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Balow SA, Coyan AG, Smith N, Russell BE, Monteil D, Hopkin RJ, Smolarek TA. Complex genomic rearrangements of the Y chromosome in a premature infant. Mol Cytogenet 2024; 17:19. [PMID: 39183314 PMCID: PMC11346217 DOI: 10.1186/s13039-024-00689-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/01/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND Chromoanagenesis is an umbrella term used to describe catastrophic "all at once" cellular events leading to the chaotic reconstruction of chromosomes. It is characterized by numerous rearrangements involving a small number of chromosomes/loci, copy number gains in combination with deletions, reconstruction of chromosomal fragments with improper order/orientation, and preserved heterozygosity in copy number neutral regions. Chromoanagesis is frequently described in association with cancer; however, it has also been described in the germline. The clinical features associated with constitutional chromoanagenesis are typically due to copy number changes and/or disruption of genes or regulatory regions. CASE PRESENTATION We present an 8-year-old male patient with complex rearrangements of the Y chromosome including a ring Y chromosome, a derivative Y;21 chromosome, and a complex rearranged Y chromosome. These chromosomes were characterized by G-banded chromosome analysis, SNP microarray, interphase FISH, and metaphase FISH. The mechanism(s) by which these rearrangements occurred is unclear; however, it is evocative of chromoanagenesis. CONCLUSION This case is a novel example of suspected germline chromoanagenesis leading to large copy number changes that are well-tolerated, possibly because only the sex chromosomes are affected.
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Affiliation(s)
- Stephanie A Balow
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Alyxis G Coyan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nicki Smith
- Seton Center, Good Samaritan Hospital, TriHealth Hospital Systems, Cincinnati, OH, USA
| | - Bianca E Russell
- Department of Human Genetics, Division of Clinical Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Danielle Monteil
- Department of Pediatrics, Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Teresa A Smolarek
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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Zhang CZ, Pellman D. Chromosome breakage-replication/fusion enables rapid DNA amplification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.17.608415. [PMID: 39229211 PMCID: PMC11370323 DOI: 10.1101/2024.08.17.608415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
DNA rearrangements are thought to arise from two classes of processes. The first class involves DNA breakage and fusion ("cut-and-paste") without net DNA gain or loss. The second class involves aberrant DNA replication ("copy-and-paste") and can produce either net DNA gain or loss. We previously demonstrated that the partitioning of chromosomes into aberrant structures of the nucleus, micronuclei or chromosome bridges, can generate cut-and-paste rearrangements by chromosome fragmentation and ligation. Surprisingly, in the progeny clones of single cells that have undergone chromosome bridge breakage, we identified large segmental duplications and short sequence insertions that are commonly attributed to copy-and-paste processes. Here, we demonstrate that both large duplications and short insertions are inherent outcomes of the replication and fusion of unligated DNA ends, a process we term breakage-replication/fusion (B-R/F). We propose that B-R/F provides a unifying explanation for complex rearrangement patterns including chromothripsis and chromoanasynthesis and enables rapid DNA amplification after chromosome fragmentation.
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Ogiwara Y, Kobori Y, Suzuki E, Hattori A, Tanase-Nakao K, Osaka A, Iwahata T, Okada H, Kuroki Y, Fukami M. Isodicentric Y Chromosome with Multiple Breakpoints in the Pseudoautosomal Region 1. Cytogenet Genome Res 2024:1-6. [PMID: 39074465 DOI: 10.1159/000540634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/26/2024] [Indexed: 07/31/2024] Open
Abstract
INTRODUCTION Isodicentric Y chromosomes are relatively common structural variants of the human genome. The underlying mechanism of isodicentric Y chromosomes with short arm breakpoints [idic(Yq)] remains to be clarified. CASE PRESENTATION We encountered a Japanese man with azoospermia and mild short stature. G-banding and array-based comparative genomic hybridization indicated that his karyotype was 45,X/46,X,idic(Y)(qter→p11.32::p11.32→qter) with a ∼1.8 Mb terminal deletion. Whole-genome sequencing suggested that the Y chromosome had four breakpoints in a ∼7 kb region of the pseudoautosomal region 1 (PAR1). CONCLUSION This case was assumed to have an idic(Yq) resulting from multiple DNA double-strand breaks in PAR1. This rearrangement may have been facilitated by the PAR1-specific chromatin architecture. The clinical features of the patient can be ascribed to SHOX haploinsufficiency and the presence of a 45,X cell line, although copy-number gains of some Yq genes and the size reduction of PAR1 may also contribute to his spermatogenic failure.
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Affiliation(s)
- Yasuko Ogiwara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan
| | - Yoshitomo Kobori
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Erina Suzuki
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Atsushi Hattori
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kanako Tanase-Nakao
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akiyoshi Osaka
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Toshiyuki Iwahata
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Hiroshi Okada
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Yoko Kuroki
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Genome Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Collaborative Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
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Daida K, Yoshino H, Malik L, Baker B, Ishiguro M, Genner R, Paquette K, Li Y, Nishioka K, Masuzugawa S, Hirano M, Takahashi K, Kolmogolv M, Billingsley KJ, Funayama M, Blauwendraat C, Hattori N. The Utility of Long-Read Sequencing in Diagnosing Genetic Autosomal Recessive Parkinson's Disease: a genetic screening study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.14.24308784. [PMID: 39108517 PMCID: PMC11302705 DOI: 10.1101/2024.06.14.24308784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Background Mutations within the genes PRKN and PINK1 are the leading cause of early onset autosomal recessive Parkinson's disease (PD). However, the genetic cause of most early-onset PD (EOPD) cases still remains unresolved. Long-read sequencing has successfully identified many pathogenic structural variants that cause disease, but this technology has not been widely applied to PD. We recently identified the genetic cause of EOPD in a pair of monozygotic twins by uncovering a complex structural variant that spans over 7 Mb, utilizing Oxford Nanopore Technologies (ONT) long-read sequencing. In this study, we aimed to expand on this and assess whether a second variant could be detected with ONT long-read sequencing in other unresolved EOPD cases reported to carry one heterozygous variant in PRKN or PINK1. Methods ONT long-read sequencing was performed on patients with one reported PRKN/PINK1 pathogenic variant. EOPD patients with an age at onset younger than 50 were included in this study. As a positive control, we also included EOPD patients who had already been identified to carry two known PRKN pathogenic variants. Initial genetic testing was performed using either short-read targeted panel sequencing for single nucleotide variants and multiplex ligation-dependent probe amplification (MLPA) for copy number variants. Results 48 patients were included in this study (PRKN "one-variant" n = 24, PINK1 "one-variant" n = 12, PRKN "two-variants" n = 12). Using ONT long-read sequencing, we detected a second pathogenic variant in six PRKN "one-variant" patients (26%, 6/23) but none in the PINK1 "one-variant" patients (0%, 0/12). Long-read sequencing identified one case with a complex inversion, two instances of structural variant overlap, and three cases of duplication. In addition, in the positive control PRKN "two-variants" group, we were able to identify both pathogenic variants in PRKN in all the patients (100%, 12/12). Conclusions This data highlights that ONT long-read sequencing is a powerful tool to identify a pathogenic structural variant at the PRKN locus that is often missed by conventional methods. Therefore, for cases where conventional methods fail to detect a second variant for EOPD, long-read sequencing should be considered as an alternative and complementary approach.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Breeana Baker
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Rylee Genner
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kimberly Paquette
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Yuanzhe Li
- Department of Neurology, Faculty of Medicine, Juntendo University, Tokyo, Japan
- Department of Diagnosis, Prevention and Treatment of Dementia, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo Tokyo Koto Geriatric Medical Center, Koto-ku, Tokyo, Japan
| | | | - Makito Hirano
- Department of Neurology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Kenta Takahashi
- Division of Neurology and Gerontology, Department of Internal Medicine, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Mikhail Kolmogolv
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Manabu Funayama
- Department of Neurology, Faculty of Medicine, Juntendo University, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nobutaka Hattori
- Department of Neurology, Faculty of Medicine, Juntendo University, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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Iwata S, Nagahara M, Ido R, Iwamoto T. A Recql5 mutant facilitates complex CRISPR/Cas9-mediated chromosomal engineering in mouse zygotes. Genetics 2024; 227:iyae054. [PMID: 38577877 PMCID: PMC11151919 DOI: 10.1093/genetics/iyae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/07/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024] Open
Abstract
Complex chromosomal rearrangements (CCRs) are often observed in clinical samples from patients with cancer and congenital diseases but are difficult to induce experimentally. Here, we report the first success in establishing animal models for CCRs. Mutation in Recql5, a crucial member of the DNA helicase RecQ family involved in DNA replication, transcription, and repair, enabled CRISPR/Cas9-mediated CCRs, establishing a mouse model containing triple fusion genes and megabase-sized inversions. Some of these structural features of individual chromosomal rearrangements use template switching and microhomology-mediated break-induced replication mechanisms and are reminiscent of the newly described phenomenon "chromoanasynthesis." These data show that Recql5 mutant mice could be a powerful tool to analyze the pathogenesis of CCRs (particularly chromoanasynthesis) whose underlying mechanisms are poorly understood. The Recql5 mutants generated in this study are to be deposited at key animal research facilities, thereby making them accessible for future research on CCRs.
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Affiliation(s)
- Satoru Iwata
- Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi 487-8501, Japan
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi 487-8501, Japan
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
- Center for Mathematical Science and Artificial Intelligence, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Miki Nagahara
- Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Risako Ido
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Takashi Iwamoto
- Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi 487-8501, Japan
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi 487-8501, Japan
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6
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Kuroki Y, Hattori A, Matsubara K, Fukami M. Long-read next-generation sequencing for molecular diagnosis of pediatric endocrine disorders. Ann Pediatr Endocrinol Metab 2024; 29:156-160. [PMID: 38956752 PMCID: PMC11220396 DOI: 10.6065/apem.2448028.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/23/2024] [Indexed: 07/04/2024] Open
Abstract
Recent advances in long-read next-generation sequencing (NGS) have enabled researchers to identify several pathogenic variants overlooked by short-read NGS, array-based comparative genomic hybridization, and other conventional methods. Long-read NGS is particularly useful in the detection of structural variants and repeat expansions. Furthermore, it can be used for mutation screening in difficultto- sequence regions, as well as for DNA-methylation analyses and haplotype phasing. This mini-review introduces the usefulness of long-read NGS in the molecular diagnosis of pediatric endocrine disorders.
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Affiliation(s)
- Yoko Kuroki
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Genome Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Atsushi Hattori
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Keiko Matsubara
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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7
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Chen CY. Chromothripsis in myeloid malignancies. Ann Hematol 2024:10.1007/s00277-024-05814-9. [PMID: 38814446 DOI: 10.1007/s00277-024-05814-9] [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: 03/06/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
Chromothripsis refers to massive genomic rearrangements developed during a catastrophic event. In total acute myeloid leukemia (AML), the incidence of chromothripsis ranges from 0 to 6.6%, in cases of complex karyotype AML, the incidence of chromothripsis ranges from 27.3 to 100%, whereas in cases of AML with TP53 mutations, the incidence ranges from 11.1 to 90%. For other types of malignancies, the incidence of chromothripsis also varies, from 0 to 10.5% in myelodysplastic syndrome to up to 61.5% in cases of myelodysplastic syndrome with TP53 mutations.Chromothripsis is typically associated with complex karyotypes and TP53 mutations, and monosomal karyotypes are associated with the condition. ERG amplifications are frequently noted in cases of chromothripsis, whereas MYC amplifications are not. Moreover, FLT3 and NPM1 mutations are negatively associated with chromothripsis. Chromothripsis typically occurs in older patients with AML with low leukocyte counts and bone marrow blast counts. Rare cases of patients with chromothripsis who received intensive induction chemotherapy revealed low response rates and poor overall prognosis. Signal pathways in chromothripsis typically involve copy number gain and upregulation of oncogene gene sets that promote cancer growth and a concomitant copy number loss and downregulation of gene sets associated with tumor suppression functions.Patients with chromothripsis showed a trend of lower complete remission rate and worse overall survival in myeloid malignancy. Large-scale studies are required to further elucidate the causes and treatments of the condition.
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Affiliation(s)
- Chien-Yuan Chen
- Department of Internal Medicine, Division of Hematology, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei, 100, Taiwan.
- Department of Pathology, Cytogenetic laboratory, National Taiwan University Hospital, Taipei, Taiwan.
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8
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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.
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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
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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.
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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.
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10
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Pati D. Role of chromosomal cohesion and separation in aneuploidy and tumorigenesis. Cell Mol Life Sci 2024; 81:100. [PMID: 38388697 PMCID: PMC10884101 DOI: 10.1007/s00018-024-05122-5] [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: 11/13/2023] [Revised: 12/28/2023] [Accepted: 01/09/2024] [Indexed: 02/24/2024]
Abstract
Cell division is a crucial process, and one of its essential steps involves copying the genetic material, which is organized into structures called chromosomes. Before a cell can divide into two, it needs to ensure that each newly copied chromosome is paired tightly with its identical twin. This pairing is maintained by a protein complex known as cohesin, which is conserved in various organisms, from single-celled ones to humans. Cohesin essentially encircles the DNA, creating a ring-like structure to handcuff, to keep the newly synthesized sister chromosomes together in pairs. Therefore, chromosomal cohesion and separation are fundamental processes governing the attachment and segregation of sister chromatids during cell division. Metaphase-to-anaphase transition requires dissolution of cohesins by the enzyme Separase. The tight regulation of these processes is vital for safeguarding genomic stability. Dysregulation in chromosomal cohesion and separation resulting in aneuploidy, a condition characterized by an abnormal chromosome count in a cell, is strongly associated with cancer. Aneuploidy is a recurring hallmark in many cancer types, and abnormalities in chromosomal cohesion and separation have been identified as significant contributors to various cancers, such as acute myeloid leukemia, myelodysplastic syndrome, colorectal, bladder, and other solid cancers. Mutations within the cohesin complex have been associated with these cancers, as they interfere with chromosomal segregation, genome organization, and gene expression, promoting aneuploidy and contributing to the initiation of malignancy. In summary, chromosomal cohesion and separation processes play a pivotal role in preserving genomic stability, and aberrations in these mechanisms can lead to aneuploidy and cancer. Gaining a deeper understanding of the molecular intricacies of chromosomal cohesion and separation offers promising prospects for the development of innovative therapeutic approaches in the battle against cancer.
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Affiliation(s)
- Debananda Pati
- Texas Children's Cancer Center, Department of Pediatrics Hematology/Oncology, Molecular and Cellular Biology, Baylor College of Medicine, 1102 Bates Avenue, Houston, TX, 77030, USA.
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Lestringant V, Guermouche-Flament H, Jimenez-Pocquet M, Gaillard JB, Penther D. Cytogenetics in the management of hematological malignancies: An overview of alternative technologies for cytogenetic characterization. Curr Res Transl Med 2024; 72:103440. [PMID: 38447270 DOI: 10.1016/j.retram.2024.103440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024]
Abstract
Genomic characterization is an essential part of the clinical management of hematological malignancies for diagnostic, prognostic and therapeutic purposes. Although CBA and FISH are still the gold standard in hematology for the detection of CNA and SV, some alternative technologies are intended to complement their deficiencies or even replace them in the more or less near future. In this article, we provide a technological overview of these alternatives. CMA is the historical and well established technique for the high-resolution detection of CNA. For SV detection, there are emerging techniques based on the study of chromatin conformation and more established ones such as RTMLPA for the detection of fusion transcripts and RNA-seq to reveal the molecular consequences of SV. Comprehensive techniques that detect both CNA and SV are the most interesting because they provide all the information in a single examination. Among these, OGM is a promising emerging higher-solution technique that offers a complete solution at a contained cost, at the expense of a relatively low throughput per machine. WGS remains the most adaptable solution, with long-read approaches enabling very high-resolution detection of CAs, but requiring a heavy bioinformatics installation and at a still high cost. However, the development of high-resolution genome-wide detection techniques for CAs allows for a much better description of chromoanagenesis. Therefore, we have included in this review an update on the various existing mechanisms and their consequences and implications, especially prognostic, in hematological malignancies.
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Affiliation(s)
| | | | | | - Jean-Baptiste Gaillard
- Unité de Génétique Chromosomique, Service de Génétique moléculaire et cytogénomique, CHU Montpellier, Montpellier, France
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12
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Mazzagatti A, Engel JL, Ly P. Boveri and beyond: Chromothripsis and genomic instability from mitotic errors. Mol Cell 2024; 84:55-69. [PMID: 38029753 PMCID: PMC10842135 DOI: 10.1016/j.molcel.2023.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023]
Abstract
Mitotic cell division is tightly monitored by checkpoints that safeguard the genome from instability. Failures in accurate chromosome segregation during mitosis can cause numerical aneuploidy, which was hypothesized by Theodor Boveri over a century ago to promote tumorigenesis. Recent interrogation of pan-cancer genomes has identified unexpected classes of chromosomal abnormalities, including complex rearrangements arising through chromothripsis. This process is driven by mitotic errors that generate abnormal nuclear structures that provoke extensive yet localized shattering of mis-segregated chromosomes. Here, we discuss emerging mechanisms underlying chromothripsis from micronuclei and chromatin bridges, as well as highlight how this mutational cascade converges on the DNA damage response. A fundamental understanding of these catastrophic processes will provide insight into how initial errors in mitosis can precipitate rapid cancer genome evolution.
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Affiliation(s)
- Alice Mazzagatti
- 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
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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13
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Poot M. Methods of Detection and Mechanisms of Origin of Complex Structural Genome Variations. Methods Mol Biol 2024; 2825:39-65. [PMID: 38913302 DOI: 10.1007/978-1-0716-3946-7_2] [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] [Indexed: 06/25/2024]
Abstract
Based on classical karyotyping, structural genome variations (SVs) have generally been considered to be either "simple" (with one or two breakpoints) or "complex" (with more than two breakpoints). Studying the breakpoints of SVs at nucleotide resolution revealed additional, subtle structural variations, such that even "simple" SVs turned out to be "complex." Genome-wide sequencing methods, such as fosmid and paired-end mapping, short-read and long-read whole genome sequencing, and single-molecule optical mapping, also indicated that the number of SVs per individual was considerably larger than expected from karyotyping and high-resolution chromosomal array-based studies. Interestingly, SVs were detected in studies of cohorts of individuals without clinical phenotypes. The common denominator of all SVs appears to be a failure to accurately repair DNA double-strand breaks (DSBs) or to halt cell cycle progression if DSBs persist. This review discusses the various DSB response mechanisms during the mitotic cell cycle and during meiosis and their regulation. Emphasis is given to the molecular mechanisms involved in the formation of translocations, deletions, duplications, and inversions during or shortly after meiosis I. Recently, CRISPR-Cas9 studies have provided unexpected insights into the formation of translocations and chromothripsis by both breakage-fusion-bridge and micronucleus-dependent mechanisms.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Wuerzburg, Wuerzburg, Germany
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14
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Ye JC, Heng HH. Tracking Karyotype Changes in Treatment-Induced Drug-Resistant Evolution. Methods Mol Biol 2024; 2825:263-280. [PMID: 38913315 DOI: 10.1007/978-1-0716-3946-7_15] [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] [Indexed: 06/25/2024]
Abstract
Karyotype coding, which encompasses the complete chromosome sets and their topological genomic relationships within a given species, encodes system-level information that organizes and preserves genes' function, and determines the macroevolution of cancer. This new recognition emphasizes the crucial role of karyotype characterization in cancer research. To advance this cancer cytogenetic/cytogenomic concept and its platforms, this study outlines protocols for monitoring the karyotype landscape during treatment-induced rapid drug resistance in cancer. It emphasizes four key perspectives: combinational analyses of phenotype and karyotype, a focus on the entire evolutionary process through longitudinal analysis, a comparison of whole landscape dynamics by including various types of NCCAs (including genome chaos), and the use of the same process to prioritize different genomic scales. This protocol holds promise for studying numerous evolutionary aspects of cancers, and it further enhances the power of karyotype analysis in cancer research.
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Affiliation(s)
- Jing Christine Ye
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Henry H Heng
- Department of Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA.
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15
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Ling C, Dai Y, Geng C, Pan S, Quan W, Ding Q, Yang X, Shen D, Tao Q, Li J, Li J, Wang Y, Jiang S, Wang Y, Chen L, Cui L, Wang D. Uncovering the true features of dystrophin gene rearrangement and improving the molecular diagnosis of Duchenne and Becker muscular dystrophies. iScience 2023; 26:108365. [PMID: 38047063 PMCID: PMC10690541 DOI: 10.1016/j.isci.2023.108365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/19/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023] Open
Abstract
Duchenne and Becker muscular dystrophies (DMD/BMD) are caused by complex mutations in the dystrophin gene (DMD). Currently, there is no integrative method for the precise detection of all potential DMD variants, a gap which we aimed to address using long-read sequencing. The captured long-read sequencing panel developed in this study was applied to 129 subjects, including 11 who had previously unsolved cases. The results showed that this method accurately detected DMD mutations, ranging from single-nucleotide variations to structural variations. Furthermore, our findings revealed that continuous exon duplication/deletion in the DMD/BMD cohort may be attributed to complex segmental rearrangements and that noncontiguous duplication/deletion is generally attributed to intragenic inversion or interchromosome translocation. Mutations in the deep introns were confirmed to produce a pseudoexon. Moreover, variations in female carriers were precisely identified. The integrated and precise DMD gene screening method proposed in this study could improve the molecular diagnosis of DMD/BMD.
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Affiliation(s)
- Chao Ling
- The Laboratory of Clinical Genetics, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Chang Geng
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Shirang Pan
- Grandomics Biosciences, Beijing 102200, China
| | | | - Qingyun Ding
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Xunzhe Yang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Dongchao Shen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Qing Tao
- Grandomics Biosciences, Beijing 102200, China
| | - Jingjing Li
- Grandomics Biosciences, Beijing 102200, China
| | - Jia Li
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yinbing Wang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Shan Jiang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yang Wang
- Grandomics Biosciences, Beijing 102200, China
| | - Lin Chen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102200, China
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16
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Espejo Valle-Inclán J, Cortés-Ciriano I. ReConPlot: an R package for the visualization and interpretation of genomic rearrangements. Bioinformatics 2023; 39:btad719. [PMID: 38058190 PMCID: PMC10710371 DOI: 10.1093/bioinformatics/btad719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 09/13/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023] Open
Abstract
MOTIVATION Whole-genome sequencing studies of human tumours have revealed that complex forms of structural variation, collectively known as complex genome rearrangements (CGRs), are pervasive across diverse cancer types. Detection, classification, and mechanistic interpretation of CGRs requires the visualization of complex patterns of somatic copy number aberrations (SCNAs) and structural variants (SVs). However, there is a lack of tools specifically designed to facilitate the visualization and study of CGRs. RESULTS We present ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing customization of plots and the generation of publication-quality figures with minimal effort. Overall, ReConPlot facilitates the exploration, interpretation, and reporting of CGR patterns. AVAILABILITY AND IMPLEMENTATION The R package ReConPlot is available at https://github.com/cortes-ciriano-lab/ReConPlot. Detailed documentation and a tutorial with examples are provided with the package.
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Affiliation(s)
- Jose Espejo Valle-Inclán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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17
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Sugimoto T, Inagaki H, Mariya T, Kawamura R, Taniguchi-Ikeda M, Mizuno S, Muramatsu Y, Tsuge I, Ohashi H, Saito N, Hasegawa Y, Ochi N, Yamaguchi M, Murotsuki J, Kurahashi H. Breakpoints in complex chromosomal rearrangements correspond to transposase-accessible regions of DNA from mature sperm. Hum Genet 2023; 142:1451-1460. [PMID: 37615740 PMCID: PMC10511381 DOI: 10.1007/s00439-023-02591-9] [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: 06/02/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023]
Abstract
Constitutional complex chromosomal rearrangements (CCRs) are rare cytogenetic aberrations arising in the germline via an unknown mechanism. Here we analyzed the breakpoint junctions of microscopically three-way or more complex translocations using comprehensive genomic and epigenomic analyses. All of these translocation junctions showed submicroscopic genomic complexity reminiscent of chromothripsis. The breakpoints were clustered within small genomic domains with junctions showing microhomology or microinsertions. Notably, all of the de novo cases were of paternal origin. The breakpoint distributions corresponded specifically to the ATAC-seq (assay for transposase-accessible chromatin with sequencing) read data peak of mature sperm and not to other chromatin markers or tissues. We propose that DNA breaks in CCRs may develop in an accessible region of densely packaged chromatin during post-meiotic spermiogenesis.
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Affiliation(s)
- Takeshi Sugimoto
- Division of Molecular Genetics, Center for Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
- Kobe Motomachi Yume Clinic, Kobe, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Center for Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Tasuku Mariya
- Division of Molecular Genetics, Center for Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Rie Kawamura
- Division of Molecular Genetics, Center for Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Mariko Taniguchi-Ikeda
- Division of Molecular Genetics, Center for Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Seiji Mizuno
- Department of Clinical Genetics, Central Hospital, Aichi Developmental Disability Center, Aichi, Japan
| | - Yukako Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Ikuya Tsuge
- Department of Pediatrics, Fujita Health University, Aichi, Japan
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan
| | | | - Yuiko Hasegawa
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Nobuhiko Ochi
- Department of Pediatrics, Aichi Prefectural Mikawa Aoitori Medical and Rehabilitation Center for Developmental Disabilities, Okazaki, Japan
| | - Masatoshi Yamaguchi
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Jun Murotsuki
- Department of Maternal and Fetal Medicine, Miyagi Children's Hospital, Sendai, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Center for Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan.
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18
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Villa N, Redaelli S, Farina S, Conconi D, Sala EM, Crosti F, Mariani S, Colombo CM, Dalprà L, Lavitrano M, Bentivegna A, Roversi G. Genomic Complexity and Complex Chromosomal Rearrangements in Genetic Diagnosis: Two Illustrative Cases on Chromosome 7. Genes (Basel) 2023; 14:1700. [PMID: 37761840 PMCID: PMC10530880 DOI: 10.3390/genes14091700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Complex chromosomal rearrangements are rare events compatible with survival, consisting of an imbalance and/or position effect of one or more genes, that contribute to a range of clinical presentations. The investigation and diagnosis of these cases are often difficult. The interpretation of the pattern of pairing and segregation of these chromosomes during meiosis is important for the assessment of the risk and the type of imbalance in the offspring. Here, we investigated two unrelated pediatric carriers of complex rearrangements of chromosome 7. The first case was a 2-year-old girl with a severe phenotype. Conventional cytogenetics evidenced a duplication of part of the short arm of chromosome 7. By array-CGH analysis, we found a complex rearrangement with three discontinuous trisomy regions (7p22.1p21.3, 7p21.3, and 7p21.3p15.3). The second case was a newborn investigated for hypodevelopment and dimorphisms. The karyotype analysis promptly revealed a structurally altered chromosome 7. The array-CGH analysis identified an even more complex rearrangement consisting of a trisomic region at 7q11.23q22 and a tetrasomic region of 4.5 Mb spanning 7q21.3 to q22.1. The mother's karyotype examination revealed a complex rearrangement of chromosome 7: the 7q11.23q22 region was inserted in the short arm at 7p15.3. Finally, array-CGH analysis showed a trisomic region that corresponds to the tetrasomic region of the son. Our work proved that the integration of several technical solutions is often required to appropriately analyze complex chromosomal rearrangements in order to understand their implications and offer appropriate genetic counseling.
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Affiliation(s)
- Nicoletta Villa
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy (G.R.)
| | - Serena Redaelli
- School of Medicine and Surgery, University of Milan-Bicocca, 20900 Monza, Italy
| | - Stefania Farina
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy (G.R.)
- School of Medicine and Surgery, University of Milan-Bicocca, 20900 Monza, Italy
| | - Donatella Conconi
- School of Medicine and Surgery, University of Milan-Bicocca, 20900 Monza, Italy
| | - Elena Maria Sala
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy (G.R.)
| | - Francesca Crosti
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy (G.R.)
| | - Silvana Mariani
- Department of Obstetrics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Carla Maria Colombo
- Neonatal Intensive Care Unit, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Leda Dalprà
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy (G.R.)
- School of Medicine and Surgery, University of Milan-Bicocca, 20900 Monza, Italy
| | | | - Angela Bentivegna
- School of Medicine and Surgery, University of Milan-Bicocca, 20900 Monza, Italy
| | - Gaia Roversi
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy (G.R.)
- School of Medicine and Surgery, University of Milan-Bicocca, 20900 Monza, Italy
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19
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van Ginkel J, Tomlinson I, Soriano I. The Evolutionary Landscape of Colorectal Tumorigenesis: Recent Paradigms, Models, and Hypotheses. Gastroenterology 2023; 164:841-846. [PMID: 36702361 DOI: 10.1053/j.gastro.2022.11.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 01/28/2023]
Abstract
Using colorectal cancer as a model, we review some of the insights into cancer evolution afforded by cancer sequencing. These include nonlinear and neutral evolution; polyclonality of driver mutations and parallel evolution in adenomas, although these are rare in carcinomas; the ability of mutational processes to shape evolution against the force of selection; the presence of rare driver genes that function in the same signaling pathways as the longstanding canonical drivers; and the existence of selective windows that constrain the functional effects of cancer driver mutations within limits. Many of these nascent evolutionary paradigms are potentially important for treating colorectal cancers as well as understanding their development.
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Affiliation(s)
- Jurriaan van Ginkel
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Ian Tomlinson
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Ignacio Soriano
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom.
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20
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Holt S, Arrey G, Regenberg B. Did circular DNA shape the evolution of mammalian genomes? Trends Biochem Sci 2023; 48:317-320. [PMID: 36280496 DOI: 10.1016/j.tibs.2022.09.010] [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: 07/13/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022]
Abstract
Extrachromosomal circular DNA (eccDNA) can shape the genomes of somatic cells, but how it impacts genomes across generations is largely unexplored. We propose that genomes can rearrange via circular intermediates across generations and show that up to 6% of a mammalian genome can have changed gene order through eccDNA.
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Affiliation(s)
- Sylvester Holt
- Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Gerard Arrey
- Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Birgitte Regenberg
- Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark.
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21
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Masson J, Pebrel-Richard C, Egloff M, Frétigny M, Beaumont M, Uguen K, Rollat-Farnier PA, Diguet F, Perthus I, Le Gudayer G, Haye D, Dupeyron MNB, Putoux A, Raskin-Champion F, Till M, Chatron N, Doray B, Bardel C, Vinciguerra C, Sanlaville D, Schluth-Bolard C. Familial transmission of chromoanagenesis leads to unpredictable unbalanced rearrangements through meiotic recombination. Clin Genet 2023; 103:401-412. [PMID: 36576162 DOI: 10.1111/cge.14291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Chromoanagenesis is a cellular mechanism that leads to complex chromosomal rearrangements (CCR) during a single catastrophic event. It may result in loss and/or gain of genetic material and may be responsible for various phenotypes. These rearrangements are usually sporadic. However, some familial cases have been reported. Here, we studied six families in whom an asymptomatic or paucisymptomatic parent transmitted a CCR to its offspring in an unbalanced manner. The rearrangements were characterized by karyotyping, fluorescent in situ hybridization, chromosomal microarray (CMA) and/or whole genome sequencing (WGS) in the carrier parents and offspring. We then hypothesized meiosis-pairing figures between normal and abnormal parental chromosomes that may have led to the formation of new unbalanced rearrangements through meiotic recombination. Our work indicates that chromoanagenesis might be associated with a normal phenotype and normal fertility, even in males, and that WGS may be the only way to identify these events when there is no imbalance. Subsequently, the CCR can be transmitted to the next generation in an unbalanced and unpredictable manner following meiotic recombination. Thereby, prenatal diagnosis using CMA should be proposed to these families to detect any pathogenic imbalances in the offspring.
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Affiliation(s)
- Julie Masson
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | | | | | - Mathilde Frétigny
- Service d'hématologie, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Bron, France
| | - Marion Beaumont
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Genetics and NIPT, Laboratoire Eylau-Unilabs, Neuilly-sur-Seine, France
| | - Kevin Uguen
- UMR 1078, GGB, CHU Brest, Inserm, Univ Brest, EFS, Brest, France
- Service de Génétique Médicale, CHRU de Brest, Brest, France
| | - Pierre-Antoine Rollat-Farnier
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Plateforme NGS, Hospices Civils de Lyon, Bron, France
| | - Flavie Diguet
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Isabelle Perthus
- Service de Génétique Médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | | | - Damien Haye
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Marie-Noëlle Bonnet Dupeyron
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Service de Génétique, CH de Valence, Valence, France
| | - Audrey Putoux
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Fabienne Raskin-Champion
- Service de Gynécologie Médicale et Obstétrique, Groupement Hospitalier Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Marianne Till
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Nicolas Chatron
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | - Bérénice Doray
- Service de Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Service de Génétique, CHU de la Réunion - Hôpital Félix Guyon, Saint-Denis, France
| | - Claire Bardel
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Plateforme NGS, Hospices Civils de Lyon, Bron, France
- ISPB, Université Claude Bernard Lyon 1, Lyon, France
| | - Christine Vinciguerra
- Service d'hématologie, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Bron, France
- ISPB, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Sanlaville
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | - Caroline Schluth-Bolard
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Team Energetic Metabolism and Neuronal Development, Neuromyogene Institute, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
- Laboratoires de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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22
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Guo W, Comai L, Henry IM. Chromoanagenesis in the asy1 meiotic mutant of Arabidopsis. G3 (BETHESDA, MD.) 2023; 13:jkac185. [PMID: 35920777 PMCID: PMC9911071 DOI: 10.1093/g3journal/jkac185] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023]
Abstract
Chromoanagenesis is a catastrophic event that involves localized chromosomal shattering and reorganization. In this study, we report a case of chromoanagenesis resulting from defective meiosis in the MEIOTIC ASYNAPTIC MUTANT 1 (asy1) background in Arabidopsis thaliana. We provide a detailed characterization of the genomic structure of this individual with a severely shattered segment of chromosome 1. We identified 260 novel DNA junctions in the affected region, most of which affect gene sequence on 1 or both sides of the junction. Our results confirm that asy1-related defective meiosis is a potential trigger for chromoanagenesis. This is the first example of chromoanagenesis associated with female meiosis and indicates the potential for genome evolution during oogenesis. PLAIN LANGUAGE SUMMARY Chromoanagenesis is a complex and catastrophic event that results in severely restructured chromosomes. It has been identified in cancer cells and in some plant samples, after specific triggering events. Here, we identified this kind of genome restructuring in a mutant that exhibits defective meiosis in the model plant system Arabidopsis thaliana.
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Affiliation(s)
- Weier Guo
- Genome Center and Dept. Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Luca Comai
- Genome Center and Dept. Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Isabelle M Henry
- Genome Center and Dept. Plant Biology, University of California, Davis, Davis, CA 95616, USA
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23
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Paternal UPD14 with sSMC derived from chromosome 14 in Kagami-Ogata syndrome. CHROMOSOME RESEARCH : AN INTERNATIONAL JOURNAL ON THE MOLECULAR, SUPRAMOLECULAR AND EVOLUTIONARY ASPECTS OF CHROMOSOME BIOLOGY 2023; 31:1. [PMID: 36656404 DOI: 10.1007/s10577-023-09712-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/27/2022] [Accepted: 01/02/2023] [Indexed: 01/20/2023]
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24
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de Groot D, Spanjaard A, Hogenbirk MA, Jacobs H. Chromosomal Rearrangements and Chromothripsis: The Alternative End Generation Model. Int J Mol Sci 2023; 24:ijms24010794. [PMID: 36614236 PMCID: PMC9821053 DOI: 10.3390/ijms24010794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
Chromothripsis defines a genetic phenomenon where up to hundreds of clustered chromosomal rearrangements can arise in a single catastrophic event. The phenomenon is associated with cancer and congenital diseases. Most current models on the origin of chromothripsis suggest that prior to chromatin reshuffling numerous DNA double-strand breaks (DSBs) have to exist, i.e., chromosomal shattering precedes rearrangements. However, the preference of a DNA end to rearrange in a proximal accessible region led us to propose chromothripsis as the reaction product of successive chromatin rearrangements. We previously coined this process Alternative End Generation (AEG), where a single DSB with a repair-blocking end initiates a domino effect of rearrangements. Accordingly, chromothripsis is the end product of this domino reaction taking place in a single catastrophic event.
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Affiliation(s)
- Daniel de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Aldo Spanjaard
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Marc A. Hogenbirk
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Agendia NV, Radarweg 60, 1043 NT Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Correspondence: ; Tel.: +31-20-512-2065
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25
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Ganguly BB, Ganguly S, Kadam NN. Spectrum of stable and unstable rearrangements in lymphocytic chromosomes investigated in Bhopal population 30 years post MIC disaster amid co-exposure to lifestyle, living, and occupational hazards. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:1997-2019. [PMID: 35922599 DOI: 10.1007/s11356-022-22053-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Immediate assessment of genetic damage in methyl isocyanate (MIC) gas-exposed population in small and heterogeneous samples using diversified study designs and solid-stained metaphases could not depict the actual genetic impact of MIC on accidentally exposed individuals. The outcome of the then large multi-center genetic screening program was not available to the public and scientific community. Also, the routine and regular epidemiological health survey does not capture the genetic and long-term effect of MIC. Therefore, genetic screening was carried out 30 years post disaster during 2015-2017 with a view to screen the present status of chromosomal consequences in lymphocytic cells. Participants were recruited from moderate (34) and severely (78) exposed and unexposed (35) cohorts with their informed consent. Analysis of ~100 mitotic cells and karyotyping of at least 10-15 and all abnormal metaphases detected structural and numerical alterations, including stable and replicable ones. Clonal abnormalities were detected with monosomal and complex karyotypes, trisomy 8, del5q/20q, loss of Y, etc. Among all, X-chromosome was frequently involved in numerical alterations. Structural aberrations appeared higher in the then exposed populations, though abnormalities cannot be linked directly to MIC exposure 30 years post disaster. Collectively, all rearrangements were markedly higher in the severely exposed population. Altogether, the detected abnormalities appeared random and indicated genomic instability, suggesting follow-up at shorter intervals for the individuals detected with clonal aberrations. G-banding has facilitated recognition of chromosomal involvement and their breakpoints and classification of structural rearrangements. The present data has been derived from the 30-year post-disaster genetic screening.
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Affiliation(s)
- Bani Bandana Ganguly
- MGM Center for Genetic Research & Diagnosis, MGM New Bombay Hospital, Navi Mumbai, India.
- MGM Institute of Health Sciences, Navi Mumbai, India.
| | - Shouvik Ganguly
- MGM Center for Genetic Research & Diagnosis, MGM New Bombay Hospital, Navi Mumbai, India
- MGM Dental College and Hospital, Navi Mumbai, India
| | - Nitin N Kadam
- MGM Center for Genetic Research & Diagnosis, MGM New Bombay Hospital, Navi Mumbai, India
- MGM Institute of Health Sciences, Navi Mumbai, India
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26
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Guo W, Comai L, Henry IM. Chromoanagenesis in plants: triggers, mechanisms, and potential impact. Trends Genet 2023; 39:34-45. [PMID: 36055901 DOI: 10.1016/j.tig.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022]
Abstract
Chromoanagenesis is a single catastrophic event that involves, in most cases, localized chromosomal shattering and reorganization, resulting in a dramatically restructured chromosome. First discovered in cancer cells, it has since been observed in various other systems, including plants. In this review, we discuss the origin, characteristics, and potential mechanisms underlying chromoanagenesis in plants. We report that multiple processes, including mutagenesis and genetic engineering, can trigger chromoanagenesis via a variety of mechanisms such as micronucleation, breakage-fusion-bridge (BFB) cycles, or chain-like translocations. The resulting rearranged chromosomes can be preserved during subsequent plant growth, and sometimes inherited to the next generation. Because of their high tolerance to genome restructuring, plants offer a unique system for investigating the evolutionary consequences and potential practical applications of chromoanagenesis.
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Affiliation(s)
- Weier Guo
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Luca Comai
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Isabelle M Henry
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA.
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27
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A Complex Genomic Rearrangement Resulting in Loss of Function of SCN1A and SCN2A in a Patient with Severe Developmental and Epileptic Encephalopathy. Int J Mol Sci 2022; 23:ijms232112900. [DOI: 10.3390/ijms232112900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Complex genomic rearrangements (CGRs) are structural variants arising from two or more chromosomal breaks, which are challenging to characterize by conventional or molecular cytogenetic analysis (karyotype and FISH). The integrated approach of standard and genomic techniques, including optical genome mapping (OGM) and genome sequencing, is crucial for disclosing and characterizing cryptic chromosomal rearrangements at high resolutions. We report on a patient with a complex developmental and epileptic encephalopathy in which karyotype analysis showed a de novo balanced translocation involving the long arms of chromosomes 2 and 18. Microarray analysis detected a 194 Kb microdeletion at 2q24.3 involving the SCN2A gene, which was considered the likely translocation breakpoint on chromosome 2. However, OGM redefined the translocation breakpoints by disclosing a paracentric inversion at 2q24.3 disrupting SCN1A. This combined genomic high-resolution approach allowed a fine characterization of the CGR, which involves two different chromosomes with four breakpoints. The patient’s phenotype resulted from the concomitant loss of function of SCN1A and SCN2A.
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28
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Bao L, Zhong X, Yang Y, Yang L. Starfish infers signatures of complex genomic rearrangements across human cancers. NATURE CANCER 2022; 3:1247-1259. [PMID: 35835961 PMCID: PMC11077613 DOI: 10.1038/s43018-022-00404-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Complex genomic rearrangements (CGRs) are common in cancer and are known to form via two aberrant cellular structures-micronuclei and chromatin bridges. However, which of these mechanisms is more relevant to CGR formation in cancer and whether there are other undiscovered mechanisms remain unknown. Here we developed a computational algorithm, 'Starfish', to analyze 2,014 CGRs from 2,428 whole-genome-sequenced (WGS) tumors and discovered six CGR signatures based on their copy number and breakpoint patterns. Extensive benchmarking showed that our CGR signatures are highly accurate and biologically meaningful. Three signatures can be attributed to known biological processes-micronuclei- and chromatin-bridge-induced chromothripsis and circular extrachromosomal DNA. Over half of the CGRs belong to the remaining three signatures, not reported previously. A unique signature, which we named 'hourglass chromothripsis', with localized breakpoints and a low amount of DNA loss, is abundant in prostate cancer. Hourglass chromothripsis is associated with mutant SPOP, which may induce genome instability.
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Affiliation(s)
- Lisui Bao
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiaoming Zhong
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Yang Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA.
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29
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Dubois F, Sidiropoulos N, Weischenfeldt J, Beroukhim R. Structural variations in cancer and the 3D genome. Nat Rev Cancer 2022; 22:533-546. [PMID: 35764888 PMCID: PMC10423586 DOI: 10.1038/s41568-022-00488-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/18/2022] [Indexed: 12/21/2022]
Abstract
Structural variations (SVs) affect more of the cancer genome than any other type of somatic genetic alteration but difficulties in detecting and interpreting them have limited our understanding. Clinical cancer sequencing also increasingly aims to detect SVs, leading to a widespread necessity to interpret their biological and clinical relevance. Recently, analyses of large whole-genome sequencing data sets revealed features that impact rates of SVs across the genome in different cancers. A striking feature has been the extent to which, in both their generation and their influence on the selective fitness of cancer cells, SVs are more specific to individual cancer types than other genetic alterations such as single-nucleotide variants. This Perspective discusses how the folding of the 3D genome, and differences in its folding across cell types, affect observed SV rates in different cancer types as well as how SVs can impact cancer cell fitness.
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Affiliation(s)
- Frank Dubois
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikos Sidiropoulos
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Joachim Weischenfeldt
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark.
- Department of Urology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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30
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Amendola M, Brusson M, Miccio A. CRISPRthripsis: The Risk of CRISPR/Cas9-induced Chromothripsis in Gene Therapy. Stem Cells Transl Med 2022; 11:1003-1009. [PMID: 36048170 PMCID: PMC9585945 DOI: 10.1093/stcltm/szac064] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/23/2022] [Indexed: 12/22/2022] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 nuclease system has allowed the generation of disease models and the development of therapeutic approaches for many genetic and non-genetic disorders. However, the generation of large genomic rearrangements has raised safety concerns for the clinical application of CRISPR/Cas9 nuclease approaches. Among these events, the formation of micronuclei and chromosome bridges due to chromosomal truncations can lead to massive genomic rearrangements localized to one or few chromosomes. This phenomenon, known as chromothripsis, was originally described in cancer cells, where it is believed to be caused by defective chromosome segregation during mitosis or DNA double-strand breaks. Here, we will discuss the factors influencing CRISPR/Cas9-induced chromothripsis, hereafter termed CRISPRthripsis, and its outcomes, the tools to characterize these events and strategies to minimize them.
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Affiliation(s)
- Mario Amendola
- Genethon, Evry, France.,Integrare Research Unit UMR_S951, Université Paris-Saclay, Univ Evry, Inserm, Genethon, Evry, France
| | - Mégane Brusson
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Université Paris Cité, Imagine Institute, Paris, France
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Université Paris Cité, Imagine Institute, Paris, France
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31
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Löytynoja A. Thousands of human mutation clusters are explained by short-range template switching. Genome Res 2022; 32:1437-1447. [PMID: 35760560 PMCID: PMC9435742 DOI: 10.1101/gr.276478.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/21/2022] [Indexed: 02/03/2023]
Abstract
Variation within human genomes is unevenly distributed, and variants show spatial clustering. DNA replication-related template switching is a poorly known mutational mechanism capable of causing major chromosomal rearrangements as well as creating short inverted sequence copies that appear as local mutation clusters in sequence comparisons. In this study, haplotype-resolved genome assemblies representing 25 human populations and multinucleotide variants aggregated from 140,000 human sequencing experiments were reanalyzed. Local template switching could explain thousands of complex mutation clusters across the human genome, the loci segregating within and between populations. During the study, computational tools were developed for identification of template switch events using both short-read sequencing data and genotype data, and for genotyping candidate loci using short-read data. The characteristics of template-switch mutations complicate their detection, and widely used analysis pipelines for short-read sequencing data, normally capable of identifying single nucleotide changes, were found to miss template-switch mutations of tens of base pairs, potentially invalidating medical genetic studies searching for a causative allele behind genetic diseases. Combined with the massive sequencing data now available for humans, the novel tools described here enable building catalogs of affected loci and studying the cellular mechanisms behind template switching in both healthy organisms and disease.
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Affiliation(s)
- Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
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32
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A Maternally Inherited Rare Case with Chromoanagenesis-Related Complex Chromosomal Rearrangements and De Novo Microdeletions. Diagnostics (Basel) 2022; 12:diagnostics12081900. [PMID: 36010250 PMCID: PMC9406357 DOI: 10.3390/diagnostics12081900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/22/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Chromoanagenesis is a phenomenon of highly complex rearrangements involving the massive genomic shattering and reconstitution of chromosomes that has had a great impact on cancer biology and congenital anomalies. Complex chromosomal rearrangements (CCRs) are structural alterations involving three or more chromosomal breakpoints between at least two chromosomes. Here, we present a 3-year-old boy exhibiting multiple congenital malformations and developmental delay. The cytogenetic analysis found a highly complex CCR inherited from the mother involving four chromosomes and five breakpoints due to forming four derivative chromosomes (2, 3, 6 and 11). FISH analysis identified an ultrarare derivative chromosome 11 containing three parts that connected the 11q telomere to partial 6q and 3q fragments. We postulate that this derivative chromosome 11 is associated with chromoanagenesis-like phenomena by which DNA repair can result in a cooccurrence of inter-chromosomal translocations. Additionally, chromosome microarray studies revealed that the child has one subtle maternal-inherited deletion at 6p12.1 and two de novo deletions at 6q14.1 and 6q16.1~6q16.3. Here, we present a familial CCR case with rare rearranged chromosomal structures and the use of multiple molecular techniques to delineate these genomic alterations. We suggest that chromoanagenesis may be a possible mechanism involved in the repair and reconstitution of these rearrangements with evidence for increasing genomic imbalances such as additional deletions in this case.
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33
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Li D, Strong A, Hou C, Downes H, Pritchard AB, Mazzeo P, Zackai EH, Conlin LK, Hakonarson H. Interstitial deletion 4p15.32p16.1 and complex chromoplexy in a female proband with severe neurodevelopmental delay, growth failure and dysmorphism. Mol Cytogenet 2022; 15:33. [PMID: 35932041 PMCID: PMC9354344 DOI: 10.1186/s13039-022-00610-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
Complex chromosomal rearrangements involve the restructuring of genetic material within a single chromosome or across multiple chromosomes. These events can cause serious human disease by disrupting coding DNA and gene regulatory elements via deletions, duplications, and structural rearrangements. Here we describe a 5-year-old female with severe developmental delay, dysmorphic features, multi-suture craniosynostosis, and growth failure found to have a complex series of balanced intra- and inter-chromosomal rearrangements involving chromosomes 4, 11, 13, and X. Initial clinical studies were performed by karyotype, chromosomal microarray, and FISH with research-based short-read genome sequencing coupled with sanger sequencing to precisely map her breakpoints to the base pair resolution to understand the molecular basis of her phenotype. Genome analysis revealed two pathogenic deletions at 4p16.1-p15.32 and 4q31.1, accounting for her developmental delay and dysmorphism. We identified over 60 breakpoints, many with blunt ends and limited homology, supporting a role for non-homologous end joining in restructuring and resolution of the seminal chromoplexy event. We propose that the complexity of our patient’s genomic rearrangements with a high number of breakpoints causes dysregulation of gene expression by three-dimensional chromatin interactions or topologically associating domains leading to growth failure and craniosynostosis. Our work supports an important role for genome sequencing in understanding the molecular basis of complex chromosomal rearrangements in human disease.
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Affiliation(s)
- Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Abramson Research Building, Suite 1016I, 3615 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA. .,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Alanna Strong
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Abramson Research Building, Suite 1016I, 3615 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cuiping Hou
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Abramson Research Building, Suite 1016I, 3615 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA
| | - Helen Downes
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Abramson Research Building, Suite 1016I, 3615 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA
| | - Amanda Barone Pritchard
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, University of Michigan Health, Ann Arbor, MI, USA
| | - Pamela Mazzeo
- Division of General Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elaine H Zackai
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Abramson Research Building, Suite 1016I, 3615 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
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34
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Ní Leathlobhair M, Lenski RE. Population genetics of clonally transmissible cancers. Nat Ecol Evol 2022; 6:1077-1089. [PMID: 35879542 DOI: 10.1038/s41559-022-01790-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
Populations of cancer cells are subject to the same core evolutionary processes as asexually reproducing, unicellular organisms. Transmissible cancers are particularly striking examples of these processes. These unusual cancers are clonal lineages that can spread through populations via physical transfer of living cancer cells from one host individual to another, and they have achieved long-term success in the colonization of at least eight different host species. Population genetic theory provides a useful framework for understanding the shift from a multicellular sexual animal into a unicellular asexual clone and its long-term effects on the genomes of these cancers. In this Review, we consider recent findings from transmissible cancer research with the goals of developing an evolutionarily informed perspective on transmissible cancers, examining possible implications for their long-term fate and identifying areas for future research on these exceptional lineages.
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Affiliation(s)
- Máire Ní Leathlobhair
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland.
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
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35
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Burssed B, Zamariolli M, Bellucco FT, Melaragno MI. Mechanisms of structural chromosomal rearrangement formation. Mol Cytogenet 2022; 15:23. [PMID: 35701783 PMCID: PMC9199198 DOI: 10.1186/s13039-022-00600-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/31/2022] [Indexed: 12/31/2022] Open
Abstract
Structural chromosomal rearrangements result from different mechanisms of formation, usually related to certain genomic architectural features that may lead to genetic instability. Most of these rearrangements arise from recombination, repair, or replication mechanisms that occur after a double-strand break or the stalling/breakage of a replication fork. Here, we review the mechanisms of formation of structural rearrangements, highlighting their main features and differences. The most important mechanisms of constitutional chromosomal alterations are discussed, including Non-Allelic Homologous Recombination (NAHR), Non-Homologous End-Joining (NHEJ), Fork Stalling and Template Switching (FoSTeS), and Microhomology-Mediated Break-Induced Replication (MMBIR). Their involvement in chromoanagenesis and in the formation of complex chromosomal rearrangements, inverted duplications associated with terminal deletions, and ring chromosomes is also outlined. We reinforce the importance of high-resolution analysis to determine the DNA sequence at, and near, their breakpoints in order to infer the mechanisms of formation of structural rearrangements and to reveal how cells respond to DNA damage and repair broken ends.
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Affiliation(s)
- Bruna Burssed
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernanda Teixeira Bellucco
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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36
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Cosenza MR, Rodriguez-Martin B, Korbel JO. Structural Variation in Cancer: Role, Prevalence, and Mechanisms. Annu Rev Genomics Hum Genet 2022; 23:123-152. [DOI: 10.1146/annurev-genom-120121-101149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Somatic rearrangements resulting in genomic structural variation drive malignant phenotypes by altering the expression or function of cancer genes. Pan-cancer studies have revealed that structural variants (SVs) are the predominant class of driver mutation in most cancer types, but because they are difficult to discover, they remain understudied when compared with point mutations. This review provides an overview of the current knowledge of somatic SVs, discussing their primary roles, prevalence in different contexts, and mutational mechanisms. SVs arise throughout the life history of cancer, and 55% of driver mutations uncovered by the Pan-Cancer Analysis of Whole Genomes project represent SVs. Leveraging the convergence of cell biology and genomics, we propose a mechanistic classification of somatic SVs, from simple to highly complex DNA rearrangement classes. The actions of DNA repair and DNA replication processes together with mitotic errors result in a rich spectrum of SV formation processes, with cascading effects mediating extensive structural diversity after an initiating DNA lesion has formed. Thanks to new sequencing technologies, including the sequencing of single-cell genomes, open questions about the molecular triggers and the biomolecules involved in SV formation as well as their mutational rates can now be addressed. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | | | - Jan O. Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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37
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Liu P, Vossaert L. Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing. Prenat Diagn 2022; 42:686-696. [PMID: 35416301 PMCID: PMC10014115 DOI: 10.1002/pd.6146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/10/2022]
Abstract
DNA sequencing technologies for clinical genetic testing have been rapidly evolving in recent years, and steadily become more important within the field of prenatal diagnostics. This review aims to give an overview of recent developments and to describe how they have the potential to fill the gaps of the currently clinically implemented methods for prenatal diagnosis of various genetic disorders. It has been shown for postnatal testing that whole genome sequencing provides a set of added benefits compared to exome sequencing, and it is to be expected that this will be the case for prenatal testing as well. RNA-sequencing, already used postnatally, can provide valuable complementary data to DNA-based testing, and aid in variant interpretation. While not ready for clinical implementation, emerging technologies such as long-read and Hi-C sequencing analyses might add to the toolbox for interpreting the expanding genetic data sets generated by genome-wide sequencing. Lastly, we also discuss some more practical implications of introducing these emerging technologies, which generate larger and larger genomic data sets, in the prenatal field.
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Affiliation(s)
- Pengfei Liu
- Baylor College of Medicine and Baylor Genetics, Houston, Texas, USA
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38
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Abstract
Distilling biologically meaningful information from cancer genome sequencing data requires comprehensive identification of somatic alterations using rigorous computational methods. As the amount and complexity of sequencing data have increased, so has the number of tools for analysing them. Here, we describe the main steps involved in the bioinformatic analysis of cancer genomes, review key algorithmic developments and highlight popular tools and emerging technologies. These tools include those that identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes. We also discuss issues in experimental design, the strengths and limitations of sequencing modalities and methodological challenges for the future.
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39
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Perovic D, Damnjanovic T, Jekic B, Dusanovic-Pjevic M, Grk M, Djuranovic A, Rasic M, Novakovic I, Maksimovic N. Chromosomal microarray in postnatal diagnosis of congenital anomalies and neurodevelopmental disorders in Serbian patients. J Clin Lab Anal 2022; 36:e24441. [PMID: 35441737 PMCID: PMC9169173 DOI: 10.1002/jcla.24441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022] Open
Abstract
Background Array‐based genomic analysis is a gold standard for the detection of copy number variations (CNVs) as an important source of benign as well as pathogenic variations in humans. The introduction of chromosomal microarray (CMA) has led to a significant leap in diagnostics of genetically caused congenital malformations and neurodevelopmental disorders, with an average diagnostic yield of 15%. Here, we present our experience from a single laboratory perspective in four years’ postnatal clinical CMA application. Methods DNA samples of 430 patients with congenital anomalies and/or neurodevelopmental disorders were analyzed by comparative genome hybridization using oligonucleotide‐based microarray platforms. Interpretation of detected CNVs was performed according to current guidelines. The detection rate (DR) of clinically significant findings (pathogenic/likely pathogenic CNVs) was calculated for the whole cohort and isolated or combined phenotypic categories. Results A total of 140 non‐benign CNVs were detected in 113/430 patients (26.5%). In 70 patients at least one CNV was considered clinically significant thus reaching a diagnostic yield of 16.3%. The more complex the phenotype, including developmental delay/intellectual disability (DD/ID) as a prevailing feature, the higher the DR of clinically significant CNVs is obtained. Isolated congenital anomalies had the lowest, while the “dysmorphism plus” category had the highest diagnostic yield. Conclusion In our study, CMA proved to be a very useful method in the diagnosis of genetically caused congenital anomalies and neurodevelopmental disorders. DD/ID and dysmorphism stand out as important phenotypic features that significantly increase the diagnostic yield of the analysis.
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Affiliation(s)
- Dijana Perovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Tatjana Damnjanovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Biljana Jekic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | | | - Milka Grk
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Ana Djuranovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Milica Rasic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Ivana Novakovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Nela Maksimovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
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40
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Zhang CZ, Pellman D. Cancer Genomic Rearrangements and Copy Number Alterations from Errors in Cell Division. ANNUAL REVIEW OF CANCER BIOLOGY 2022. [DOI: 10.1146/annurev-cancerbio-070620-094029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Analysis of cancer genomes has shown that a large fraction of chromosomal changes originate from catastrophic events including whole-genome duplication, chromothripsis, breakage-fusion-bridge cycles, and chromoplexy. Through sophisticated computational analysis of cancer genomes and experimental recapitulation of these catastrophic alterations, we have gained significant insights into the origin, mechanism, and evolutionary dynamics of cancer genome complexity. In this review, we summarize this progress and survey the major unresolved questions, with particular emphasis on the relative contributions of chromosome fragmentation and DNA replication errors to complex chromosomal alterations.
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Affiliation(s)
- Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - David Pellman
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts, USA
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41
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Bakloushinskaya I. Chromosome Changes in Soma and Germ Line: Heritability and Evolutionary Outcome. Genes (Basel) 2022; 13:genes13040602. [PMID: 35456408 PMCID: PMC9029507 DOI: 10.3390/genes13040602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 12/13/2022] Open
Abstract
The origin and inheritance of chromosome changes provide the essential foundation for natural selection and evolution. The evolutionary fate of chromosome changes depends on the place and time of their emergence and is controlled by checkpoints in mitosis and meiosis. Estimating whether the altered genome can be passed to subsequent generations should be central when we consider a particular genome rearrangement. Through comparative analysis of chromosome rearrangements in soma and germ line, the potential impact of macromutations such as chromothripsis or chromoplexy appears to be fascinating. What happens with chromosomes during the early development, and which alterations lead to mosaicism are other poorly studied but undoubtedly essential issues. The evolutionary impact can be gained most effectively through chromosome rearrangements arising in male meiosis I and in female meiosis II, which are the last divisions following fertilization. The diversity of genome organization has unique features in distinct animals; the chromosome changes, their internal relations, and some factors safeguarding genome maintenance in generations under natural selection were considered for mammals.
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Affiliation(s)
- Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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42
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Insight into the Molecular Basis Underlying Chromothripsis. Int J Mol Sci 2022; 23:ijms23063318. [PMID: 35328739 PMCID: PMC8948871 DOI: 10.3390/ijms23063318] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
Chromoanagenesis constitutes a group of events that arise from single cellular events during early development. This particular class of complex rearrangements is a newfound occurrence that may lead to chaotic and complex genomic realignments. By that, chromoanagenesis is thought to be a crucial factor regarding macroevolution of the genome, and consequently is affecting the karyotype revolution together with genomic plasticity. One of chromoanagenesis-type of events is chromothripsis. It is characterised by the breakage of the chromosomal structure and its reassembling in random order and orientation which results in the establishment of derivative forms of chromosomes. Molecular mechanisms that underlie this phenomenon are mostly related to chromosomal sequestration throughout the micronuclei formation process. Chromothripsis is linked both to congenital and cancer diseases, moreover, it might be detected in subjects characterised by a normal phenotype. Chromothripsis, as well as the other chromoanagenetic variations, may be confined to one or more chromosomes, which makes up a non-uniform variety of karyotypes among chromothriptic patients. The detection of chromothripsis is enabled via tools like microarray-based comparative genomic hybridisation, next generation sequencing or authorial protocols aimed for the recognition of structural variations.
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Dahiya R, Hu Q, Ly P. Mechanistic origins of diverse genome rearrangements in cancer. Semin Cell Dev Biol 2022; 123:100-109. [PMID: 33824062 PMCID: PMC8487437 DOI: 10.1016/j.semcdb.2021.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/08/2021] [Indexed: 12/14/2022]
Abstract
Cancer genomes frequently harbor structural chromosomal rearrangements that disrupt the linear DNA sequence order and copy number. To date, diverse classes of structural variants have been identified across multiple cancer types. These aberrations span a wide spectrum of complexity, ranging from simple translocations to intricate patterns of rearrangements involving multiple chromosomes. Although most somatic rearrangements are acquired gradually throughout tumorigenesis, recent interrogation of cancer genomes have uncovered novel categories of complex rearrangements that arises rapidly through a one-off catastrophic event, including chromothripsis and chromoplexy. Here we review the cellular and molecular mechanisms contributing to the formation of diverse structural rearrangement classes during cancer development. Genotoxic stress from a myriad of extrinsic and intrinsic sources can trigger DNA double-strand breaks that are subjected to DNA repair with potentially mutagenic outcomes. We also highlight how aberrant nuclear structures generated through mitotic cell division errors, such as rupture-prone micronuclei and chromosome bridges, can instigate massive DNA damage and the formation of complex rearrangements in cancer genomes.
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Affiliation(s)
- Rashmi Dahiya
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Qing Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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44
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Heng J, Heng HH. Genome Chaos, Information Creation, and Cancer Emergence: Searching for New Frameworks on the 50th Anniversary of the "War on Cancer". Genes (Basel) 2021; 13:genes13010101. [PMID: 35052441 PMCID: PMC8774498 DOI: 10.3390/genes13010101] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 12/26/2022] Open
Abstract
The year 2021 marks the 50th anniversary of the National Cancer Act, signed by President Nixon, which declared a national “war on cancer.” Powered by enormous financial support, this past half-century has witnessed remarkable progress in understanding the individual molecular mechanisms of cancer, primarily through the characterization of cancer genes and the phenotypes associated with their pathways. Despite millions of publications and the overwhelming volume data generated from the Cancer Genome Project, clinical benefits are still lacking. In fact, the massive, diverse data also unexpectedly challenge the current somatic gene mutation theory of cancer, as well as the initial rationales behind sequencing so many cancer samples. Therefore, what should we do next? Should we continue to sequence more samples and push for further molecular characterizations, or should we take a moment to pause and think about the biological meaning of the data we have, integrating new ideas in cancer biology? On this special anniversary, we implore that it is time for the latter. We review the Genome Architecture Theory, an alternative conceptual framework that departs from gene-based theories. Specifically, we discuss the relationship between genes, genomes, and information-based platforms for future cancer research. This discussion will reinforce some newly proposed concepts that are essential for advancing cancer research, including two-phased cancer evolution (which reconciles evolutionary contributions from karyotypes and genes), stress-induced genome chaos (which creates new system information essential for macroevolution), the evolutionary mechanism of cancer (which unifies diverse molecular mechanisms to create new karyotype coding during evolution), and cellular adaptation and cancer emergence (which explains why cancer exists in the first place). We hope that these ideas will usher in new genomic and evolutionary conceptual frameworks and strategies for the next 50 years of cancer research.
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Affiliation(s)
- Julie Heng
- Harvard College, 16 Divinity Ave, Cambridge, MA 02138, USA;
| | - Henry H. Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Correspondence:
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45
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The Abscission Checkpoint: A Guardian of Chromosomal Stability. Cells 2021; 10:cells10123350. [PMID: 34943860 PMCID: PMC8699595 DOI: 10.3390/cells10123350] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022] Open
Abstract
The abscission checkpoint contributes to the fidelity of chromosome segregation by delaying completion of cytokinesis (abscission) when there is chromatin lagging in the intercellular bridge between dividing cells. Although additional triggers of an abscission checkpoint-delay have been described, including nuclear pore defects, replication stress or high intercellular bridge tension, this review will focus only on chromatin bridges. In the presence of such abnormal chromosomal tethers in mammalian cells, the abscission checkpoint requires proper localization and optimal kinase activity of the Chromosomal Passenger Complex (CPC)-catalytic subunit Aurora B at the midbody and culminates in the inhibition of Endosomal Sorting Complex Required for Transport-III (ESCRT-III) components at the abscission site to delay the final cut. Furthermore, cells with an active checkpoint stabilize the narrow cytoplasmic canal that connects the two daughter cells until the chromatin bridges are resolved. Unsuccessful resolution of chromatin bridges in checkpoint-deficient cells or in cells with unstable intercellular canals can lead to chromatin bridge breakage or tetraploidization by regression of the cleavage furrow. In turn, these outcomes can lead to accumulation of DNA damage, chromothripsis, generation of hypermutation clusters and chromosomal instability, which are associated with cancer formation or progression. Recently, many important questions regarding the mechanisms of the abscission checkpoint have been investigated, such as how the presence of chromatin bridges is signaled to the CPC, how Aurora B localization and kinase activity is regulated in late midbodies, the signaling pathways by which Aurora B implements the abscission delay, and how the actin cytoskeleton is remodeled to stabilize intercellular canals with DNA bridges. Here, we review recent progress toward understanding the mechanisms of the abscission checkpoint and its role in guarding genome integrity at the chromosome level, and consider its potential implications for cancer therapy.
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46
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Robert M, Crasta K. Breaking the vicious circle: Extrachromosomal circular DNA as an emerging player in tumour evolution. Semin Cell Dev Biol 2021; 123:140-150. [PMID: 34857471 DOI: 10.1016/j.semcdb.2021.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 12/16/2022]
Abstract
Extrachromosomal circular DNA (ecDNA) or double minutes have gained renewed interest since its discovery more than five decades ago, emerging as potent drivers of tumour evolution. This has largely been motivated by recent discovery that the tumour-exclusive ecDNA are highly prevalent in almost all cancers unlike previously thought. EcDNAs contribute to elevated oncogene expression, intratumoural heterogeneity, tumour adaptation and therapy resistance independently of canonical chromosomal alterations. Importantly, ecDNAs play a critical role in patient survival as ecDNA-based oncogene amplification adversely affects clinical outcome to a significantly greater extent than intrachromosomal amplification. Chromothripsis, a major driver of ecDNA biogenesis and gene amplification, is a mutational process characterised by chromosomal shattering and localised complex genome rearrangement. Chemotherapeutic drugs can lead to chromothriptic rearrangements and therapy resistance. In this review, we examine how ecDNAs mediate oncogene overexpression, facilitate accelerated tumour malignancy and enhance rapid adaptation independently of linear chromosomes. We delve into discoveries pertaining to mechanisms of biogenesis, distinctive features of ecDNA, gene regulation and topological interactions with active chromatin. We also discuss the critical role of chromothripsis in engendering ecDNA amplification and evolution. One envisions that insights into ecDNA biology not only hold importance for the cancer genome and tumour evolutionary dynamics, but could also inform prognostication and clinical intervention, particularly for cancers characterised by high oncogene amplification.
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Affiliation(s)
- Matius Robert
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Healthy Longevity Translational Research Program, National University of Singapore, Singapore
| | - Karen Crasta
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Healthy Longevity Translational Research Program, National University of Singapore, Singapore; NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Agency for Science, Technology & Research (A⁎STAR), Institute of Molecular and Cell Biology, Singapore.
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47
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Keuper K, Wieland A, Räschle M, Storchova Z. Processes shaping cancer genomes - From mitotic defects to chromosomal rearrangements. DNA Repair (Amst) 2021; 107:103207. [PMID: 34425515 DOI: 10.1016/j.dnarep.2021.103207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 11/19/2022]
Abstract
Sequencing of cancer genomes revealed a rich landscape of somatic single nucleotide variants, structural changes of chromosomes, as well as chromosomal copy number alterations. These chromosome changes are highly variable, and simple translocations, deletions or duplications have been identified, as well as complex events that likely arise through activity of several interconnected processes. Comparison of the cancer genome sequencing data with our knowledge about processes important for maintenance of genome stability, namely DNA replication, repair and chromosome segregation, provides insights into the mechanisms that may give rise to complex chromosomal patterns, such as chromothripsis, a complex form of multiple focal chromosome rearrangements. In addition, observations gained from model systems that recapitulate the rearrangements patterns under defined experimental conditions suggest that mitotic errors and defective DNA replication and repair contribute to their formation. Here, we review the molecular mechanisms that contribute to formation of chromosomal aberrations observed in cancer genomes.
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Affiliation(s)
- Kristina Keuper
- Department of Molecular Genetics, Paul-Ehrlich Strasse 24, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Angela Wieland
- Department of Molecular Genetics, Paul-Ehrlich Strasse 24, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Markus Räschle
- Department of Molecular Genetics, Paul-Ehrlich Strasse 24, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Zuzana Storchova
- Department of Molecular Genetics, Paul-Ehrlich Strasse 24, University of Kaiserslautern, 67663, Kaiserslautern, Germany.
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48
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Lupski JR. Clan genomics: From OMIM phenotypic traits to genes and biology. Am J Med Genet A 2021; 185:3294-3313. [PMID: 34405553 PMCID: PMC8530976 DOI: 10.1002/ajmg.a.62434] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/29/2021] [Accepted: 07/04/2021] [Indexed: 12/20/2022]
Abstract
Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
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49
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Giunta S. Decoding human cancer with whole genome sequencing: a review of PCAWG Project studies published in February 2020. Cancer Metastasis Rev 2021; 40:909-924. [PMID: 34097189 PMCID: PMC8180541 DOI: 10.1007/s10555-021-09969-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022]
Abstract
Cancer is underlined by genetic changes. In an unprecedented international effort, the Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) sequenced the tumors of over two thousand five hundred patients across 38 different cancer types, as well as the corresponding healthy tissue, with the aim of identifying genome-wide mutations exclusively found in cancer and uncovering new genetic changes that drive tumor formation. What set this project apart from earlier efforts is the use of whole genome sequencing (WGS) that enabled to explore alterations beyond the coding DNA, into cancer's non-coding genome. WGS of the entire cohort allowed to tease apart driving mutations that initiate and support carcinogenesis from passenger mutations that do not play an overt role in the disease. At least one causative mutation was found in 95% of all cancers, with many tumors showing an average of 5 driver mutations. The PCAWG Project also assessed the transcriptional output altered in cancer and rebuilt the evolutionary history of each tumor showing that initial driver mutations can occur years if not decades prior to a diagnosis. Here, I provide a concise review of the Pan-Cancer Project papers published on February 2020, along with key computational tools and the digital framework generated as part of the project. This represents an historic effort by hundreds of international collaborators, which provides a comprehensive understanding of cancer genetics, with publicly available data and resources representing a treasure trove of information to advance cancer research for years to come.
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Affiliation(s)
- Simona Giunta
- Laboratory of Genome Evolution, Department of Biology & Biotechnology "Charles Darwin", University of Rome Sapienza, Rome, Italy.
- The Rockefeller University, 1230 York Avenue, New York, NY, USA.
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50
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Guo W, Comai L, Henry IM. Chromoanagenesis from radiation-induced genome damage in Populus. PLoS Genet 2021; 17:e1009735. [PMID: 34432802 PMCID: PMC8423247 DOI: 10.1371/journal.pgen.1009735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/07/2021] [Accepted: 07/22/2021] [Indexed: 11/18/2022] Open
Abstract
Chromoanagenesis is a genomic catastrophe that results in chromosomal shattering and reassembly. These extreme single chromosome events were first identified in cancer, and have since been observed in other systems, but have so far only been formally documented in plants in the context of haploid induction crosses. The frequency, origins, consequences, and evolutionary impact of such major chromosomal remodeling in other situations remain obscure. Here, we demonstrate the occurrence of chromoanagenesis in poplar (Populus sp.) trees produced from gamma-irradiated pollen. Specifically, in this population of siblings carrying indel mutations, two individuals exhibited highly frequent copy number variation (CNV) clustered on a single chromosome, one of the hallmarks of chromoanagenesis. Using short-read sequencing, we confirmed the presence of clustered segmental rearrangement. Independently, we identified and validated novel DNA junctions and confirmed that they were clustered and corresponded to these rearrangements. Our reconstruction of the novel sequences suggests that the chromosomal segments have reorganized randomly to produce a novel rearranged chromosome but that two different mechanisms might be at play. Our results indicate that gamma irradiation can trigger chromoanagenesis, suggesting that this may also occur when natural or induced mutagens cause DNA breaks. We further demonstrate that such events can be tolerated in poplar, and even replicated clonally, providing an attractive system for more in-depth investigations of their consequences. Plant breeders often use radiation treatment to produce variation, with the goal of identifying new varieties with superior traits. We studied a population of poplar trees produced by gamma irradiation of pollen, and asked what kind of DNA changes were associated with this variation. We found many changes, most often in the form of added (insertions) or removed (deletions) pieces of DNA. We also found two lines with much more drastic changes. In those lines, we observed massive reorganization. We characterized these two lines in detail and found that catastrophic pulverization and random reassembly only occurred on a single chromosome. Looking closely at how the pieces were put back together suggest that the rearrangements in these two lines may have resulted from two slightly different mechanisms. This type of rearrangement is commonly observed in human cancer cells, but has rarely been observed in plants. We demonstrated here that they can be induced by gamma irradiation, indicating this type of event might be more widespread than we expected. Characterizing such genome restructuring instances helps to understand how genome instability can remodel chromosomes and affect genome function.
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Affiliation(s)
- Weier Guo
- Genome Center and Dept. Plant Biology, University of California Davis, Davis, California, United States of America
| | - Luca Comai
- Genome Center and Dept. Plant Biology, University of California Davis, Davis, California, United States of America
| | - Isabelle M. Henry
- Genome Center and Dept. Plant Biology, University of California Davis, Davis, California, United States of America
- * E-mail:
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