easy and beneficial method of determining the structures of complex chromosomal rearrangements.
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22
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Dierckxsens N, Li T, Vermeesch JR, Xie Z. A benchmark of structural variation detection by long reads through a realistic simulated model. Genome Biol 2021; 22:342. [PMID: 34911553 PMCID: PMC8672642 DOI: 10.1186/s13059-021-02551-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
Accurate simulations of structural variation distributions and sequencing data are crucial for the development and benchmarking of new tools. We develop Sim-it, a straightforward tool for the simulation of both structural variation and long-read data. These simulations from Sim-it reveal the strengths and weaknesses for current available structural variation callers and long-read sequencing platforms. With these findings, we develop a new method (combiSV) that can combine the results from structural variation callers into a superior call set with increased recall and precision, which is also observed for the latest structural variation benchmark set developed by the GIAB Consortium.
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Affiliation(s)
- Nicolas Dierckxsens
- Center for Human Genetics, University Hospital Leuven and KU Leuven, Leuven, Belgium. .,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
| | - Tong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Joris R Vermeesch
- Center for Human Genetics, University Hospital Leuven and KU Leuven, Leuven, Belgium
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
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23
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Papenhausen PR, Kelly CA, Harris S, Caldwell S, Schwartz S, Penton A. Clinical significance and mechanisms associated with segmental UPD. Mol Cytogenet 2021; 14:38. [PMID: 34284807 PMCID: PMC8290618 DOI: 10.1186/s13039-021-00555-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/22/2021] [Indexed: 11/14/2022] Open
Abstract
Whole chromosome uniparental disomy (UPD) has been well documented with mechanisms largely understood. However, the etiology of segmental limited UPD (segUPD) is not as clear. In a 10-year period of confirming (> 300) cases of whole chromosome UPD, we identified 86 segmental cases in both prenatal and postnatal samples. Thirty-two of these cases showed mosaic segmental UPD at 11p due to somatic selection associated with Beckwith–Wiedemann syndrome. This study focuses on apparent mechanisms associated with the remaining cases, many of which appear to represent corrections of genomic imbalance such as deletions and derivative chromosomes. In some cases, segmental UPD was associated with the generation of additional genomic imbalance while in others it apparently resulted in restoration of euploidy. Multiple tests utilizing noninvasive prenatal testing (NIPT), chorionic villus sampling (CVS) and amniotic fluid samples from the same pregnancy revealed temporal evidence of correction and a “hotspot” at 1p. Although in many cases the genomic imbalance was dosage “repaired” in the analyzed tissue, clinical effects could be sustained due to early developmental effects of the original imbalance or due to its continued existence in other tissues. In addition, if correction did not occur in the gametes there would be recurrence risks for the offspring of those individuals. Familial microarray allele patterns are presented that differentiate lack of gamete correction from somatic derived gonadal mosaicism. These results suggest that the incidence of segUPD mediated correction is underestimated and may explain the etiology of some clinical phenotypes which are undetected by routine microarray analysis and many exome sequencing studies.
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Affiliation(s)
- Peter R Papenhausen
- Cytogenetics Department, Laboratory Corporation of America, Research Triangle Park, NC, 27709, USA
| | - Carla A Kelly
- Cytogenetics Department, Laboratory Corporation of America, Research Triangle Park, NC, 27709, USA
| | - Samuel Harris
- Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Samantha Caldwell
- Cytogenetics Department, Laboratory Corporation of America, Research Triangle Park, NC, 27709, USA
| | - Stuart Schwartz
- Cytogenetics Department, Laboratory Corporation of America, Research Triangle Park, NC, 27709, USA
| | - Andrea Penton
- Cytogenetics Department, Laboratory Corporation of America, Research Triangle Park, NC, 27709, USA.
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24
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Genomic profiling of platinum-resistant ovarian cancer: The road into druggable targets. Semin Cancer Biol 2020; 77:29-41. [PMID: 33161141 DOI: 10.1016/j.semcancer.2020.10.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 02/07/2023]
Abstract
Ovarian cancer is the most lethal gynecologic cancer. High-grade serous carcinoma (HGSC) is the most frequent histologic subtype and while it is a highly platinum-sensitive cancer at initial treatment, nearly 90 % of stage IIIC patients recur in 5 years and eventually become resistant to platinum treatment. Historically, the definition of platinum-resistant disease is based on the time interval between last platinum therapy and recurrence shorter than 6 months. Nowadays the use of sophisticated imaging techniques and serum markers to detect recurrence makes the accuracy of this clinical definition less clear and even more debatable as we begin to better understand the molecular landscape of HGSC and markers of platinum resistance and sensitivity. HGSC is characterized by a low frequency of recurrent mutations, great genomic instability with widespread copy number variations, universal TP53 mutations, and homologous recombination deficiency in more than 50 % of cases. Platinum agents form DNA adducts and intra- and inter-strand cross-links in the DNA. Most of DNA repair pathways are involved at some point in the repair of platinum induced DNA damaging, most notably homologous recombination, Fanconi Anemia, and nucleotide excision repair pathways. Mechanisms of platinum resistance are related mostly to the limitation of platinum-DNA adduct formation by changing cellular pharmacology, and to the prevention of cell death after DNA damage due to alterations in DNA repair pathways and cell cycle regulation. Understanding these mechanisms of sensitivity and resistance may help to define the utility of platinum re-challenge in each situation and guide new therapeutic opportunities. Moreover, the discovery of mechanisms of synthetic lethality related to alterations in DNA repair and cell cycle regulation pathways has opened up a new avenue for drug therapy in the last decade. In the present article, we review pathways involved in platinum-induced DNA damage repair and their relationship with genomic alterations present in HGSC. Moreover, we report new treatment strategies that are underway to target these alterations.
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25
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Spealman P, Burrell J, Gresham D. Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy. Nucleic Acids Res 2020; 48:4940-4945. [PMID: 32255181 PMCID: PMC7229812 DOI: 10.1093/nar/gkaa206] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/14/2020] [Accepted: 04/03/2020] [Indexed: 12/27/2022] Open
Abstract
Inverted duplicated DNA sequences are a common feature of structural variants (SVs) and copy number variants (CNVs). Analysis of CNVs containing inverted duplicated DNA sequences using nanopore sequencing identified recurrent aberrant behavior characterized by low confidence, incorrect and missed base calls. Inverted duplicate DNA sequences in both yeast and human samples were observed to have systematic elevation in the electrical current detected at the nanopore, increased translocation rates and decreased sampling rates. The coincidence of inverted duplicated DNA sequences with dramatically reduced sequencing accuracy and an increased translocation rate suggests that secondary DNA structures may interfere with the dynamics of transit of the DNA through the nanopore.
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Affiliation(s)
- Pieter Spealman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Jaden Burrell
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
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26
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Li BZ, Putnam CD, Kolodner RD. Mechanisms underlying genome instability mediated by formation of foldback inversions in Saccharomyces cerevisiae. eLife 2020; 9:58223. [PMID: 32762846 PMCID: PMC7467729 DOI: 10.7554/elife.58223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/04/2020] [Indexed: 01/09/2023] Open
Abstract
Foldback inversions, also called inverted duplications, have been observed in human genetic diseases and cancers. Here, we used a Saccharomyces cerevisiae genetic system that generates gross chromosomal rearrangements (GCRs) mediated by foldback inversions combined with whole-genome sequencing to study their formation. Foldback inversions were mediated by formation of single-stranded DNA hairpins. Two types of hairpins were identified: small-loop hairpins that were suppressed by MRE11, SAE2, SLX1, and YKU80 and large-loop hairpins that were suppressed by YEN1, TEL1, SWR1, and MRC1. Analysis of CRISPR/Cas9-induced double strand breaks (DSBs) revealed that long-stem hairpin-forming sequences could form foldback inversions when proximal or distal to the DSB, whereas short-stem hairpin-forming sequences formed foldback inversions when proximal to the DSB. Finally, we found that foldback inversion GCRs were stabilized by secondary rearrangements, mostly mediated by different homologous recombination mechanisms including single-strand annealing; however, POL32-dependent break-induced replication did not appear to be involved forming secondary rearrangements.
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Affiliation(s)
- Bin-Zhong Li
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, San Diego, United States
| | - Christopher D Putnam
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, San Diego, United States.,Departments of Medicine, University of California School of Medicine, San Diego, San Diego, United States
| | - Richard David Kolodner
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, San Diego, United States.,Cellular and Molecular Medicine, University of California School of Medicine, San Diego, San Diego, United States.,Moores-UCSD Cancer Center, University of California School of Medicine, San Diego, San Diego, United States.,Institute of Genomic Medicine, University of California School of Medicine, San Diego, San Diego, United States
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27
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Todd RT, Selmecki A. Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs. eLife 2020; 9:e58349. [PMID: 32687060 PMCID: PMC7371428 DOI: 10.7554/elife.58349] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Previously, we identified long repeat sequences that are frequently associated with genome rearrangements, including copy number variation (CNV), in many diverse isolates of the human fungal pathogen Candida albicans (Todd et al., 2019). Here, we describe the rapid acquisition of novel, high copy number CNVs during adaptation to azole antifungal drugs. Single-cell karyotype analysis indicates that these CNVs appear to arise via a dicentric chromosome intermediate and breakage-fusion-bridge cycles that are repaired using multiple distinct long inverted repeat sequences. Subsequent removal of the antifungal drug can lead to a dramatic loss of the CNV and reversion to the progenitor genotype and drug susceptibility phenotype. These findings support a novel mechanism for the rapid acquisition of antifungal drug resistance and provide genomic evidence for the heterogeneity frequently observed in clinical settings.
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Affiliation(s)
- Robert T Todd
- Department of Microbiology and Immunology, University of Minnesota Medical SchoolMinneapolis, MinnesotaUnited States
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical SchoolMinneapolis, MinnesotaUnited States
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28
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Dutta M, Nakagawa H, Kato H, Maejima K, Sasagawa S, Nakano K, Sasaki-Oku A, Fujimoto A, Mateos RN, Patil A, Tanaka H, Miyano S, Yasuda T, Nakai K, Fujita M. Whole genome sequencing analysis identifies recurrent structural alterations in esophageal squamous cell carcinoma. PeerJ 2020; 8:e9294. [PMID: 32617189 PMCID: PMC7323713 DOI: 10.7717/peerj.9294] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/14/2020] [Indexed: 12/17/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the predominant type of esophageal cancer in the Asian region, including Japan. A previous study reported mutational landscape of Japanese ESCCs by using exome sequencing. However, somatic structural alterations were yet to be explored. To provide a comprehensive mutational landscape, we performed whole genome sequencing (WGS) analysis of biopsy specimens from 20 ESCC patients in a Japanese population. WGS analysis identified non-silent coding mutations of TP53, ZNF750 and FAT1 in ESCC. We detected six mutational signatures in ESCC, one of which showed significant association with smoking status. Recurrent structural variations, many of which were chromosomal deletions, affected genes such as LRP1B, TTC28, CSMD1, PDE4D, SDK1 and WWOX in 25%–30% of tumors. Somatic copy number amplifications at 11q13.3 (CCND1), 3q26.33 (TP63/SOX2), and 8p11.23 (FGFR1) and deletions at 9p21.3 (CDKN2A) were identified. Overall, these multi-dimensional view of genomic alterations improve the understanding of the ESCC development at molecular level and provides future prognosis and therapeutic implications for ESCC in Japan.
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Affiliation(s)
- Munmee Dutta
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroaki Kato
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kaoru Nakano
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Aya Sasaki-Oku
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akihiro Fujimoto
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Raúl Nicolás Mateos
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ashwini Patil
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroko Tanaka
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takushi Yasuda
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Kenta Nakai
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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29
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Kato T, Inagaki H, Miyai S, Suzuki F, Naru Y, Shinkai Y, Kato A, Kanyama K, Mizuno S, Muramatsu Y, Yamamoto T, Shinya M, Tazaki Y, Hiwatashi S, Ikeda T, Ozaki M, Kurahashi H. The involvement of U-type dicentric chromosomes in the formation of terminal deletions with or without adjacent inverted duplications. Hum Genet 2020; 139:1417-1427. [PMID: 32488466 DOI: 10.1007/s00439-020-02186-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/22/2020] [Indexed: 11/28/2022]
Abstract
An inverted duplication with a terminal deletion (inv-dup-del) is one of the complex constitutional structural rearrangements that can occur in a chromosome. Although breakages of dicentric chromosome have been suggested, the precise mechanism of this is yet to be fully understood. In our present study, we investigated the genomic structure of 10 inv-dup-del cases to elucidate this mechanism. Two recurrent 8p inv-dup-del cases harbored a large copy-number-neutral region between the duplication and deletion in common. Although the other non-recurrent cases did not appear to have this copy-number-neutral region, refined sequencing analysis identified that they contained a small intervening region at the junction between the inverted and non-inverted segment. The size of this small intervening region ranged from 1741 to 3728 bp. Combined with a presence of microhomology at the junction, a resolution of the replication fork stalling through template switching within the same replication fork is suggested. We further observed two cases with mosaicism of the dicentric chromosome and various structural rearrangements related to the dicentric chromosome. Refined analysis allowed us to identify different breakpoints on the same chromosome in the same case, implicating multiple rounds of U-type formation and its breakage. From these results, we propose that a replication-based mechanism generates unstable dicentric chromosomes and that their breakage leads to the formation of inv-dup-dels and other related derivative chromosomes.
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Affiliation(s)
- Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Syunsuke Miyai
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Fumihiko Suzuki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yuki Naru
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yasuko Shinkai
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Asuka Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Kazuo Kanyama
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Seiji Mizuno
- Department of Clinical Genetics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Kasugai, Japan
| | - Yukako Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Shinjuku, Japan
| | - Mitsuhisa Shinya
- Genetic Counseling Room, Kagoshima University Hospital, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine, Kagoshima, Japan
| | - Yukiko Tazaki
- Genetic Counseling Room, Kagoshima University Hospital, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine, Kagoshima, Japan
| | - Sayuri Hiwatashi
- Genetic Counseling Room, Kagoshima University Hospital, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine, Kagoshima, Japan
| | - Toshiro Ikeda
- Genetic Counseling Room, Kagoshima University Hospital, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine, Kagoshima, Japan
| | - Mamoru Ozaki
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan. .,Department of Clinical Genetics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Kasugai, Japan.
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30
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Identifying NAHR mechanism between two distinct Alu elements through breakpoint junction mapping by NGS. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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31
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Cleal K, Baird DM. Catastrophic Endgames: Emerging Mechanisms of Telomere-Driven Genomic Instability. Trends Genet 2020; 36:347-359. [PMID: 32294415 DOI: 10.1016/j.tig.2020.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/31/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022]
Abstract
When cells progress to malignancy, they must overcome a final telomere-mediated proliferative lifespan barrier called replicative crisis. Crisis is characterized by extensive telomere fusion that drives widespread genomic instability, mitotic arrest, hyperactivation of autophagy, and cell death. Recently, it has become apparent that that the resolution of dicentric chromosomes, which arise from telomere fusions during crisis, can initiate a sequence of events that leads to chromothripsis, a form of extreme genomic catastrophe. Chromothripsis is characterized by localized genomic regions containing tens to thousands of rearrangements and it is becoming increasingly apparent that chromothripsis occurs widely across tumor types and has a clinical impact. Here we discuss how telomere dysfunction can initiate genomic complexity and the emerging mechanisms of chromothripsis.
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Affiliation(s)
- Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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32
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Chromosome 3p Inverted Duplication with Terminal Deletion: Second Postnatal Case Report with Additional Clinical Features. Case Rep Genet 2019; 2019:5384295. [PMID: 31428485 PMCID: PMC6683815 DOI: 10.1155/2019/5384295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/26/2019] [Accepted: 07/11/2019] [Indexed: 12/05/2022] Open
Abstract
Distal deletions and duplications of 3p are individually well-characterized chromosome abnormalities. Here, we report an inverted duplication of 3p with an adjacent terminal 3p deletion in a 17-month-old girl who had prenatal intrauterine growth restriction and cardiac defects. Other findings included hemangiomas, neutropenia, umbilical hernia, hypotonia, gross motor delay, microcephaly, and ptosis. Family history was noncontributory. Microarray analysis revealed a 5.37 Mb deletion of chromosome bands 3p26.1 to 3p26.3 and a 13.68 Mb duplication of 3p24.3 to 3p26.1. FISH analysis confirmed that the duplication was inverted. Upon literature review, only one postnatal patient and one second trimester pregnancy have been reported with this finding. Many of our patient's features are present in both 3p deletion and 3p duplication syndromes, including congenital heart disease, growth restriction, microcephaly, hypotonia, and developmental delay. Our patient has additional features not commonly reported in 3p deletion or duplication patients, such as aortic dilation, hemangiomas, and neutropenia. The identification of this patient contributes to additional understanding of features associated with concurrent deletion and inverted duplication in the distal 3p chromosome. This report may assist clinicians working with patients who have constellations of similar features or similar cytogenomic abnormalities.
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33
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Cleal K, Jones RE, Grimstead JW, Hendrickson EA, Baird DM. Chromothripsis during telomere crisis is independent of NHEJ, and consistent with a replicative origin. Genome Res 2019; 29:737-749. [PMID: 30872351 PMCID: PMC6499312 DOI: 10.1101/gr.240705.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 03/11/2019] [Indexed: 01/02/2023]
Abstract
Telomere erosion, dysfunction, and fusion can lead to a state of cellular crisis characterized by large-scale genome instability. We investigated the impact of a telomere-driven crisis on the structural integrity of the genome by undertaking whole-genome sequence analyses of clonal populations of cells that had escaped crisis. Quantification of large-scale structural variants revealed patterns of rearrangement consistent with chromothripsis but formed in the absence of functional nonhomologous end-joining pathways. Rearrangements frequently consisted of short fragments with complex mutational patterns, with a repair topology that deviated from randomness showing preferential repair to local regions or exchange between specific loci. We find evidence of telomere involvement with an enrichment of fold-back inversions demarcating clusters of rearrangements. Our data suggest that chromothriptic rearrangements caused by a telomere crisis arise via a replicative repair process involving template switching.
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Affiliation(s)
- Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - Rhiannon E Jones
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - Julia W Grimstead
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
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34
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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: 9] [Impact Index Per Article: 1.5] [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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35
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De novo unbalanced translocations have a complex history/aetiology. Hum Genet 2018; 137:817-829. [DOI: 10.1007/s00439-018-1941-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022]
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36
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Pristyazhnyuk IE, Menzorov AG. Ring chromosomes: from formation to clinical potential. PROTOPLASMA 2018; 255:439-449. [PMID: 28894962 DOI: 10.1007/s00709-017-1165-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
Ring chromosomes (RCs) are circular DNA molecules, which occur rarely in eukaryotic nuclear genomes. Lilian Vaughan Morgan first described them in the fruit fly. Human embryos very seldom have RCs, about 1:50,000. Carriers of RCs may have varying degrees of symptoms, from healthy phenotype to serious pathologies in physical and intellectual development. Many authors describe common symptoms of RC presence: short stature and some developmental delay that could be described as a "ring chromosome syndrome." As a rule, RCs arise de novo through the end-joining of two DNA double-strand breaks, telomere-subtelomere junction, or inv dup del rearrangement in both meiosis and mitosis. There are family cases of RC inheritance. The presence of RCs causes numerous secondary chromosome rearrangements in vivo and in vitro. RCs can change their size, become lost, or increase their copy number and cause additional deletions, duplication, and translocations, affecting both RCs and other chromosomes. In this review, we examine RC inheritance, instability, mechanisms of formation, and potential clinical applications of artificially created RCs for large-scale chromosome rearrangement treatment.
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Affiliation(s)
- Inna E Pristyazhnyuk
- Sector of Genomic Mechanisms of Ontogenesis, Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, 630090.
| | - Aleksei G Menzorov
- Sector of Cell Collections, Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, 630090
- Natural Sciences Department, Novosibirsk State University, Novosibirsk, Russia, 630090
- Research Institute of Medical Genetics, Tomsk National Research Medical Center Russian Academy of Sciences, Tomsk, Russia, 634050
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Cleal K, Norris K, Baird D. Telomere Length Dynamics and the Evolution of Cancer Genome Architecture. Int J Mol Sci 2018; 19:E482. [PMID: 29415479 PMCID: PMC5855704 DOI: 10.3390/ijms19020482] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 02/06/2023] Open
Abstract
Telomeres are progressively eroded during repeated rounds of cell division due to the end replication problem but also undergo additional more substantial stochastic shortening events. In most cases, shortened telomeres induce a cell-cycle arrest or trigger apoptosis, although for those cells that bypass such signals during tumour progression, a critical length threshold is reached at which telomere dysfunction may ensue. Dysfunction of the telomere nucleoprotein complex can expose free chromosome ends to the DNA double-strand break (DSB) repair machinery, leading to telomere fusion with both telomeric and non-telomeric loci. The consequences of telomere fusions in promoting genome instability have long been appreciated through the breakage-fusion-bridge (BFB) cycle mechanism, although recent studies using high-throughput sequencing technologies have uncovered evidence of involvement in a wider spectrum of genomic rearrangements including chromothripsis. A critical step in cancer progression is the transition of a clone to immortality, through the stabilisation of the telomere repeat array. This can be achieved via the reactivation of telomerase, or the induction of the alternative lengthening of telomeres (ALT) pathway. Whilst telomere dysfunction may promote genome instability and tumour progression, by limiting the replicative potential of a cell and enforcing senescence, telomere shortening can act as a tumour suppressor mechanism. However, the burden of senescent cells has also been implicated as a driver of ageing and age-related pathology, and in the promotion of cancer through inflammatory signalling. Considering the critical role of telomere length in governing cancer biology, we review questions related to the prognostic value of studying the dynamics of telomere shortening and fusion, and discuss mechanisms and consequences of telomere-induced genome rearrangements.
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Affiliation(s)
- Kez Cleal
- Division of Cancer and Genetics, School of Medicine, UHW Main Building, Cardiff CF14 4XN, UK.
| | - Kevin Norris
- Division of Cancer and Genetics, School of Medicine, UHW Main Building, Cardiff CF14 4XN, UK.
| | - Duncan Baird
- Division of Cancer and Genetics, School of Medicine, UHW Main Building, Cardiff CF14 4XN, UK.
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38
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Grygalewicz B, Woroniecka R, Rymkiewicz G, Rygier J, Borkowska K, Kotyl A, Blachnio K, Bystydzienski Z, Nowakowska B, Pienkowska-Grela B. The 11q-Gain/Loss Aberration Occurs Recurrently in MYC-Negative Burkitt-like Lymphoma With 11q Aberration, as Well as MYC-Positive Burkitt Lymphoma and MYC-Positive High-Grade B-Cell Lymphoma, NOS. Am J Clin Pathol 2017; 149:17-28. [PMID: 29272887 PMCID: PMC5848380 DOI: 10.1093/ajcp/aqx139] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Objectives The latest revision of lymphoma’s World Health Organization classification describes the new provisional entity “Burkitt-like lymphoma with 11q aberration” (BLL, 11q) as lacking MYC rearrangement, but harboring the specific11q-gain/loss aberration. We report genetic characteristics of 11 lymphoma cases with this aberration. Methods Classical cytogenetics, fluorescence in situ hybridization (FISH), and single nucleotide polymorphism/array comparative genomic hybridization. Results The 11q aberrations were described as duplication, inversion, and deletion. Array comparative genomic hybridization showed two types of duplication: bigger than 50 megabase pairs (Mbp) and smaller than 20 Mbp, which were associated with bulky tumor larger than 20 cm and amplification of the 11q23.3 region, including KMT2A. Six cases revealed a normal FISH status of MYC and were diagnosed as BLL,11q. Five cases showed MYC rearrangement and were diagnosed as Burkitt lymphoma (BL) or high-grade B-cell lymphoma, not otherwise specified (HGBL, NOS). Conclusions The 11q-gain/loss is not specific for BLL, 11q, but occurs recurrently in MYC-positive BL and MYC-positive HGBL.
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Affiliation(s)
- Beata Grygalewicz
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Renata Woroniecka
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Grzegorz Rymkiewicz
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
- Flow Cytometry Laboratory, Pathology and Laboratory Diagnostics Department, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Jolanta Rygier
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Klaudia Borkowska
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Aleksandra Kotyl
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Katarzyna Blachnio
- Flow Cytometry Laboratory, Pathology and Laboratory Diagnostics Department, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Zbigniew Bystydzienski
- Flow Cytometry Laboratory, Pathology and Laboratory Diagnostics Department, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Beata Nowakowska
- Department of Medical Genetics, Mother and Child Institute, Warsaw, Poland
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39
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Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes. Nat Genet 2017; 49:856-865. [DOI: 10.1038/ng.3849] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 03/28/2017] [Indexed: 12/15/2022]
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40
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Carvalho CMB, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet 2016; 17:224-38. [PMID: 26924765 DOI: 10.1038/nrg.2015.25] [Citation(s) in RCA: 406] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, MG 30190-002, Brazil
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Texas Children's Hospital, Houston, Texas 77030, USA
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41
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Whole-Genome Sequencing Reveals Diverse Models of Structural Variations in Esophageal Squamous Cell Carcinoma. Am J Hum Genet 2016; 98:256-74. [PMID: 26833333 PMCID: PMC4746371 DOI: 10.1016/j.ajhg.2015.12.013] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 12/15/2015] [Indexed: 01/02/2023] Open
Abstract
Comprehensive identification of somatic structural variations (SVs) and understanding their mutational mechanisms in cancer might contribute to understanding biological differences and help to identify new therapeutic targets. Unfortunately, characterization of complex SVs across the whole genome and the mutational mechanisms underlying esophageal squamous cell carcinoma (ESCC) is largely unclear. To define a comprehensive catalog of somatic SVs, affected target genes, and their underlying mechanisms in ESCC, we re-analyzed whole-genome sequencing (WGS) data from 31 ESCCs using Meerkat algorithm to predict somatic SVs and Patchwork to determine copy-number changes. We found deletions and translocations with NHEJ and alt-EJ signature as the dominant SV types, and 16% of deletions were complex deletions. SVs frequently led to disruption of cancer-associated genes (e.g., CDKN2A and NOTCH1) with different mutational mechanisms. Moreover, chromothripsis, kataegis, and breakage-fusion-bridge (BFB) were identified as contributing to locally mis-arranged chromosomes that occurred in 55% of ESCCs. These genomic catastrophes led to amplification of oncogene through chromothripsis-derived double-minute chromosome formation (e.g., FGFR1 and LETM2) or BFB-affected chromosomes (e.g., CCND1, EGFR, ERBB2, MMPs, and MYC), with approximately 30% of ESCCs harboring BFB-derived CCND1 amplification. Furthermore, analyses of copy-number alterations reveal high frequency of whole-genome duplication (WGD) and recurrent focal amplification of CDCA7 that might act as a potential oncogene in ESCC. Our findings reveal molecular defects such as chromothripsis and BFB in malignant transformation of ESCCs and demonstrate diverse models of SVs-derived target genes in ESCCs. These genome-wide SV profiles and their underlying mechanisms provide preventive, diagnostic, and therapeutic implications for ESCCs.
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42
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Conover HN, Argueso JL. Contrasting mechanisms of de novo copy number mutagenesis suggest the existence of different classes of environmental copy number mutagens. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:3-9. [PMID: 26247157 DOI: 10.1002/em.21967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 07/05/2015] [Accepted: 07/07/2015] [Indexed: 05/23/2023]
Abstract
While gene copy number variations (CNVs) are abundant in the human genome, and often are associated with disease consequences, the mutagenic pathways and environmental exposures that cause these large structural mutations are understudied relative to conventional nucleotide substitutions in DNA. The members of the environmental mutagenesis community are currently seeking to remedy this deficiency, and there is a renewed interest in the development of mutagenicity assays to identify and characterize compounds that may induce de novo CNVs in humans. To achieve this goal, it is critically important to acknowledge that CNVs exist in two very distinct classes: nonrecurrent and recurrent CNVs. The goal of this commentary is to emphasize the deep contrasts that exist between the proposed pathways that lead to these two mutation classes. Nonrecurrent de novo CNVs originate primarily in mitotic cells through replication-dependent DNA repair pathways that involve microhomologies (<10 bp), and are detected at higher frequency in children of older fathers. In contrast, recurrent de novo CNVs are most often formed in meiotic cells through homologous recombination between nonallelic large low-copy repeats (>10,000 bp), without an associated paternal age effect. Given the biological differences between the two CNV classes, it is our belief that nonrecurrent and recurrent CN mutagens will probably differ substantially in their modes of action. Therefore, each CNV class may require their own uniquely designed assays, so that we as a field may succeed in uncovering the broadest possible spectrum of environmental CN mutagens.
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Affiliation(s)
- Hailey N Conover
- Department of Environmental and Radiological Health Sciences, Cell and Molecular Biology Graduate Program, Institute for Genome Architecture and Function, Colorado State University, Fort Collins, Colorado
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Cell and Molecular Biology Graduate Program, Institute for Genome Architecture and Function, Colorado State University, Fort Collins, Colorado
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43
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Liu Q, Hesson LB, Nunez AC, Packham D, Williams R, Ward RL, Sloane MA. A cryptic paracentric inversion of MSH2 exons 2-6 causes Lynch syndrome. Carcinogenesis 2015; 37:10-17. [PMID: 26498247 DOI: 10.1093/carcin/bgv154] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/19/2015] [Indexed: 12/28/2022] Open
Abstract
Lynch syndrome is an autosomal dominant disorder that predisposes carriers of DNA mismatch repair (MMR) gene mutations to early-onset cancer. Germline testing screens exons and splice sites for mutations, but does not examine introns or RNA transcripts for alterations. Pathogenic mutations have not been detected in ~30% of suspected Lynch syndrome cases with standard screening practices. We present a 38-year-old male with a clinicopathological and family history consistent with Lynch syndrome, including loss of MSH2 expression in his tumor. Germline testing revealed normal MSH2 coding sequence, splice sites and exon copy number, however, cDNA sequencing identified an aberrant MSH2 transcript lacking exons 2-6. An inversion PCR on germline DNA identified an ~18kb unbalanced, paracentric inversion within MSH2, with breakpoints in a long terminal repeat in intron 1 and an Alu repeat in intron 6. The 3' end of the inversion had a 1.2 kb deletion and an 8 bp insertion at the junction with intron 6. Screening of 55 additional Australian patients presenting with MSH2-deficient tumors who were negative in germline genetic tests for MSH2 mutations identified another inversion-positive patient. We propose an Alu-mediated recombination model to explain the origin of the inversion. Our study illustrates the potential value of cDNA screening to identify patients with cryptic MMR gene rearrangements, clarifies why standard testing may not detect some pathogenic alterations, and provides a genetic test for screening individuals with suspected Lynch syndrome that present with unexplained MSH2-deficient tumors.
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Affiliation(s)
- Qing Liu
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Luke B Hesson
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Andrea C Nunez
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Deborah Packham
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Rachel Williams
- Hereditary Cancer Clinic , Prince of Wales Hospital , Randwick, New South Wales 2031 , Australia and
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney New South Wales 2052, Australia.,Level 3 Brian Wilson Chancellery, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mathew A Sloane
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
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44
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Weckselblatt B, Rudd MK. Human Structural Variation: Mechanisms of Chromosome Rearrangements. Trends Genet 2015; 31:587-599. [PMID: 26209074 PMCID: PMC4600437 DOI: 10.1016/j.tig.2015.05.010] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 01/05/2023]
Abstract
Chromosome structural variation (SV) is a normal part of variation in the human genome, but some classes of SV can cause neurodevelopmental disorders. Analysis of the DNA sequence at SV breakpoints can reveal mutational mechanisms and risk factors for chromosome rearrangement. Large-scale SV breakpoint studies have become possible recently owing to advances in next-generation sequencing (NGS) including whole-genome sequencing (WGS). These findings have shed light on complex forms of SV such as triplications, inverted duplications, insertional translocations, and chromothripsis. Sequence-level breakpoint data resolve SV structure and determine how genes are disrupted, fused, and/or misregulated by breakpoints. Recent improvements in breakpoint sequencing have also revealed non-allelic homologous recombination (NAHR) between paralogous long interspersed nuclear element (LINE) or human endogenous retrovirus (HERV) repeats as a cause of deletions, duplications, and translocations. This review covers the genomic organization of simple and complex constitutional SVs, as well as the molecular mechanisms of their formation.
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Affiliation(s)
- Brooke Weckselblatt
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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45
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Weckselblatt B, Hermetz KE, Rudd MK. Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis. Genome Res 2015; 25:937-47. [PMID: 26070663 PMCID: PMC4484391 DOI: 10.1101/gr.191247.115] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 05/15/2015] [Indexed: 12/17/2022]
Abstract
Unbalanced translocations are a relatively common type of copy number variation and a major contributor to neurodevelopmental disorders. We analyzed the breakpoints of 57 unique unbalanced translocations to investigate the mechanisms of how they form. Fifty-one are simple unbalanced translocations between two different chromosome ends, and six rearrangements have more than three breakpoints involving two to five chromosomes. Sequencing 37 breakpoint junctions revealed that simple translocations have between 0 and 4 base pairs (bp) of microhomology (n = 26), short inserted sequences (n = 8), or paralogous repeats (n = 3) at the junctions, indicating that translocations do not arise primarily from nonallelic homologous recombination but instead form most often via nonhomologous end joining or microhomology-mediated break-induced replication. Three simple translocations fuse genes that are predicted to produce in-frame transcripts of SIRPG-WWOX, SMOC2-PROX1, and PIEZO2-MTA1, which may lead to gain of function. Three complex translocations have inversions, insertions, and multiple breakpoint junctions between only two chromosomes. Whole-genome sequencing and fluorescence in situ hybridization analysis of two de novo translocations revealed at least 18 and 33 breakpoints involving five different chromosomes. Breakpoint sequencing of one maternally inherited translocation involving four chromosomes uncovered multiple breakpoints with inversions and insertions. All of these breakpoint junctions had 0-4 bp of microhomology consistent with chromothripsis, and both de novo events occurred on paternal alleles. Together with other studies, these data suggest that germline chromothripsis arises in the paternal genome and may be transmitted maternally. Breakpoint sequencing of our large collection of chromosome rearrangements provides a comprehensive analysis of the molecular mechanisms behind translocation formation.
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Affiliation(s)
- Brooke Weckselblatt
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Karen E Hermetz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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46
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Tan RNGB, Witlox RSGM, Hilhorst-Hofstee Y, Peeters-Scholte CMPCD, den Hollander NS, Ruivenkamp CAL, Hoffer MJ, Hansson KB, van Roosmalen MJ, Kloosterman WP, Santen GWE. Clinical and molecular characterization of an infant with a tandem duplication and deletion of 19p13. Am J Med Genet A 2015; 167A:1884-9. [DOI: 10.1002/ajmg.a.37076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 03/06/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Ratna N. G. B. Tan
- Department of Pediatrics; Leiden University Medical Center; Leiden the Netherlands
| | | | | | | | | | | | - Mariëtte J.V. Hoffer
- Department of Clinical Genetics; Leiden University Medical Center; Leiden the Netherlands
| | - Kerstin B. Hansson
- Department of Clinical Genetics; Leiden University Medical Center; Leiden the Netherlands
| | - Mark J. van Roosmalen
- Center for Molecular Medicine; Department of Medical Genetics; University Medical Center Utrecht; Utrecht the Netherlands
| | - Wigard P. Kloosterman
- Center for Molecular Medicine; Department of Medical Genetics; University Medical Center Utrecht; Utrecht the Netherlands
| | - Gijs W. E. Santen
- Department of Clinical Genetics; Leiden University Medical Center; Leiden the Netherlands
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47
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Escaramís G, Docampo E, Rabionet R. A decade of structural variants: description, history and methods to detect structural variation. Brief Funct Genomics 2015; 14:305-14. [PMID: 25877305 DOI: 10.1093/bfgp/elv014] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In the past decade, the view on genomic structural variation (SV) has been changed completely. SVs, previously considered rare events, are now recognized as the largest source of interindividual genetic variation affecting more bases than single nucleotide polymorphisms, variable number of tandem repeats and other small genetic variants. They have also been shown to play a role in phenotypic variation and in disease. In this review, the authors will provide an introduction to SV; a short historical perspective on the research of this source of genomic variation; a description of the types of structural variants, and on how they may have arisen; and an overview on methods of detecting structural variants, focusing on the analysis of high-throughput sequencing data.
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48
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Zampini É, Lepage É, Tremblay-Belzile S, Truche S, Brisson N. Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans. Genome Res 2015; 25:645-54. [PMID: 25800675 PMCID: PMC4417113 DOI: 10.1101/gr.188573.114] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/19/2015] [Indexed: 12/15/2022]
Abstract
Failure to maintain organelle genome stability has been linked to numerous phenotypes, including variegation and cytosolic male sterility (CMS) in plants, as well as cancer and neurodegenerative diseases in mammals. Here we describe a next-generation sequencing approach that precisely maps and characterizes organelle DNA rearrangements in a single genome-wide experiment. In addition to displaying global portraits of genomic instability, it surprisingly unveiled an abundance of short-range rearrangements in Arabidopsis thaliana and human organelles. Among these, short-range U-turn-like inversions reach 25% of total rearrangements in wild-type Arabidopsis plastids and 60% in human mitochondria. Furthermore, we show that replication stress correlates with the accumulation of this type of rearrangement, suggesting that U-turn-like rearrangements could be the outcome of a replication-dependent mechanism. We also show that U-turn-like rearrangements are mostly generated using microhomologies and are repressed in plastids by Whirly proteins WHY1 and WHY3. A synergistic interaction is also observed between the genes for the plastid DNA recombinase RECA1 and those encoding plastid Whirly proteins, and the triple mutant why1why3reca1 accumulates almost 60 times the WT levels of U-turn-like rearrangements. We thus propose that the process leading to U-turn-like rearrangements may constitute a RecA-independent mechanism to restart stalled forks. Our results reveal that short-range rearrangements, and especially U-turn-like rearrangements, are a major factor of genomic instability in organelles, and this raises the question of whether they could have been underestimated in diseases associated with mitochondrial dysfunction.
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Affiliation(s)
- Éric Zampini
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada H3C 3J7
| | - Étienne Lepage
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada H3C 3J7
| | - Samuel Tremblay-Belzile
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada H3C 3J7
| | - Sébastien Truche
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada H3C 3J7
| | - Normand Brisson
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada H3C 3J7
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Complex genomic rearrangements at the PLP1 locus include triplication and quadruplication. PLoS Genet 2015; 11:e1005050. [PMID: 25749076 PMCID: PMC4352052 DOI: 10.1371/journal.pgen.1005050] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/02/2015] [Indexed: 02/07/2023] Open
Abstract
Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals-16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology-or homeology-driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.
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50
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Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints. Am J Hum Genet 2015; 96:208-20. [PMID: 25640679 DOI: 10.1016/j.ajhg.2014.12.017] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/15/2014] [Indexed: 11/23/2022] Open
Abstract
Interpreting the genomic and phenotypic consequences of copy-number variation (CNV) is essential to understanding the etiology of genetic disorders. Whereas deletion CNVs lead obviously to haploinsufficiency, duplications might cause disease through triplosensitivity, gene disruption, or gene fusion at breakpoints. The mutational spectrum of duplications has been studied at certain loci, and in some cases these copy-number gains are complex chromosome rearrangements involving triplications and/or inversions. However, the organization of clinically relevant duplications throughout the genome has yet to be investigated on a large scale. Here we fine-mapped 184 germline duplications (14.7 kb-25.3 Mb; median 532 kb) ascertained from individuals referred for diagnostic cytogenetics testing. We performed next-generation sequencing (NGS) and whole-genome sequencing (WGS) to sequence 130 breakpoints from 112 subjects with 119 CNVs and found that most (83%) were tandem duplications in direct orientation. The remainder were triplications embedded within duplications (8.4%), adjacent duplications (4.2%), insertional translocations (2.5%), or other complex rearrangements (1.7%). Moreover, we predicted six in-frame fusion genes at sequenced duplication breakpoints; four gene fusions were formed by tandem duplications, one by two interconnected duplications, and one by duplication inserted at another locus. These unique fusion genes could be related to clinical phenotypes and warrant further study. Although most duplications are positioned head-to-tail adjacent to the original locus, those that are inverted, triplicated, or inserted can disrupt or fuse genes in a manner that might not be predicted by conventional copy-number assays. Therefore, interpreting the genetic consequences of duplication CNVs requires breakpoint-level analysis.
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