1
|
Hu Q, Espejo Valle-Inclán J, Dahiya R, Guyer A, Mazzagatti A, Maurais EG, Engel JL, Lu H, Davis AJ, Cortés-Ciriano I, Ly P. Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors. Nat Commun 2024; 15:5611. [PMID: 38965240 PMCID: PMC11224358 DOI: 10.1038/s41467-024-49985-5] [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: 08/02/2023] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Mitotic errors generate micronuclei entrapping mis-segregated chromosomes, which are susceptible to catastrophic fragmentation through chromothripsis. The reassembly of fragmented chromosomes by error-prone DNA double-strand break (DSB) repair generates diverse genomic rearrangements associated with human diseases. How specific repair pathways recognize and process these lesions remains poorly understood. Here we use CRISPR/Cas9 to systematically inactivate distinct DSB repair pathways and interrogate the rearrangement landscape of fragmented chromosomes. Deletion of canonical non-homologous end joining (NHEJ) components substantially reduces complex rearrangements and shifts the rearrangement landscape toward simple alterations without the characteristic patterns of chromothripsis. Following reincorporation into the nucleus, fragmented chromosomes localize within sub-nuclear micronuclei bodies (MN bodies) and undergo ligation by NHEJ within a single cell cycle. In the absence of NHEJ, chromosome fragments are rarely engaged by alternative end-joining or recombination-based mechanisms, resulting in delayed repair kinetics, persistent 53BP1-labeled MN bodies, and cell cycle arrest. Thus, we provide evidence supporting NHEJ as the exclusive DSB repair pathway generating complex rearrangements from mitotic errors.
Collapse
Affiliation(s)
- Qing Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jose Espejo Valle-Inclán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rashmi Dahiya
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alison Guyer
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alice Mazzagatti
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth G Maurais
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Justin L Engel
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huiming Lu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anthony J Davis
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
2
|
Vitetta G, Desiderio L, Baccolini I, Uliana V, Lanzoni G, Ghi T, Pilu G, Ambrosini E, Caggiati P, Barili V, Trotta AC, Liuti MR, Malpezzi E, Pittalis MC, Percesepe A. Mosaic derivative chromosomes at chorionic villi (CV) sampling are expression of genomic instability and precursors of cryptic disease-causing rearrangements: report of further four cases. Mol Cytogenet 2024; 17:8. [PMID: 38589928 PMCID: PMC11003029 DOI: 10.1186/s13039-024-00675-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/12/2024] [Indexed: 04/10/2024] Open
Abstract
Mosaic chromosomal anomalies arising in the product of conception and the final fetal chromosomal arrangement are expression of complex biological mechanisms. The rescue of unbalanced chromosome with selection of the most viable cell line/s in the embryo and the unfavourable imbalances in placental tissues was documented in our previous paper and in the literature. We report four additional cases with mosaic derivative chromosomes in different feto-placental tissues, further showing the instability of an intermediate gross imbalance as a frequent mechanism of de novo cryptic deletions and duplications. In conclusion we underline how the extensive remodeling of unbalanced chromosomes in placental tissues represents the 'backstage' of de novo structural rearrangements, as the early phases of a long selection process that the genome undergo during embryogenesis.
Collapse
Affiliation(s)
- Giulia Vitetta
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Laura Desiderio
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Ilaria Baccolini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Vera Uliana
- Medical Genetics Unit, University Hospital of Parma, Parma, Italy
| | - Giulia Lanzoni
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tullio Ghi
- Obstetrics & Gynecology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Gianluigi Pilu
- Obstetric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Enrico Ambrosini
- Medical Genetics Unit, University Hospital of Parma, Parma, Italy
| | | | - Valeria Barili
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | - Elisabetta Malpezzi
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Maria Carla Pittalis
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | - Antonio Percesepe
- Medical Genetics Unit, University Hospital of Parma, Parma, Italy
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| |
Collapse
|
3
|
Krupina K, Goginashvili A, Cleveland DW. Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements. Nat Rev Genet 2024; 25:196-210. [PMID: 37938738 PMCID: PMC10922386 DOI: 10.1038/s41576-023-00663-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 11/09/2023]
Abstract
Complex chromosome rearrangements, known as chromoanagenesis, are widespread in cancer. Based on large-scale DNA sequencing of human tumours, the most frequent type of complex chromosome rearrangement is chromothripsis, a massive, localized and clustered rearrangement of one (or a few) chromosomes seemingly acquired in a single event. Chromothripsis can be initiated by mitotic errors that produce a micronucleus encapsulating a single chromosome or chromosomal fragment. Rupture of the unstable micronuclear envelope exposes its chromatin to cytosolic nucleases and induces chromothriptic shattering. Found in up to half of tumours included in pan-cancer genomic analyses, chromothriptic rearrangements can contribute to tumorigenesis through inactivation of tumour suppressor genes, activation of proto-oncogenes, or gene amplification through the production of self-propagating extrachromosomal circular DNAs encoding oncogenes or genes conferring anticancer drug resistance. Here, we discuss what has been learned about the mechanisms that enable these complex genomic rearrangements and their consequences in cancer.
Collapse
Affiliation(s)
- Ksenia Krupina
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Alexander Goginashvili
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
| |
Collapse
|
4
|
Wang L, Dong B, Xie Y, Kang H, Wu Y. The molecular mechanisms of recombinant chromosome 18 with parental pericentric inversions and a review of the literature. J Hum Genet 2023; 68:625-634. [PMID: 37161033 DOI: 10.1038/s10038-023-01157-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/07/2023] [Accepted: 04/26/2023] [Indexed: 05/11/2023]
Abstract
Chromosomal rearrangements mostly result from non-allelic homologous recombination mediated by low-copy repeats (LCRs) or segmental duplications (SDs). Recent studies on recombinant chromosome 18 (rec (18)) have focused on diagnoses and clinical phenotypes. We diagnosed two cases of prenatal rec (18) and identified precise breakpoint intervals using karyotype and chromosomal microarray analyses. We analyzed the distribution characteristics of breakpoint repetitive elements to infer rearrangement mechanisms and reviewed relevant literature to identify genetic trends. Among the 12 families with 25 pregnancies analyzed, 68% rec (18), 24% spontaneous abortions, and 8% normal births were reported. In the 17 rec (18) cases, 65% presented maternal origin and 35% were paternal. Short-arm breakpoints at p11.31 were reported in 10 cases, whereas the long-arm breakpoints were located at q21.3 (6 cases) and q12 (4 cases). Breakpoints of pericentric inversions on chromosome 18 are concentrated in p11.31, q21.3, and q12 regions. Rearrangements at 18p11.31 are non-recurrent events. ALUs, LINE1s, and MIRs were enriched at the breakpoint regions (1.85 to 3.42-fold enrichment over the entire chromosome 18), while SDs and LCRs were absent. ALU subfamilies had sequence identities of 85.94% and 83.01% between two pair breakpoints. Small repetitive elements may mediate recombination-coupled DNA repair processes, facilitating rearrangements on chromosome 18. Maternal inversion carriers are more prone to abnormal recombination in prenatal families with rec (18). Recombinant chromosomes may present preferential segregation during gamete formation.
Collapse
Affiliation(s)
- Lingxi Wang
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China.
| | - Bing Dong
- Department of Eugenics, Meishan Women and Children's Hospital, Alliance Hospital of West China Second University Hospital, Sichuan University, Meishan, 620000, China
| | - Yamei Xie
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Han Kang
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yong Wu
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| |
Collapse
|
5
|
Hu Q, Valle-Inclan JE, Dahiya R, Guyer A, Mazzagatti A, Maurais EG, Engel JL, Cortés-Ciriano I, Ly P. Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552800. [PMID: 37609143 PMCID: PMC10441393 DOI: 10.1101/2023.08.10.552800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Errors in mitosis can generate micronuclei that entrap mis-segregated chromosomes, which are susceptible to catastrophic fragmentation through a process termed chromothripsis. The reassembly of fragmented chromosomes by error-prone DNA double-strand break (DSB) repair generates a spectrum of simple and complex genomic rearrangements that are associated with human cancers and disorders. How specific DSB repair pathways recognize and process these lesions remains poorly understood. Here we used CRISPR/Cas9 to systematically inactivate distinct DSB processing or repair pathways and interrogated the rearrangement landscape of fragmented chromosomes from micronuclei. Deletion of canonical non-homologous end joining (NHEJ) components, including DNA-PKcs, LIG4, and XLF, substantially reduced the formation of complex rearrangements and shifted the rearrangement landscape toward simple alterations without the characteristic patterns of cancer-associated chromothripsis. Following reincorporation into the nucleus, fragmented chromosomes localize within micronuclei bodies (MN bodies) and undergo successful ligation by NHEJ within a single cell cycle. In the absence of NHEJ, chromosome fragments were rarely engaged by polymerase theta-mediated alternative end-joining or recombination-based mechanisms, resulting in delayed repair kinetics and persistent 53BP1-labeled MN bodies in the interphase nucleus. Prolonged DNA damage signaling from unrepaired fragments ultimately triggered cell cycle arrest. Thus, we provide evidence supporting NHEJ as the exclusive DSB repair pathway generating complex rearrangements following chromothripsis from mitotic errors.
Collapse
Affiliation(s)
- Qing Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Jose Espejo Valle-Inclan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Rashmi Dahiya
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Alison Guyer
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Present address: Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Alice Mazzagatti
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Elizabeth G. Maurais
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Justin L. Engel
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| |
Collapse
|
6
|
Masson J, Pebrel-Richard C, Egloff M, Frétigny M, Beaumont M, Uguen K, Rollat-Farnier PA, Diguet F, Perthus I, Le Gudayer G, Haye D, Dupeyron MNB, Putoux A, Raskin-Champion F, Till M, Chatron N, Doray B, Bardel C, Vinciguerra C, Sanlaville D, Schluth-Bolard C. Familial transmission of chromoanagenesis leads to unpredictable unbalanced rearrangements through meiotic recombination. Clin Genet 2023; 103:401-412. [PMID: 36576162 DOI: 10.1111/cge.14291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Chromoanagenesis is a cellular mechanism that leads to complex chromosomal rearrangements (CCR) during a single catastrophic event. It may result in loss and/or gain of genetic material and may be responsible for various phenotypes. These rearrangements are usually sporadic. However, some familial cases have been reported. Here, we studied six families in whom an asymptomatic or paucisymptomatic parent transmitted a CCR to its offspring in an unbalanced manner. The rearrangements were characterized by karyotyping, fluorescent in situ hybridization, chromosomal microarray (CMA) and/or whole genome sequencing (WGS) in the carrier parents and offspring. We then hypothesized meiosis-pairing figures between normal and abnormal parental chromosomes that may have led to the formation of new unbalanced rearrangements through meiotic recombination. Our work indicates that chromoanagenesis might be associated with a normal phenotype and normal fertility, even in males, and that WGS may be the only way to identify these events when there is no imbalance. Subsequently, the CCR can be transmitted to the next generation in an unbalanced and unpredictable manner following meiotic recombination. Thereby, prenatal diagnosis using CMA should be proposed to these families to detect any pathogenic imbalances in the offspring.
Collapse
Affiliation(s)
- Julie Masson
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | | | | | - Mathilde Frétigny
- Service d'hématologie, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Bron, France
| | - Marion Beaumont
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Genetics and NIPT, Laboratoire Eylau-Unilabs, Neuilly-sur-Seine, France
| | - Kevin Uguen
- UMR 1078, GGB, CHU Brest, Inserm, Univ Brest, EFS, Brest, France
- Service de Génétique Médicale, CHRU de Brest, Brest, France
| | - Pierre-Antoine Rollat-Farnier
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Plateforme NGS, Hospices Civils de Lyon, Bron, France
| | - Flavie Diguet
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Isabelle Perthus
- Service de Génétique Médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | | | - Damien Haye
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Marie-Noëlle Bonnet Dupeyron
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Service de Génétique, CH de Valence, Valence, France
| | - Audrey Putoux
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Fabienne Raskin-Champion
- Service de Gynécologie Médicale et Obstétrique, Groupement Hospitalier Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Marianne Till
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Nicolas Chatron
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | - Bérénice Doray
- Service de Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Service de Génétique, CHU de la Réunion - Hôpital Félix Guyon, Saint-Denis, France
| | - Claire Bardel
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Plateforme NGS, Hospices Civils de Lyon, Bron, France
- ISPB, Université Claude Bernard Lyon 1, Lyon, France
| | - Christine Vinciguerra
- Service d'hématologie, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Bron, France
- ISPB, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Sanlaville
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | - Caroline Schluth-Bolard
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
- Laboratoires de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| |
Collapse
|
7
|
The spectrum of chromosomal translocations in the Arab world: ethnic-specific chromosomal translocations and their relevance to diseases. Chromosoma 2022; 131:127-146. [PMID: 35907041 PMCID: PMC9470631 DOI: 10.1007/s00412-022-00775-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/13/2022] [Accepted: 06/23/2022] [Indexed: 11/04/2022]
Abstract
Chromosomal translocations (CTs) are the most common type of structural chromosomal abnormalities in humans. CTs have been reported in several studies in the Arab world, but the frequency and spectrum of these translocations are not well characterized. The aim of this study is to conduct a systematic review to estimate the frequency and spectrum of CTs in the 22 Arab countries. Four literature databases were searched: PubMed, Science Direct, Scopus, and Web of Science, from the time of inception until July 2021. A combination of broad search terms was used to collect all possible CTs reported in the Arab world. In addition to the literature databases, all captured CTs were searched in three chromosomal rearrangement databases (Mitelman Database, CytoD 1.0 Database, and the Atlas of Genetics and Cytogenetics in Oncology and Hematology), along with PubMed and Google Scholar, to check whether the CTs are unique to the Arabs or shared between Arabs and non-Arabs. A total of 9,053 titles and abstracts were screened, of which 168 studies met our inclusion criteria, and 378 CTs were identified in 15 Arab countries, of which 57 CTs were unique to Arab patients. Approximately 89% of the identified CTs involved autosomal chromosomes. Three CTs, t(9;22), t(13;14), and t(14;18), showed the highest frequency, which were associated with hematological malignancies, recurrent pregnancy loss, and follicular lymphoma, respectively. Complex CTs were commonly reported among Arabs, with a total of 44 CTs, of which 12 were unique to Arabs. This is the first study to focus on the spectrum of CTs in the Arab world and compressively map the ethnic-specific CTs relevant to cancer. It seems that there is a distinctive genotype of Arabs with CTs, of which some manifested with unique clinical phenotypes. Although ethnic-specific CTs are highly relevant to disease mechanism, they are understudied and need to be thoroughly addressed.
Collapse
|
8
|
Li Y, Zhang G, Cui J. Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates. Viruses 2022; 14:v14071370. [PMID: 35891351 PMCID: PMC9323773 DOI: 10.3390/v14071370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 01/27/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are viral “fossils” in the human genome that originated from the ancient integration of exogenous retroviruses. Although HERVs have sporadically been reported in nonhuman primate genomes, their deep origination in pan-primates remains to be explored. Hence, based on the in silico genomic mining of full-length HERVs in 49 primates, we performed the largest systematic survey to date of the distribution, phylogeny, and functional predictions of HERVs. Most importantly, we obtained conclusive evidence of nonhuman origin for most contemporary HERVs. We found that various supergroups, including HERVW9, HUERSP, HSERVIII, HERVIPADP, HERVK, and HERVHF, were widely distributed in Strepsirrhini, Platyrrhini (New World monkeys) and Catarrhini (Old World monkeys and apes). We found that numerous HERVHFs are spread by vertical transmission within Catarrhini and one HERVHF was traced in 17 species, indicating its ancient nature. We also discovered that 164 HERVs were likely involved in genomic rearrangement and 107 HERVs were potentially coopted in the form of noncoding RNAs (ncRNAs) in humans. In summary, we provided comprehensive data on the deep origination of modern HERVs in pan-primates.
Collapse
Affiliation(s)
- Yian Li
- CAS Key Laboratory of Molecular Virology & Immunology, Institute Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai 200031, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-1353 Copenhagen, Denmark;
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Institute Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai 200031, China;
- Correspondence:
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Liang Y, Xie Y, Kong S, Pan Q, Qiu W, Wang D, Li M, Lin S, Liu Z, Sun X. Complex Chromosomal Rearrangement Causes Male Azoospermia: A Case Report and Literature Review. Front Genet 2022; 13:792539. [PMID: 35281846 PMCID: PMC8907855 DOI: 10.3389/fgene.2022.792539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Male carriers of complex chromosomal rearrangements (CCRs) may have decreased fertility and usually present with azoospermia, oligospermia or teratospermia.Methods: High-resolution karyotype analysis using G-banding on peripheral blood lymphocytes was performed in an azoospermic male. Copy number variations (CNVs) were detected by chromosomal microarray analysis, and genetic variations were determined by long-read nanopore sequencing with Sanger sequencing for breakpoint confirmation.Results: The karyotype of the patient was 46,XY,t(4;21)(p11;p11),t(5;6;14)(p13q22;p22q22;q22), which did not involve CNVs with clinical significance. Twelve breakpoints in chromosomes 5, 6, and 14 were found by long-read nanopore sequencing. Reports on 17 males carrying CCRs with azoospermia were also reviewed.Conclusion: The extent of asynaptic regions in synaptonemal complexes during pachytene and the disruption of genes involved in male gametogenesis may cause azoospermia in CCR carriers.
Collapse
Affiliation(s)
- Yi Liang
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shu Kong
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qianying Pan
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenjun Qiu
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ding Wang
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mengting Li
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Sisi Lin
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Zihang Liu
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Xiaofang Sun
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Xiaofang Sun,
| |
Collapse
|
11
|
Verdi G, Li D, Elsea SH, Nelson B, Bhoj EJ, Hakonarson H, Yearwood KR, Upadhya S, Gluschitz S, Smith JL, Sobering AK. A novel unbalanced translocation between chromosomes 5p and 18q leading to dysmorphology and global developmental delay. Mol Genet Genomic Med 2022; 10:e1900. [PMID: 35189041 PMCID: PMC9000934 DOI: 10.1002/mgg3.1900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/23/2021] [Accepted: 02/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background Individuals with various sized terminal duplications of chromosome 5p or terminal deletions of chromosome 18q have been described. These aberrations may cause congenital malformations and intellectual disability of varying severity. Methods Via an international collaborative effort, we obtained a cytogenetic diagnosis for a 5‐year‐old boy of Afro‐Caribbean ancestry who has global developmental delay, dysmorphology, hypotonia, feeding difficulties, bilateral club feet, and intellectual disability. Results Conventional G‐banded karyotyping showed additional chromatin of unknown origin on the long arm of chromosome 18. SNP microarray confirmed the loss of ~6.4 Mb from chromosome 18q: arr[hg19] 18q22.3‐q23(71,518,518‐77,943,115)x1. The source of the additional chromatin was determined from the microarray to be ~32 Mb from the short arm of chromosome 5 (arr[hg19] 5p13.3‐p15.33(51,045‐32,062,984)x3). The unbalanced translocation was verified by fluorescent in situ hybridization (FISH). Both parents are healthy and have normal karyotypes suggesting that this abnormality arose de novo in the proband, although gonadal mosaicism in a parent cannot be excluded. Conclusion The combination of clinical features in this individual is most likely due to the partial deletion of 18q and partial duplication of 5p, which to our knowledge has not been previously described.
Collapse
Affiliation(s)
- Giavanna Verdi
- Department of Biochemistry St. George's University School of Medicine True Blue Grenada
| | - Dong Li
- Center for Applied Genomics The Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas USA
| | - Beverly Nelson
- Clinical Teaching Unit St. George's University School of Medicine True Blue Grenada
| | - Elizabeth J. Bhoj
- Center for Applied Genomics The Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Hakon Hakonarson
- Center for Applied Genomics The Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | | | - Sharmila Upadhya
- Department of Biochemistry St. George's University School of Medicine True Blue Grenada
| | - Sarah Gluschitz
- Department of Anatomical Sciences St. George's University True Blue Grenada
| | - Janice L. Smith
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas USA
| | - Andrew K. Sobering
- Department of Biochemistry St. George's University School of Medicine True Blue Grenada
- AU/UGA Medical Partnership Athens Georgia USA
- Windward Islands Research and Education Foundation St. George's Grenada
| |
Collapse
|
12
|
Abstract
Our understanding of genetic disease(s) has increased exponentially since the completion of human genome sequencing and the development of numerous techniques to detect genetic variants. These techniques have not only allowed us to diagnose genetic disease, but in so doing, also provide increased understanding of the pathogenesis of these diseases to aid in developing appropriate therapeutic options. Additionally, the advent of next-generation or massively parallel sequencing (NGS/MPS) is increasingly being used in the clinical setting, as it can detect a number of abnormalities from point mutations to chromosomal rearrangements as well as aberrations within the transcriptome. In this article, we will discuss the use of multiple techniques that are used in genetic diagnosis. © 2020 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Rashmi S Goswami
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.,Sunnybrook Research Institute, Biological Sciences, Odette Cancer Research Program, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shuko Harada
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| |
Collapse
|
13
|
Blyth U, Craciunas L, Hudson G, Choudhary M. Maternal germline factors associated with aneuploid pregnancy loss: a systematic review. Hum Reprod Update 2021; 27:866-884. [PMID: 33969392 DOI: 10.1093/humupd/dmab010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/02/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Miscarriage describes the spontaneous loss of pregnancy before the threshold of viability; the vast majority occur before 12 weeks of gestation. Miscarriage affects one in four couples and is the most common complication of pregnancy. Chromosomal abnormalities of the embryo are identified in ∼50% of first trimester miscarriages; aneuploidy accounts for 86% of these cases. The majority of trisomic miscarriages are of maternal origin with errors occurring during meiotic division of the oocytes. Chromosome segregation errors in oocytes may be sporadic events secondary to advancing maternal age; however, there is increasing evidence to suggest possible maternal germline contributions to this. OBJECTIVE AND RATIONALE The objective of this review was to appraise critically the existing evidence relating to maternal germline factors associated with pregnancy loss secondary to embryo aneuploidy, identify limitations in the current evidence base and establish areas requiring further research. SEARCH METHODS The initial literature search was performed in September 2019 and updated in January 2021 using the electronic databases OVID MEDLINE, EMBASE and the Cochrane Library. No time or language restrictions were applied to the searches and only primary research was included. Participants were women who had suffered pregnancy loss secondary to numerical chromosomal abnormalities of the embryo. Study identification and subsequent data extraction were performed by two authors independently. The Newcastle-Ottawa Scale was used to judge the quality of the included studies. The results were synthesized narratively. OUTCOMES The literature search identified 2198 titles once duplicates were removed, of which 21 were eligible for inclusion in this systematic review. They reported on maternal germline factors having variable degrees of association with pregnancy loss of aneuploid origin. The Online Mendelian Inheritance in Man (OMIM) gene ontology database was used as a reference to establish the functional role currently attributed to the genes reported. The majority of the cases reported and included were secondary to the inheritance of maternal structural factors such as Robertsonian translocations, deletions and insertions. Germline factors with a plausible role in aneuploid pregnancy loss of maternal origin included skewed X-inactivation and CGG repeats in the fragile X mental retardation (FMR1) gene. Studies that reported the association of single gene mutations with aneuploid pregnancy loss were conflicting. Single gene mutations with an uncertain or no role in aneuploid pregnancy loss included mutations in synaptonemal complex protein 3 (SYCP3), mitotic polo-like kinase 4 (PLK4) and meiotic stromal antigen 3 (STAG3) spindle integrity variants and 5,10-methylenetetrahydrofolate reductase (MTHFR). WIDER IMPLICATIONS Identifying maternal genetic factors associated with an increased risk of aneuploidy will expand our understanding of cell division, non-disjunction and miscarriage secondary to embryo aneuploidy. The candidate germline factors identified may be incorporated in a screening panel for women suffering miscarriage of aneuploidy aetiology to facilitate counselling for subsequent pregnancies.
Collapse
Affiliation(s)
- Ursula Blyth
- Newcastle Fertility Centre at Life, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Laurentiu Craciunas
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gavin Hudson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Meenakshi Choudhary
- Newcastle Fertility Centre at Life, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| |
Collapse
|
14
|
Talavera-López C, Messenger LA, Lewis MD, Yeo M, Reis-Cunha JL, Matos GM, Bartholomeu DC, Calzada JE, Saldaña A, Ramírez JD, Guhl F, Ocaña-Mayorga S, Costales JA, Gorchakov R, Jones K, Nolan MS, Teixeira SMR, Carrasco HJ, Bottazzi ME, Hotez PJ, Murray KO, Grijalva MJ, Burleigh B, Grisard EC, Miles MA, Andersson B. Repeat-Driven Generation of Antigenic Diversity in a Major Human Pathogen, Trypanosoma cruzi. Front Cell Infect Microbiol 2021; 11:614665. [PMID: 33747978 PMCID: PMC7966520 DOI: 10.3389/fcimb.2021.614665] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
Trypanosoma cruzi, a zoonotic kinetoplastid protozoan parasite, is the causative agent of American trypanosomiasis (Chagas disease). Having a very plastic, repetitive and complex genome, the parasite displays a highly diverse repertoire of surface molecules, with pivotal roles in cell invasion, immune evasion and pathogenesis. Before 2016, the complexity of the genomic regions containing these genes impaired the assembly of a genome at chromosomal level, making it impossible to study the structure and function of the several thousand repetitive genes encoding the surface molecules of the parasite. We here describe the genome assembly of the Sylvio X10/1 genome sequence, which since 2016 has been used as a reference genome sequence for T. cruzi clade I (TcI), produced using high coverage PacBio single-molecule sequencing. It was used to analyze deep Illumina sequence data from 34 T. cruzi TcI isolates and clones from different geographic locations, sample sources and clinical outcomes. Resolution of the surface molecule gene distribution showed the unusual duality in the organization of the parasite genome, a synteny of the core genomic region with related protozoa flanked by unique and highly plastic multigene family clusters encoding surface antigens. The presence of abundant interspersed retrotransposons in these multigene family clusters suggests that these elements are involved in a recombination mechanism for the generation of antigenic variation and evasion of the host immune response on these TcI strains. The comparative genomic analysis of the cohort of TcI strains revealed multiple cases of such recombination events involving surface molecule genes and has provided new insights into T. cruzi population structure.
Collapse
Affiliation(s)
- Carlos Talavera-López
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- European Bioinformatics Institute, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Louisa A. Messenger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael D. Lewis
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - João Luís Reis-Cunha
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel Machado Matos
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal Santa Catarina, Florianópolis, Brazil
| | | | - José E. Calzada
- Departamento de Parasitología, Instituto Conmemorativo Gorgas de Estudios de la Salud, Ciudad de Panamá, Panama
| | - Azael Saldaña
- Departamento de Parasitología, Instituto Conmemorativo Gorgas de Estudios de la Salud, Ciudad de Panamá, Panama
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Felipe Guhl
- Grupo de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Tropical Parasitology Research Center, Universidad de Los Andes, Bogotá, Colombia
| | - Sofía Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina (CISeAL), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jaime A. Costales
- Centro de Investigación para la Salud en América Latina (CISeAL), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Rodion Gorchakov
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Kathryn Jones
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Melissa S. Nolan
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Santuza M. R. Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hernán José Carrasco
- Laboratorio de Biología Molecular de Protozoarios, Instituto de Medicina Tropical, Facultad de Medicina, Universidad Central de Venezuela, Caracas, Venezuela
| | - Maria Elena Bottazzi
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Peter J. Hotez
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Kristy O. Murray
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Mario J. Grijalva
- Centro de Investigación para la Salud en América Latina (CISeAL), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Infectious and Tropical Disease Institute, Ohio University, Athens, OH, United States
| | - Barbara Burleigh
- Department of Immunology and Infectious Diseases, T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - Edmundo C. Grisard
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal Santa Catarina, Florianópolis, Brazil
| | - Michael A. Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
15
|
Pellestor F, Gaillard JB, Schneider A, Puechberty J, Gatinois V. Chromoanagenesis, the mechanisms of a genomic chaos. Semin Cell Dev Biol 2021; 123:90-99. [PMID: 33608210 DOI: 10.1016/j.semcdb.2021.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023]
Abstract
Designated under the name of chromoanagenesis, the phenomena of chromothripsis, chromanasynthesis and chromoplexy constitute new types of complex rearrangements, including many genomic alterations localized on a few chromosomal regions, and whose discovery over the last decade has changed our perception about the formation of chromosomal abnormalities and their etiology. Although exhibiting specific features, these new catastrophic mechanisms generally occur within a single cell cycle and their emergence is closely linked to genomic instability. Various non-exclusive exogenous or cellular mechanisms capable of generating chromoanagenesis have been evoked. However, recent experimental data shed light on 2 major processes, which following a defect in the mitotic segregation of chromosomes, can generate a cascade of cellular events leading to chromoanagenesis. These mechanisms are the formation of micronuclei integrating isolated chromosomal material, and the occurrence of chromatin bridges around chromosomal material resulting from telomeric fusions. In both cases, the cellular and molecular mechanisms of fragmentation, repair and transmission of damaged chromosomal material are consistent with the features of chromoanagenesis-related complex chromosomal rearrangements. In this review, we introduce each type of chromoanagenesis, and describe the experimental models that have allowed to validate the existence of chromoanagenesis events and to better understand their cellular mechanisms of formation and transmission, as well as their impact on the stability and the plasticity of the genome.
Collapse
Affiliation(s)
- F Pellestor
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France; INSERM 1183 Unit "Genome and Stem Cell Plasticity in Development and Aging" Institute of Regenerative Medecine and Biotherapies, St Eloi Hospital, Montpellier, France.
| | - J B Gaillard
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - A Schneider
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - J Puechberty
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - V Gatinois
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France; INSERM 1183 Unit "Genome and Stem Cell Plasticity in Development and Aging" Institute of Regenerative Medecine and Biotherapies, St Eloi Hospital, Montpellier, France
| |
Collapse
|
16
|
Arya P, Hodge JC, Matlock PA, Vance GH, Breman AM. Two Patients with Complex Rearrangements Suggestive of Germline Chromoanagenesis. Cytogenet Genome Res 2021; 160:671-679. [PMID: 33535208 DOI: 10.1159/000512898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/09/2020] [Indexed: 11/19/2022] Open
Abstract
Chromoanagenesis, a phenomenon characterized by complex chromosomal rearrangement and reorganization events localized to a limited number of genomic regions, includes the subcategories chromothripsis, chromoanasynthesis, and chromoplexy. Although definitions of these terms are evolving, constitutional chromoanagenesis events have been reported in a limited number of patients with variable phenotypes. We report on 2 cases with complex genomic events characterized by multiple copy number gains and losses confined to a single chromosome region, which are suggestive of constitutional chromoanagenesis. Case 1 is a 43-year-old male with intellectual disability and recently developed generalized tonic-clonic seizures. Chromosomal microarray analysis identified a complex rearrangement involving chromosome region 14q31.1q32.2, consisting of 16 breakpoints ranging in size from 0.2 to 6.2 Mb, with 5 segments of normal copy number present between these alterations. Interestingly, this case represents the oldest known patient with a complex rearrangement indicative of constitutional chromoanagenesis. Case 2 is a 2-year-old female with developmental delay, speech delay, low muscle tone, and seizures. Chromosomal microarray analysis identified a complex rearrangement consisting of 28 breakpoints localized to 18q21.32q23. The size of the copy number alterations ranged from 0.042 to 5.1 Mb, flanked by 12 small segments of normal copy number. These cases add to a growing body of literature demonstrating complex chromosomal rearrangements as a disease mechanism for congenital anomalies.
Collapse
Affiliation(s)
- Priyanka Arya
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jennelle C Hodge
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Peggy A Matlock
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Gail H Vance
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Amy M Breman
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA,
| |
Collapse
|
17
|
Osei-Owusu IA, Norris AL, Joynt AT, Thorpe J, Cho S, Tierney E, Schmidt J, Hagopian L, Harris J, Pevsner J. Characterization of an unbalanced translocation causing 3q28qter duplication and 10q26.2qter deletion in a patient with global developmental delay and self-injury. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005884. [PMID: 33335013 PMCID: PMC7784495 DOI: 10.1101/mcs.a005884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/08/2020] [Indexed: 01/17/2023] Open
Abstract
Chromosomal structural variation can cause severe neurodevelopmental and neuropsychiatric phenotypes. Here we present a nonverbal female adolescent with severe stereotypic movement disorder with severe problem behavior (e.g., self-injurious behavior, aggression, and disruptive and destructive behaviors), autism spectrum disorder, severe intellectual disability, attention deficit hyperactivity disorder, and global developmental delay. Previous cytogenetic analysis revealed balanced translocations present in the patient's apparently normal mother. We hypothesized the presence of unbalanced translocations in the patient due to maternal history of spontaneous abortions. Whole-genome sequencing and whole-genome optical mapping, complementary next-generation genomic technologies capable of the accurate and robust detection of structural variants, identified t(3;10), t(10;14), and t(3;14) three-way balanced translocations in the mother and der(10)t(3;14;10) and der(14)t(3;14;10) translocations in the patient. Instead of a t(3;10), she inherited a normal maternal copy of Chromosome 3, resulting in an unbalanced state of a 3q28qter duplication and 10q26.2qter deletion. Copy-imbalanced genes in one or both of these regions, such as DLG1, DOCK1, and EBF3, may contribute to the patient's phenotype that spans neurodevelopmental, musculoskeletal, and psychiatric domains, with the possible contribution of a maternally inherited 15q13.2q13.3 deletion.
Collapse
Affiliation(s)
- Ikeoluwa A Osei-Owusu
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Alexis L Norris
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Anya T Joynt
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Jeremy Thorpe
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Soonweng Cho
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Elaine Tierney
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Psychiatry, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Jonathan Schmidt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Behavioral Psychology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Louis Hagopian
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Behavioral Psychology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Jacqueline Harris
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Jonathan Pevsner
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| |
Collapse
|
18
|
Abstract
The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.
Collapse
Affiliation(s)
- Joana Damas
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Marco Corbo
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Harris A Lewin
- The Genome Center, University of California, Davis, California 95616, USA; , , .,Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616, USA
| |
Collapse
|
19
|
Anoshkin KI, Karandasheva KO, Goryacheva KM, Pyankov DV, Koshkin PA, Pavlova TV, Bobin AN, Shpot EV, Chernov YN, Vinarov AZ, Zaletaev DV, Kutsev SI, Strelnikov VV. Multiple Chromoanasynthesis in a Rare Case of Sporadic Renal Leiomyosarcoma: A Case Report. Front Oncol 2020; 10:1653. [PMID: 32974204 PMCID: PMC7466669 DOI: 10.3389/fonc.2020.01653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/28/2020] [Indexed: 01/25/2023] Open
Abstract
We present the genetic profile of kidney giant leiomyosarcoma characterized by sequencing of 409 cancer related genes and chromosomal microarray analysis. Renal leiomyosarcomas are extremely rare neoplasms with aggressive behavior and poor survival prognosis. Most frequent somatic events in leiomyosarcomas are mutations in the TP53, RB1, ATRX, and PTEN genes, chromosomal instability (CIN) and chromoanagenesis. 67-year-old woman presented with a right kidney completely replaced by tumor. Immunohistochemical reaction on surgical material was positive to desmin and smooth muscle actin. Molecular genetic analysis revealed that tumor harbored monosomy of chromosomes 3 and 11, gain of Xp (ATRX) arm and three chromoanasynthesis regions (6q21-q27, 7p22.3-p12.1, and 12q13.11-q21.2), with MDM2 and CDK4 oncogenes copy number gains, whereas no copy number variations (CNVs) or tumor specific single nucleotide variants (SNVs) in TP53, RB1, and PTEN genes were present. We hypothesize that chromoanasynthesis in 12q13.11-q21.2 could be a trigger of observed CIN in this tumor.
Collapse
|
20
|
Bonaglia MC, Bertuzzo S, Ciaschini AM, Discepoli G, Castiglia L, Romaniello R, Zuffardi O, Fichera M. Targeted next-generation sequencing identifies the disruption of the SHANK3 and RYR2 genes in a patient carrying a de novo t(1;22)(q43;q13.3) associated with signs of Phelan-McDermid syndrome. Mol Cytogenet 2020; 13:22. [PMID: 32536973 PMCID: PMC7291734 DOI: 10.1186/s13039-020-00490-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/26/2020] [Indexed: 11/10/2022] Open
Abstract
Background It has been known for more than 30 years that balanced translocations, especially if de novo, can associate with congenital malformations and / or neurodevelopmental disorders, following the disruption of a disease gene or its cis-regulatory elements at one or both breakpoints. Case presentation We describe a 10-year-old girl with a non-specific neurodevelopmental disorder characterized by moderate intellectual disability (ID), gross motor clumsiness, social and communication deficits. She carries a de novo reciprocal translocation between chromosomes 1q43 and 22q13.3, the latter suggesting the involvement of SHANK3. Indeed, its haploinsufficiency associates with Phelan-McDermid Syndrome, whose main symptoms are characterized by global developmental delay and absent or severely delayed expressive speech. A deep molecular approach, including next-generation sequencing of SHANK3 locus, allowed demonstrating the breakage of RYR2 and SHANK3 on the derivative chromosomes 1 and 22 respectively, and the formation of two fusion genes SHANK3-RYR2 and RYR2-SHANK3 with concomitant cryptic deletion of 3.6 and 4.1 kilobases at translocation junction of both derivatives chromosomes 22 and 1, respectively. Conclusions Although the interruption of SHANK3 accounts for the patient’s psychomotor retardation and autism-like behavior, we do not exclude that the interruption of RYR2 may also have a role on her disorder, or result in further pathogenicity in the future. Indeed, RYR2 that has a well-established role in the etiology of two autosomal dominant adulthood cardiac disorders (#600996 and #604772) is also expressed in the brain (cerebellum, hippocampus, and cerebral cortex) and about half of RYR2 mutation carriers present late onset primary generalized epilepsy without cardiac arrhythmogenic disorders. Moreover, RYR2 variants have also been sporadically reported in individuals with early onset schizophrenia or ID, and its constraint values suggest intolerance to loss-of-function. This study not only confirms the usefulness of the molecular mapping of de novo balanced rearrangements in symptomatic individuals, but also underscores the need for long-term clinical evaluation of the patients, for better evaluating the pathogenicity of the chromosomal breakpoints.
Collapse
Affiliation(s)
- Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Sara Bertuzzo
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Anna Maria Ciaschini
- Lab. di Genetica Medica SOS Malattie Rare, AOU Ospedali Riuniti Umberto I-G.M.Lancisi-G.Salesi, Ancona, Italy
| | - Giancarlo Discepoli
- Lab. di Genetica Medica SOS Malattie Rare, AOU Ospedali Riuniti Umberto I-G.M.Lancisi-G.Salesi, Ancona, Italy
| | | | - Romina Romaniello
- Neuropsychiatry and Neurorehabilitation Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, 23842 Lecco, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Marco Fichera
- Oasi Research Institute-IRCCS, Troina, Italy.,Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
| |
Collapse
|
21
|
Pellestor F, Gatinois V. Chromoanagenesis: a piece of the macroevolution scenario. Mol Cytogenet 2020; 13:3. [PMID: 32010222 PMCID: PMC6988253 DOI: 10.1186/s13039-020-0470-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/05/2020] [Indexed: 01/04/2023] Open
Abstract
Over the last decade, new types of massive and complex chromosomal rearrangements based on the chaotic shattering and restructuring of chromosomes have been identified in cancer cells as well as in patients with congenital diseases and healthy individuals. These unanticipated phenomena are named chromothripsis, chromoanasynthesis and chromoplexy, and are grouped under the term of chromoanagenesis. As mechanisms for rapid and profound genome modifications in germlines and early development, these processes can be regarded as credible pathways for genomic evolution and speciation process. Their discovery confirms the importance of genome-centric investigations to fully understand organismal evolution. Because they oppose the model of progressive acquisition of driver mutations or rearrangements, these phenomena conceptually give support to the concept of macroevolution, known through the models of “Hopeful Monsters” and the “Punctuated Equilibrium”. In this review, we summarize mechanisms underlying chromoanagenesis processes and we show that numerous cases of chromosomal speciation and short-term adaptation could be correlated to chromoanagenesis-related mechanisms. In the frame of a modern and integrative analysis of eukaryote evolutionary processes, it seems important to consider the unexpected chromoanagenesis phenomena.
Collapse
Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
| | - Vincent Gatinois
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
| |
Collapse
|
22
|
Xefteris A, Sekerli E, Arampatzi A, Charisiou S, Oikonomidou E, Efstathiou G, Peroulis N, Malamidou A, Tsoulou-Panidou E, Agakidou E, Sarafidis K, Psarakis A, Kataras T, Daskalakis G. Expanded Prader-Willi Syndrome due to an Unbalanced de novo Translocation t(14;15): Report and Review of the Literature. Cytogenet Genome Res 2019; 159:109-118. [PMID: 31816617 DOI: 10.1159/000504159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2019] [Indexed: 11/19/2022] Open
Abstract
In the present study, we report a case of a female infant with a de novo unbalanced t(14;15) translocation resulting in a 14-Mb deletion of the 15q11.1q14 region. The deletion includes the 15q11.2q13 Prader-Willi syndrome (PWS) critical region, while no known deleted genes are found in the 14qter region. According to literature review, patients with similar or larger deletions in the 15q region exhibit an expanded phenotype of PWS with case-specific atypical features such as severe retardation, absence of speech, microcephaly, retrognathia, bifid uvula, ear malformations, and heart defects in addition to typical features of PWS. Our proband exhibited increased deep tendon reflexes, an atypical feature which is not reported in the reviewed literature. The severity of the phenotype is not directly associated with the size of the deletion; however, using a combination of methods, the identification of breakpoints and the deleted genes can be helpful for the prognostication in patients with atypical PWS deletions.
Collapse
|
23
|
Gudipati MA, Waters E, Greene C, Goel N, Hoppman NL, Pitel BA, Webley MR, Zou Y. Stable transmission of complex chromosomal rearrangements involving chromosome 1q derived from constitutional chromoanagenesis. Mol Cytogenet 2019; 12:43. [PMID: 31695749 PMCID: PMC6822454 DOI: 10.1186/s13039-019-0455-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/16/2019] [Indexed: 01/10/2023] Open
Abstract
Background Chromoanagenesis events encompassing chromoanasynthesis, chromoplexy, and chromothripsis are described in cancers and can result in highly complex chromosomal rearrangements derived from ‘all-at-once’ catastrophic cellular events. The complexity of these rearrangements and the original descriptions in cancer cells initially led to the assumption that it was an acquired anomaly. While rare, these phenomena involving chromosome 1 have been reported a few individuals in a constitutional setting. Case presentation Here, we describe a newborn baby who was initially referred for cytogenetic testing for multiple congenital anomalies including cystic encephalomalacia, patent ductus arteriosus, inguinal hernia, and bilateral undescended testicles. Chromosome analysis was performed and revealed a derivative chromosome 1 with an 1q24-q31 segment inserted into 1q42.13 resulting in gain of 1q24-q31. Whole genome SNP microarray analysis showed a complex pattern of copy number variants with four gains and one loss involving 1q24-q31. Mate pair next-generation sequencing analysis revealed 18 chromosome breakpoints, six gains along an 1q24-q31 segment, one deletion of 1q31.3 segment and one deletion of 1q42.13 segment, which is strongly evocative of a chromoanasynthesis event for developing this complex rearrangement. Parental chromosome analyses were performed and showed the same derivative chromosome 1 in the mother. Conclusions To our knowledge, our case is the first case with familial constitutional chromoanagenesis involving chromosome 1q24-q42. This report emphasizes the value of performing microarray and mate pair next-generation sequencing analysis for individuals with germline abnormal or complex chromosome rearrangements.
Collapse
Affiliation(s)
- Mary A Gudipati
- 1Department of Pathology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Elizabeth Waters
- 1Department of Pathology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Carol Greene
- 2Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD USA
| | - Nidhi Goel
- 3Department of Internal Medicine, University of Maryland School of Medicine, Baltimore, MD USA
| | - Nicole L Hoppman
- 4Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Beth A Pitel
- 4Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Matthew R Webley
- 4Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Ying Zou
- 1Department of Pathology, University of Maryland School of Medicine, Baltimore, MD USA.,5Department of Pathology, Johns Hopkins University, 1812 Ashland Ave., Suite 200, Room 221, Baltimore, MD 2120 USA
| |
Collapse
|
24
|
Schimmel J, van Schendel R, den Dunnen JT, Tijsterman M. Templated Insertions: A Smoking Gun for Polymerase Theta-Mediated End Joining. Trends Genet 2019; 35:632-644. [PMID: 31296341 DOI: 10.1016/j.tig.2019.06.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/27/2019] [Accepted: 06/06/2019] [Indexed: 01/23/2023]
Abstract
A recognized source of disease-causing genome alterations is erroneous repair of broken chromosomes, which can be executed by two distinct mechanisms: non-homologous end joining (NHEJ) and the recently discovered polymerase theta-mediated end joining (TMEJ) pathway. While TMEJ has previously been considered to act as an alternative mechanism backing up NHEJ, recent work points to a role for TMEJ in the repair of replication-associated DNA breaks that are excluded from repair through homologous recombination. Because of its mode of action, TMEJ is intrinsically mutagenic and sometimes leaves behind a recognizable genomic scar when joining chromosome break ends (i.e., 'templated insertions'). This review article focuses on the intriguing observation that this polymerase theta signature is frequently observed in disease alleles, arguing for a prominent role of this double-strand break repair pathway in genome diversification and disease-causing spontaneous mutagenesis in humans.
Collapse
Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
| |
Collapse
|
25
|
Mechanisms of Genomic Instability in Breast Cancer. Trends Mol Med 2019; 25:595-611. [DOI: 10.1016/j.molmed.2019.04.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 12/22/2022]
|
26
|
Pellestor F, Gatinois V. Chromoanasynthesis: another way for the formation of complex chromosomal abnormalities in human reproduction. Hum Reprod 2019; 33:1381-1387. [PMID: 30325427 DOI: 10.1093/humrep/dey231] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Indexed: 12/24/2022] Open
Abstract
Chromoanasynthesis has been described as a novel cause of massive constitutional chromosomal rearrangements. Based on DNA replication machinery defects, chromoanasynthesis is characterized by the presence of chromosomal duplications and triplications locally clustered on one single chromosome, or a few chromosomes, associated with various other types of structural rearrangements. Two distinct mechanisms have been described for the formation of these chaotic genomic disorders, i.e. the fork stalling and template switching and the microhomology-mediated break-induced replication. Micronucleus-based processes have been evidenced as a causative mechanism, thus, highlighting the close connection between segregation errors and structural rearrangements. Accumulating data indicate that chromoanasynthesis is operating in human germline cells and during early embryonic development. The development of new tools for quantifying chromoanasynthesis events should provide further insight into the impact of this catastrophic cellular phenomenon in human reproduction.
Collapse
Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, Montpellier, France
| | - Vincent Gatinois
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, Montpellier, France
| |
Collapse
|
27
|
Koltsova AS, Pendina AA, Efimova OA, Chiryaeva OG, Kuznetzova TV, Baranov VS. On the Complexity of Mechanisms and Consequences of Chromothripsis: An Update. Front Genet 2019; 10:393. [PMID: 31114609 PMCID: PMC6503150 DOI: 10.3389/fgene.2019.00393] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/11/2019] [Indexed: 12/28/2022] Open
Abstract
In the present review, we focus on the phenomenon of chromothripsis, a new type of complex chromosomal rearrangements. We discuss the challenges of chromothripsis detection and its distinction from other chromoanagenesis events. Along with already known causes and mechanisms, we introduce aberrant epigenetic regulation as a possible pathway to chromothripsis. We address the issue of chromothripsis characteristics in cancers and benign tumours, as well as chromothripsis inheritance in cases of its occurrence in germ cells, zygotes and early embryos. Summarising the presented data on different phenotypic effect of chromothripsis, we assume that its consequences are most likely determined not by the chromosome shattering and reassembly themselves, but by the genome regions involved in the rearrangement.
Collapse
Affiliation(s)
- Alla S Koltsova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Anna A Pendina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Olga A Efimova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Olga G Chiryaeva
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Tatyana V Kuznetzova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Vladislav S Baranov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| |
Collapse
|
28
|
Zepeda-Mendoza CJ, Morton CC. The Iceberg under Water: Unexplored Complexity of Chromoanagenesis in Congenital Disorders. Am J Hum Genet 2019; 104:565-577. [PMID: 30951674 DOI: 10.1016/j.ajhg.2019.02.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/25/2019] [Indexed: 01/16/2023] Open
Abstract
Structural variation, composed of balanced and unbalanced genomic rearrangements, is an important contributor to human genetic diversity with prominent roles in somatic and congenital disease. At the nucleotide level, structural variants (SVs) have been shown to frequently harbor additional breakpoints and copy-number imbalances, a complexity predicted to emerge wholly as a single-cell division event. Chromothripsis, chromoplexy, and chromoanasynthesis, collectively referred to as chromoanagenesis, are three major mechanisms that explain the occurrence of complex germline and somatic SVs. While chromothripsis and chromoplexy have been shown to be key signatures of cancer, chromoanagenesis has been detected in numerous cases of developmental disease and phenotypically normal individuals. Such observations advocate for a deeper study of the polymorphic and pathogenic properties of complex germline SVs, many of which go undetected by traditional clinical molecular and cytogenetic methods. This review focuses on congenital chromoanagenesis, mechanisms leading to occurrence of these complex rearrangements, and their impact on chromosome organization and genome function. We highlight future applications of routine screening of complex and balanced SVs in the clinic, as these represent a potential and often neglected genetic disease source, a true "iceberg under water."
Collapse
Affiliation(s)
- Cinthya J Zepeda-Mendoza
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Cynthia C Morton
- Departments of Obstetrics and Gynecology and of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Manchester Center for Audiology and Deafness, School of Health Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9NT, UK.
| |
Collapse
|
29
|
Ly P, Brunner SF, Shoshani O, Kim DH, Lan W, Pyntikova T, Flanagan AM, Behjati S, Page DC, Campbell PJ, Cleveland DW. Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Nat Genet 2019; 51:705-715. [PMID: 30833795 PMCID: PMC6441390 DOI: 10.1038/s41588-019-0360-8] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 01/23/2019] [Indexed: 01/05/2023]
Abstract
Cancer genomes are frequently characterized by numerical and structural chromosomal abnormalities. Here we integrated a centromere-specific inactivation approach with selection for a conditionally essential gene, a strategy termed CEN-SELECT, to systematically interrogate the structural landscape of mis-segregated chromosomes. We show that single-chromosome mis-segregation into a micronucleus can directly trigger a broad spectrum of genomic rearrangement types. Cytogenetic profiling revealed that mis-segregated chromosomes exhibit 120-fold-higher susceptibility to developing seven major categories of structural aberrations, including translocations, insertions, deletions, and complex reassembly through chromothripsis coupled to classical non-homologous end joining. Whole-genome sequencing of clonally propagated rearrangements identified random patterns of clustered breakpoints with copy-number alterations resulting in interspersed gene deletions and extrachromosomal DNA amplification events. We conclude that individual chromosome segregation errors during mitotic cell division are sufficient to drive extensive structural variations that recapitulate genomic features commonly associated with human disease.
Collapse
Affiliation(s)
- Peter Ly
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | | | - Ofer Shoshani
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Dong Hyun Kim
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Weijie Lan
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | | | - Adrienne M Flanagan
- University College London Cancer Institute, London, UK
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - David C Page
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Don W Cleveland
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
| |
Collapse
|
30
|
Pellestor F. Chromoanagenesis: cataclysms behind complex chromosomal rearrangements. Mol Cytogenet 2019; 12:6. [PMID: 30805029 PMCID: PMC6371609 DOI: 10.1186/s13039-019-0415-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background During the last decade, genome sequencing projects in cancer genomes as well as in patients with congenital diseases and healthy individuals have led to the identification of new types of massive chromosomal rearrangements arising during single chaotic cellular events. These unanticipated catastrophic phenomenon are termed chromothripsis, chromoanasynthesis and chromoplexis., and are grouped under the name of “chromoanagenesis”. Results For each process, several specific features have been described, allowing each phenomenon to be distinguished from each other and to understand its mechanism of formation and to better understand its aetiology. Thus, chromothripsis derives from chromosome shattering followed by the random restitching of chromosomal fragments with low copy-number change whereas chromoanasynthesis results from erroneous DNA replication of a chromosome through serial fork stalling and template switching with variable copy-number gains, and chromoplexy refers to the occurrence of multiple inter-and intra-chromosomal translocations and deletions with little or no copy-number alterations in prostate cancer. Cumulating data and experimental models have shown that chromothripsis and chromoanasynthesis may essentially result from lagging chromosome encapsulated in micronuclei or telomere attrition and end-to-end telomere fusion. Conclusion The concept of chromanagenesis has provided new insight into the aetiology of complex structural rearrangements, the connection between defective cell cycle progression and genomic instability, and the complexity of cancer evolution. Increasing reported chromoanagenesis events suggest that these chaotic mechanisms are probably much more frequent than anticipated.
Collapse
Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371, avenue du Doyen Gaston Giraud, 34295 Montpellier cedex 5, France.,INSERM 1183 Unit «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
| |
Collapse
|
31
|
Cioppi F, Casamonti E, Krausz C. Age-Dependent De Novo Mutations During Spermatogenesis and Their Consequences. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1166:29-46. [DOI: 10.1007/978-3-030-21664-1_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
32
|
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]
|
33
|
Pellestor F, Gatinois V. Chromothripsis, a credible chromosomal mechanism in evolutionary process. Chromosoma 2018; 128:1-6. [DOI: 10.1007/s00412-018-0679-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 01/17/2023]
|
34
|
Slamova Z, Nazaryan-Petersen L, Mehrjouy MM, Drabova J, Hancarova M, Marikova T, Novotna D, Vlckova M, Vlckova Z, Bak M, Zemanova Z, Tommerup N, Sedlacek Z. Very short DNA segments can be detected and handled by the repair machinery during germline chromothriptic chromosome reassembly. Hum Mutat 2018; 39:709-716. [DOI: 10.1002/humu.23408] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Zuzana Slamova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Lusine Nazaryan-Petersen
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Mana M. Mehrjouy
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Jana Drabova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Tatana Marikova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Drahuse Novotna
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Marketa Vlckova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | | | - Mads Bak
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Zuzana Zemanova
- Institute of Medical Biochemistry and Laboratory Diagnostics; General University Hospital and Charles University 1st Faculty of Medicine; Prague Czech Republic
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Zdenek Sedlacek
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| |
Collapse
|
35
|
Large genomic insertion at the Shh locus results in hammer toes through enhancer adoption. Proc Natl Acad Sci U S A 2018; 115:839-841. [PMID: 29330329 DOI: 10.1073/pnas.1721351115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
36
|
Abstract
The highly complex structural genome variations chromothripsis, chromoanasynthesis, and chromoplexy are subsumed under the term chromoanagenesis, which means chromosome rebirth. Precipitated by numerous DNA double-strand breaks, they differ in number of and distances between breakpoints, associated copy number variations, order and orientation of segments, and flanking sequences at joining points. Results from patients with the autosomal dominant cancer susceptibility disorder Li-Fraumeni syndrome implicated somatic TP53 mutations in chromothripsis. TP53 participates in the G2/M phase checkpoint, halting cell cycling after premature chromosome compaction during the second half of the S phase, thus preventing chromosome shattering. By experimental TP53 ablation and micronucleus induction, one or a few isolated chromosomes underwent desynchronized replication and chromothripsis. Secondly, chromothripsis occurred after experimental induction of telomere crisis after which dicentric chromosomes sustained TREX1-mediated resolution of chromosome bridges and kataegis. Third, DNA polymerase Polθ-dependent chromothripsis has been documented. Finally, a family with chromothripsis after L1 element-dependent retrotransposition and Alu/Alu homologous recombination has been reported. Human chromosomal instability syndromes share defects in responses to DNA double-strand breaks, characteristic cell cycle perturbations, elevated rates of micronucleus formation, premature chromosome compaction, and apoptosis. They are also associated with elevated susceptibility to malignant disease, such as medulloblastomas and gliomas in ataxia-telangiectasia, leukemia and lymphoma in Bloom syndrome, and osteosarcoma and soft tissue sarcoma in Werner syndrome. The latter syndrome is characterized by a premature aging-like progressive decline of mesenchymal tissues. In all thus far studied cases, constitutional chromothripsis occurred in the male germline and male patients with defects in the double-strand break response genes ATM, MRE11, BLM, LIG4, WRN, and Ku70 show impaired fertility. Conceivably, chromothripsis may, in a stochastic rather than deterministic way, be implicated in germline structural variation, malignant disease, premature aging, genome mosaicism in somatic tissues, and male infertility.
Collapse
Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany.
| |
Collapse
|
37
|
Fukami M, Kurahashi H. Clinical Consequences of Chromothripsis and Other Catastrophic Cellular Events. Methods Mol Biol 2018; 1769:21-33. [PMID: 29564815 DOI: 10.1007/978-1-4939-7780-2_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Chromothripsis was initially described as a novel cause of chromosomal rearrangements in cancer cells and was subsequently implicated in the development of gross chromosomal rearrangements in the germline. Other catastrophic cellular events such as chromoanasynthesis and chromoplexy have also been observed in human cells. Such events have been associated with various phenotypes including mental retardation and congenital malformations. Here, we introduce representative cases of human disorders arising from somatic or germline chromothripsis or similar catastrophic events. In this chapter, we use the term "chromoanagenesis" to indicate all catastrophic events including chromothripsis.
Collapse
Affiliation(s)
- Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan.
| |
Collapse
|
38
|
Marcozzi A, Pellestor F, Kloosterman WP. The Genomic Characteristics and Origin of Chromothripsis. Methods Mol Biol 2018; 1769:3-19. [PMID: 29564814 DOI: 10.1007/978-1-4939-7780-2_1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In 2011 a phenomenon involving complex chromosomal rearrangements was discovered in cancer genomes. This phenomenon has been termed chromothripsis, on the basis of its chromosomal hallmarks, which point to an underlying process involving chromosome (chromo) shattering (thripsis). The prevailing hypothesis of cancer genome evolution as a gradual process of mutation and selection was challenged by the discovery of chromothripsis, because its patterns of chromosome rearrangement rather indicated an one-off catastrophic burst of genome rearrangement. The initial discovery of chromothripsis has led to many more examples of chromothripsis both in cancer genomes as well as in patients with congenital diseases and in the genomes of healthy individuals. Since then, a burning topic has been the study of the molecular mechanism that leads to chromothripsis. Cumulating evidence has shown that chromothripsis may result from lagging chromosomes encapsulated in micronuclei, as well as from telomere fusions followed by chromosome bridge formation. In this chapter, we will outline the genomic characteristics of chromothripsis, and we present genomic methodologies that enable the detection of chromothripsis. Furthermore, we will give an overview of recent insights into the mechanisms underlying chromothripsis.
Collapse
Affiliation(s)
- Alessio Marcozzi
- Division of Biomedical Genetics, Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Franck Pellestor
- Laboratory of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, Montpellier, France.,INSERM Unit Plasticity of the Genome and Aging, Institute of Functional Genomics, Montpellier, France
| | - Wigard P Kloosterman
- Division of Biomedical Genetics, Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.
| |
Collapse
|
39
|
Brunet E, Jasin M. Induction of Chromosomal Translocations with CRISPR-Cas9 and Other Nucleases: Understanding the Repair Mechanisms That Give Rise to Translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:15-25. [PMID: 29956288 DOI: 10.1007/978-981-13-0593-1_2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Chromosomal translocations are associated with several tumor types, including hematopoietic malignancies, sarcomas, and solid tumors of epithelial origin, due to their activation of a proto-oncogene or generation of a novel fusion protein with oncogenic potential. In many cases, the availability of suitable human models has been lacking because of the difficulty in recapitulating precise expression of the fusion protein or other reasons. Further, understanding how translocations form mechanistically has been a goal, as it may suggest ways to prevent their occurrence. Chromosomal translocations arise when DNA ends from double-strand breaks (DSBs) on two heterologous chromosomes are improperly joined. This review provides a summary of DSB repair mechanisms and their contribution to translocation formation, the various programmable nuclease platforms that have been used to generate translocations, and the successes that have been achieved in this area.
Collapse
Affiliation(s)
- Erika Brunet
- Genome Dynamics in the Immune System Laboratory, Institut Imagine, INSERM UMR 1163, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
40
|
Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
Collapse
Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
| |
Collapse
|
41
|
Tian C, Li D, Liu P, Jiao L, Gao X, Qiao J. A de novo complex chromosome rearrangement associated with multisystematic abnormalities, a case report. Mol Cytogenet 2017; 10:32. [PMID: 28878823 PMCID: PMC5581479 DOI: 10.1186/s13039-017-0332-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/10/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Complex chromosomal rearrangements (CCRs) are constitutional structural rearrangements that involve three or more chromosomes or that have more than two breakpoints. CASE PRESENTATION Here, we describe a four-way CCR involving chromosomes 4, 5, 6 and 8. The patient had mild multisystematic abnormalities during his development, including defects in his eyes and teeth, exomphalos and asthenozoospermia. His wife had two spontaneous abortions during the first trimester. The translocations in 4q27, 5q22, 6q22.3, and 8p11.2 were diagnosed by conventional cytogenetic analysis and confirmed by fluorescence in situ hybridization(FISH). After analysis using a SNP array, we defined three microdeletions, including 0.89 Mb on chromosome 4, 5.39 Mb on chromosome 5 and 0.43 Mb on chromosome 8. His mother had a chimera karyotype of 47, XXX[5]/45, X[4]/46, XX[91]; the other chromosomes were normal. After one cycle of in vitro fertility (IVF) treatment followed by preimplantation genetic diagnosis (PGD), they obtained two embryos, but neither was balanced. CONCLUSIONS The patient's phenotype resulted from the CCR and microdeletion of chromosomes 4, 5 and 8. The couple decided to use artificial insemination by donor (AID) technology.
Collapse
Affiliation(s)
- Chan Tian
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191 China.,Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191 China
| | - Dan Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191 China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191 China.,Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191 China
| | - Liping Jiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191 China
| | - Xuefeng Gao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191 China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191 China.,Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191 China
| |
Collapse
|
42
|
Abstract
Genetic abnormalities are present in all tumor types, although the frequency and type can vary. Chromosome abnormalities include highly aberrant structures, particularly chromothriptic chromosomes. The generation of massive sequencing data has illuminated the scope of the mutational burden in cancer genomes, identifying patterns of mutations (mutation signatures), which have the potential to shed light on the relatedness and etiologies of cancers and impact therapy response. Some mutation patterns are clearly attributable to disruptions in pathways that maintain genomic integrity. Here we review recent advances in our understanding of genetic changes occurring in cancers and the roles of genome maintenance pathways.
Collapse
Affiliation(s)
- Elizabeth M Kass
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Mary Ellen Moynahan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
43
|
Caballero Pérez V, López-Pisón FJ, Miramar Gallart MD, González Álvarez A, García Jiménez MC. Clinical impact of translocation t(7;15) (p22;q26) on several family members. An Pediatr (Barc) 2017. [DOI: 10.1016/j.anpede.2016.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
44
|
Caballero Pérez V, López-Pisón FJ, Miramar Gallart MD, González Álvarez A, García Jiménez MC. Repercusión clínica de la traslocación t(7;15) (p22;q26) en varios miembros de una misma familia. An Pediatr (Barc) 2017; 87:113-115. [DOI: 10.1016/j.anpedi.2016.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 11/25/2022] Open
|
45
|
Trpchevska N, Dimova I, Arabadji T, Milachich T, Angelova S, Dimitrova M, Hristova-Savova M, Andreeva P, Timeva T, Shterev A. A family study of complex chromosome rearrangement involving chromosomes 1, 8, and 11 and its reproductive consequences. J Assist Reprod Genet 2017; 34:659-669. [PMID: 28236108 PMCID: PMC5427656 DOI: 10.1007/s10815-017-0893-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/09/2017] [Indexed: 10/20/2022] Open
Abstract
Complex chromosome translocations are structural chromosomal rearrangements involving three or more chromosomes and more than two breakpoints. A complex chromosome rearrangement was detected in a phenotypically normal female patient that was referred to the hospital for genetic counseling due to reproductive failure. A cytogenetic evaluation was performed, according to standard method of chromosomal analysis, using G-banding technique. The patient's karyotype showed a balanced complex chromosome rearrangement (BCCR) involving chromosomes 1, 8, and 11 with three breakpoints 1p31, 8q13, and 11q23. The karyotype designed according to ISCN (2013), is 46,XX,t(1;8;11)(p31;q13;q23) (8qter→8q13::1p31→1qter;8pter→8q13::11q23→11qter;11pter→11q23::1p31→1pter). Additionally, the proband's mother and brother were tested, resulting in the same exact translocation. In this study, we describe all possible meiotic segregations regarding this translocation, as well as the clinical phenotypes which could arise, if unbalanced products of conception survive. This is a rare case of familial complex chromosome rearrangement, giving a view for its reproductive consequences.
Collapse
Affiliation(s)
- Natalia Trpchevska
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria.
- Laboratory of Cytogenetics and Molecular Genetics, National Specialized Hospital for Active Therapy of Hematological Diseases, Plovdivsko pole str 6, 1756, Sofia, Bulgaria.
| | - Ivanka Dimova
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
- Department of Medical Genetics, Medical University Sofia, Zdrave str 2, 1431, Sofia, Bulgaria
| | - Tatyana Arabadji
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
| | - Tanya Milachich
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
| | - Svetlana Angelova
- Laboratory of Cytogenetics and Molecular Genetics, National Specialized Hospital for Active Therapy of Hematological Diseases, Plovdivsko pole str 6, 1756, Sofia, Bulgaria
| | | | | | - Petya Andreeva
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
| | - Tania Timeva
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
| | - Atanas Shterev
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
| |
Collapse
|
46
|
Collins RL, Brand H, Redin CE, Hanscom C, Antolik C, Stone MR, Glessner JT, Mason T, Pregno G, Dorrani N, Mandrile G, Giachino D, Perrin D, Walsh C, Cipicchio M, Costello M, Stortchevoi A, An JY, Currall BB, Seabra CM, Ragavendran A, Margolin L, Martinez-Agosto JA, Lucente D, Levy B, Sanders SJ, Wapner RJ, Quintero-Rivera F, Kloosterman W, Talkowski ME. Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome. Genome Biol 2017; 18:36. [PMID: 28260531 PMCID: PMC5338099 DOI: 10.1186/s13059-017-1158-6] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/20/2017] [Indexed: 12/13/2022] Open
Abstract
Background Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies. Results We sequenced 689 participants with autism spectrum disorder (ASD) and other developmental abnormalities to construct a genome-wide map of large SV. Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution. Our results encompass 11,735 distinct large SV sites, 38.1% of which are novel and 16.8% of which are balanced or complex. We characterize 16 recurrent subclasses of complex SV (cxSV), revealing that: (1) cxSV are larger and rarer than canonical SV; (2) each genome harbors 14 large cxSV on average; (3) 84.4% of large cxSVs involve inversion; and (4) most large cxSV (93.8%) have not been delineated in previous studies. Rare SVs are more likely to disrupt coding and regulatory non-coding loci, particularly when truncating constrained and disease-associated genes. We also identify multiple cases of catastrophic chromosomal rearrangements known as chromoanagenesis, including somatic chromoanasynthesis, and extreme balanced germline chromothripsis events involving up to 65 breakpoints and 60.6 Mb across four chromosomes, further defining rare categories of extreme cxSV. Conclusions These data provide a foundational map of large SV in the morbid human genome and demonstrate a previously underappreciated abundance and diversity of cxSV that should be considered in genomic studies of human disease. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1158-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ryan L Collins
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, 02115, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Harrison Brand
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Claire E Redin
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Carrie Hanscom
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Caroline Antolik
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Matthew R Stone
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Joseph T Glessner
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Tamara Mason
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Giulia Pregno
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Naghmeh Dorrani
- Department of Pathology & Laboratory Medicine and UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, UCLA, Los Angeles, CA, 90095, USA
| | - Giorgia Mandrile
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Danielle Perrin
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Cole Walsh
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Michelle Cipicchio
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Maura Costello
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Alexei Stortchevoi
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Joon-Yong An
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, 94103, USA
| | - Benjamin B Currall
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Catarina M Seabra
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA.,GABBA Program, University of Porto, Porto, 4099-002, Portugal
| | - Ashok Ragavendran
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Lauren Margolin
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Julian A Martinez-Agosto
- Department of Pathology & Laboratory Medicine and UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, UCLA, Los Angeles, CA, 90095, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Brynn Levy
- Department of Pathology, Columbia University, New York, NY, 10032, USA
| | - Stephan J Sanders
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, 94103, USA
| | - Ronald J Wapner
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology & Laboratory Medicine and UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, UCLA, Los Angeles, CA, 90095, USA
| | - Wigard Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, 3584CG, The Netherlands
| | - Michael E Talkowski
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA. .,Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, 02115, USA. .,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA.
| |
Collapse
|
47
|
Gu S, Szafranski P, Akdemir ZC, Yuan B, Cooper ML, Magriñá MA, Bacino CA, Lalani SR, Breman AM, Smith JL, Patel A, Song RH, Bi W, Cheung SW, Carvalho CMB, Stankiewicz P, Lupski JR. Mechanisms for Complex Chromosomal Insertions. PLoS Genet 2016; 12:e1006446. [PMID: 27880765 PMCID: PMC5120786 DOI: 10.1371/journal.pgen.1006446] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/24/2016] [Indexed: 12/21/2022] Open
Abstract
Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue, constituting ~2% of nonrecurrent copy-number gains. Little is known about the molecular mechanisms of their formation. We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on 10 individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing in 6 individuals to glean insights into potential mechanisms of formation. We observed microhomologies and templated insertions at the breakpoint junctions, resembling the breakpoint junction signatures found in complex genomic rearrangements generated by replication-based mechanism(s) with iterative template switches. In addition, we analyzed 5 families with apparently balanced insertion in one parent detected by FISH analysis and found that 3 parents had additional small copy-number variants (CNVs) at one or both sides of the inserting fragments as well as at the inserted sites. We propose that replicative repair can result in interchromosomal complex insertions generated through chromothripsis-like chromoanasynthesis involving two or three chromosomes, and cause a significant fraction of apparently balanced insertions harboring small flanking CNVs. By traditional cytogenetic techniques, the incidence of microscopically visible chromosomal insertions was estimated to be 1 in 80,000 live births. More recently, by aCGH in conjunction with FISH confirmation of the aCGH findings, insertion events were demonstrated to occur much more frequently (1 in ~500 individuals tested). Although frequently detected, little is known about the molecular mechanisms of their formation. In this study, we identified 16 individuals with complex chromosomal insertions among 56,000 individuals tested at Baylor Genetics using clinical microarray analysis (CMA) and FISH. Custom high-density aCGH was performed on 10 individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing in 6 individuals to glean insights into potential mechanisms of formation. In addition, we analyzed 5 families with apparently balanced insertion in one parent detected by FISH analysis and found that 3 parents had additional small copy-number variants (CNVs) at one or both sides of the inserting fragments as well as at the inserted sites. We propose that replicative repair can result in interchromosomal complex insertions generated through chromothripsis-like chromoanasynthesis involving two or three chromosomes, and cause a significant fraction of apparently balanced insertions harboring small flanking CNVs.
Collapse
Affiliation(s)
- Shen Gu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zeynep Coban Akdemir
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Bo Yuan
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mitchell L. Cooper
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Maria A. Magriñá
- Medical Specialties Unit From City Hall São José dos Campos, São Paulo, Brazil
| | - Carlos A. Bacino
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Seema R. Lalani
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Amy M. Breman
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Janice L. Smith
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ankita Patel
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Rodger H. Song
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Weimin Bi
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sau Wai Cheung
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Claudia M. B. Carvalho
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (JRL); (PS)
| | - James R. Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
- * E-mail: (JRL); (PS)
| |
Collapse
|
48
|
Pylyp LY, Mykytenko DO, Spinenko LO, Lavrova KV, Verhoglyad NV, Zukin VD. A case of prenatal detection of a de novo unbalanced complex chromosomal rearrangement involving four chromosomes. CYTOL GENET+ 2016. [DOI: 10.3103/s009545271605011x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
49
|
Poot M. Chromothripsis after Stumbling through DNA Replication. Mol Syndromol 2016; 6:207-9. [PMID: 26997940 DOI: 10.1159/000441081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2015] [Indexed: 11/19/2022] Open
|
50
|
Shamseldin HE, Anazi S, Wakil SM, Faqeih E, El Khashab HY, Salih MA, Al-Qattan MM, Hashem M, Alsedairy H, Alkuraya FS. Novel copy number variants and major limb reduction malformation: Report of three cases. Am J Med Genet A 2016; 170A:1245-50. [PMID: 26749485 DOI: 10.1002/ajmg.a.37550] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/25/2015] [Indexed: 12/13/2022]
Abstract
Limb reduction malformations are highly heterogeneous in their clinical presentation and so, predicting the underlying mutation on a clinical basis can be challenging. Molecular karyotyping is a powerful genomic tool that has quickly become the mainstay for the study of children with malformation syndromes. We describe three patients with major limb reduction anomalies in whom pathogenic copy number variants were identified on molecular karyotyping. These include a patient with hypoplastic phalanges and absent hallux bilaterally with de novo deletion of 11.9 Mb on 7p21.1-22.1 spanning 63 genes including RAC1, another patient with severe Holt-Oram syndrome and a large de novo deletion 2.2 Mb on 12q24.13-24.21 spanning 20 genes including TBX3 and TBX5, and a third patient with acheiropodia who had a nullizygous deletion of 102 kb on 7q36.3 spanning LMBR1. We discuss the potential of these novel genomic rearrangements to improve our understanding of limb development in humans.
Collapse
Affiliation(s)
- Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shams Anazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Salma M Wakil
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Department of Pediatric Specialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Heba Y El Khashab
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Pediatrics, Children's Hospital, Ain Shams University, Cairo, Egypt
| | - Mustafa A Salih
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad M Al-Qattan
- Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Haifa Alsedairy
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| |
Collapse
|