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Kohlrausch FB, Wang F, McKerrow W, Grivainis M, Fenyo D, Keefe DL. Mapping of long interspersed element-1 (L1) insertions by TIPseq provides information about sub chromosomal genetic variation in human embryos. J Assist Reprod Genet 2024:10.1007/s10815-024-03176-9. [PMID: 38951360 DOI: 10.1007/s10815-024-03176-9] [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: 07/14/2023] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
PURPOSE Retrotransposons play important roles during early development when they are transiently de-repressed during epigenetic reprogramming. Long interspersed element-1 (L1), the only autonomous retrotransposon in humans, comprises 17% of the human genome. We applied the Single Cell Transposon Insertion Profiling by Sequencing (scTIPseq) to characterize and map L1 insertions in human embryos. METHODS Sixteen cryopreserved, genetically tested, human blastocysts, were accessed from consenting couples undergoing IVF at NYU Langone Fertility Center. Additionally, four trios (father, mother, and embryos) were also evaluated. scTIPseq was applied to map L1 insertions in all samples, using L1 locations reported in the 1000 Genomes as controls. RESULTS Twenty-nine unknown and unique insertions were observed in the sixteen embryos. Most were intergenic; no insertions were located in exons or immediately upstream of genes. The location or number of unknown insertions did not differ between euploid and aneuploid embryos, suggesting they are not merely markers of aneuploidy. Rather, scTIPseq provides novel information about sub-chromosomal structural variation in human embryos. Trio analyses showed a parental origin of all L1 insertions in embryos. CONCLUSION Several studies have measured L1 expression at different stages of development in mice, but this study for the first time reports unknown insertions in human embryos that were inherited from one parent, confirming no de novo L1 insertions occurred in parental germline or during embryogenesis. Since one-third of euploid embryo transfers fail, future studies would be useful for understanding whether these sub-chromosomal genetic variants or de novo L1 insertions affect embryo developmental potential.
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Affiliation(s)
- Fabiana B Kohlrausch
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, 24210-201, Brazil.
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA.
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - Mark Grivainis
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - David Fenyo
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA
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2
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Budrewicz J, Chavez SL. Insights into embryonic chromosomal instability: mechanisms of DNA elimination during mammalian preimplantation development. Front Cell Dev Biol 2024; 12:1344092. [PMID: 38374891 PMCID: PMC10875028 DOI: 10.3389/fcell.2024.1344092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/15/2024] [Indexed: 02/21/2024] Open
Abstract
Mammalian preimplantation embryos often contend with aneuploidy that arose either by the inheritance of meiotic errors from the gametes, or from mitotic mis-segregation events that occurred following fertilization. Regardless of the origin, mis-segregated chromosomes become encapsulated in micronuclei (MN) that are spatially isolated from the main nucleus. Much of our knowledge of MN formation comes from dividing somatic cells during tumorigenesis, but the error-prone cleavage-stage of early embryogenesis is fundamentally different. One unique aspect is that cellular fragmentation (CF), whereby small subcellular bodies pinch off embryonic blastomeres, is frequently observed. CF has been detected in both in vitro and in vivo-derived embryos and likely represents a response to chromosome mis-segregation since it only appears after MN formation. There are multiple fates for MN, including sequestration into CFs, but the molecular mechanism(s) by which this occurs remains unclear. Due to nuclear envelope rupture, the chromosomal material contained within MN and CFs becomes susceptible to double stranded-DNA breaks. Despite this damage, embryos may still progress to the blastocyst stage and exclude chromosome-containing CFs, as well as non-dividing aneuploid blastomeres, from participating in further development. Whether these are attempts to rectify MN formation or eliminate embryos with poor implantation potential is unknown and this review will discuss the potential implications of DNA removal by CF/blastomere exclusion. We will also extrapolate what is known about the intracellular pathways mediating MN formation and rupture in somatic cells to preimplantation embryogenesis and how nuclear budding and DNA release into the cytoplasm may impact overall development.
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Affiliation(s)
- Jacqueline Budrewicz
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR, United States
| | - Shawn L. Chavez
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR, United States
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
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3
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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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4
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Comaills V, Castellano-Pozo M. Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution. BIOLOGY 2023; 12:biology12050671. [PMID: 37237485 DOI: 10.3390/biology12050671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures, and for this purpose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanisms leading to the creation of genomic heterogeneity by altering the number of chromosomes and changing their structures. In this review, we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, the human genome shows an induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as the whole genome doubling to more discrete changes as the complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double-strand breaks (DSBs) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs, and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar patterns observed during tumorigenesis. Then, we will also list several diseases associated with CIN, resulting in fertility issues, miscarriage, rare genetic diseases, and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.
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Affiliation(s)
- Valentine Comaills
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
| | - Maikel Castellano-Pozo
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
- Genetic Department, Faculty of Biology, University of Seville, 41080 Seville, Spain
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5
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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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Regin M, Spits C, Sermon K. On the origins and fate of chromosomal abnormalities in human preimplantation embryos: an unsolved riddle. Mol Hum Reprod 2022; 28:6566308. [DOI: 10.1093/molehr/gaac011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
About 8 out of 10 human embryos obtained in vitro harbour chromosomal abnormalities of either meiotic or mitotic origin. Abnormalities of mitotic origin lead to chromosomal mosaicism, a phenomenon which has sparked much debate lately as it confounds results obtained through preimplantation genetic testing for aneuploidy (PGT-A). PGT-A in itself is still highly debated, not only on the modalities of its execution, but also on whether it should be offered to patients at all.
We will focus on post-zygotic chromosomal abnormalities leading to mosaicism. First, we will summarize what is known of the rates of chromosomal abnormalities at different developmental stages. Next, based on the current understanding of the origin and cellular consequences of chromosomal abnormalities, which is largely based on studies on cancer cells and model organisms, we will offer a number of hypotheses on which mechanisms may be at work in early human development. Finally, and very briefly, we will touch upon the impact our current knowledge has on the practice of PGT-A. What is the level of abnormal cells that an embryo can tolerate before it loses its potential for full development? And is blastocyst biopsy as harmless as it seems?
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Affiliation(s)
- Marius Regin
- Research group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, 1090, Belgium
| | - Claudia Spits
- Research group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, 1090, Belgium
| | - Karen Sermon
- Research group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, 1090, Belgium
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7
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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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8
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Preimplantation genetic testing for aneuploidy (PGT-A)-a single-center experience. J Assist Reprod Genet 2022; 39:729-738. [PMID: 35119550 PMCID: PMC8995221 DOI: 10.1007/s10815-022-02413-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/25/2022] [Indexed: 10/19/2022] Open
Abstract
PURPOSE The aim of this study was to determine the prevalence and nature of human embryonic aneuploidy based on the preimplantation genetic testing for aneuploidy (PGT-A), the distribution of aneuploidy across the individual chromosomes, and their relationship to maternal age. METHODS This is a retrospective cohort study conducted at a single center. The study includes subjects who opted for PGT-A in their in vitro fertilization (IVF) cycle from 2016 to 2020. PGT-A was performed on 1501 embryos from 488 patients in 535 cycles. PGT-A was performed using NGS-based technique on Ion Torrent PGM (Life Technologies). Analysis was performed to determine the (i) frequency of the aneuploidy, (ii) the chromosome most commonly affected, (iii) relationship between maternal age and the rate of aneuploidy, and (iv) incidence of segmental aneuploidy. RESULTS The overall frequency of aneuploidy was observed to be 46.8%. The incidence of aneuploidy rate was ~ 28% at maternal age < 30 years which steadily increased to ~ 67% in women above 40 years. High frequency of aneuploidy was observed in chromosomes 16, 22, 21, and 15. Segmental abnormalities, involving loss or gain of chromosomal fragments, were observed at a frequency of 5.3%, and highest incidence of segmental gain was observed on the q-arm of chromosome 9. CONCLUSION The study provides important information regarding the frequency of the aneuploidy in IVF cohort and the most frequent chromosomal abnormality. The study further emphasizes the relationship between maternal age and aneuploidy. This study has important implications which help clinicians and genetic counselors in providing information in patient counseling.
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9
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Fukami M, Miyado M. Mosaic loss of the Y chromosome and men's health. Reprod Med Biol 2022; 21:e12445. [PMID: 35386373 PMCID: PMC8967293 DOI: 10.1002/rmb2.12445] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Maki Fukami
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
| | - Mami Miyado
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
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10
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Liu J. Giant cells: Linking McClintock's heredity to early embryogenesis and tumor origin throughout millennia of evolution on Earth. Semin Cancer Biol 2021; 81:176-192. [PMID: 34116161 DOI: 10.1016/j.semcancer.2021.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/12/2021] [Accepted: 06/06/2021] [Indexed: 02/08/2023]
Abstract
The "life code" theory postulates that egg cells, which are giant, are the first cells in reproduction and that damaged or aged giant somatic cells are the first cells in tumorigenesis. However, the hereditary basis for giant cells remains undefined. Here I propose that stress-induced genomic reorganization proposed by Nobel Laureate Barbara McClintock may represent the underlying heredity for giant cells, referred to as McClintock's heredity. Increase in cell size may serve as a response to environmental stress via switching proliferative mitosis to intranuclear replication for reproduction. Intranuclear replication activates McClintock's heredity to reset the genome following fertilization for reproduction or restructures the somatic genome for neoplastic transformation via formation of polyploid giant cancer cells (PGCCs). The genome-based McClintock heredity functions together with gene-based Mendel's heredity to regulate the genomic stability at two different stages of life cycle or tumorigenesis. Thus, giant cells link McClintock's heredity to both early embryogenesis and tumor origin. Cycling change in cell size together with ploidy number switch may represent the most fundamental mechanism on how both germ and soma for coping with environmental stresses for the survival across the tree of life which evolved over millions of years on Earth.
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Affiliation(s)
- Jinsong Liu
- Department of Anatomical Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, United States.
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11
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Soler N, Bautista-Llàcer R, Escrich L, Oller A, Grau N, Tena R, Insua MF, Ferrer P, Escribà MJ, Vendrell X. Rescuing monopronucleated-derived human blastocysts: a model to study chromosomal topography and fingerprinting. Fertil Steril 2021; 116:583-596. [PMID: 33926715 DOI: 10.1016/j.fertnstert.2021.03.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVE To quantify the percentage of monopronuclear-derived blastocysts (MNBs) that are potentially useful for reproductive purposes using classic and state-of-the-art chromosome analysis approaches, and to study chromosomal distribution in the inner cell mass (ICM) and trophectoderm (TE) for intertissue/intratissue concordance comparison. DESIGN Prospective experimental study. SETTING Single-center in vitro fertilization clinic and reproductive genetics laboratory. PATIENT(S) A total of 1,128 monopronuclear zygotes were obtained between June 2016 and December 2018. INTERVENTION(S) MNBs were whole-fixed or biopsied to obtain a portion of ICM and 2 TE portions (TE1 and TE2) and were subsequently analyzed by fluorescence in situ hybridization, new whole-genome sequencing, and fingerprinting by single-nucleotide polymorphism array-based techniques (a-SNP). MAIN OUTCOME MEASURE(S) We assessed MNB rate, ploidy rate, and chromosomal constitution by new whole-genome sequencing, and parental composition by comparative a-SNP, performed in a "trio"-format (embryo/parents). The 24-chromosome distribution was compared between the TE and the ICM and within the TE. RESULT(S) A total of 18.4% of monopronuclear zygotes progressed to blastocysts; 77.6% of MNBs were diploid; 20% of MNBs were male and euploid, which might be reproductively useful. Seventy-five percent of MNBs were biparental and half of them were euploid, indicating that 40% might be reproductively useful. Intratissue concordance (TE1/TE2) was established for 93.3% and 73.3% for chromosome matching. Intertissue concordance (TE/ICM) was established for 78.8%, but 57.6% for chromosome matching. When segmental aneuploidy was not considered, intratissue concordance and chromosome matching increased to 100% and 80%, respectively, and intertissue concordance and chromosome matching increased to 84.8% and 75.8%, respectively. CONCLUSION(S) The a-SNP-trio strategy provides information about ploidy, euploidy, and parental origin in a single biopsy. This approach enabled us to identify 40% of MNBs with reproductive potential, which can have a significant effect in the clinical setting. Additionally, segmental aneuploidy is relevant for mismatched preimplantation genetic testing of aneuploidies, both within and between MNB tissues. Repeat biopsy might clarify whether segmental aneuploidy is a prone genetic character.
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Affiliation(s)
- Nuria Soler
- IVF Laboratory, IVI-RMA-València, Valencia, Spain; IVI Foundation, Valencia, Spain; Department of Pediatrics, Obstetrics and Gynaecology, University of Valencia, Valencia, Spain
| | | | | | - Andrea Oller
- Reproductive Genetics Unit, Sistemas Genómicos, Paterna, Valencia, Spain
| | - Noelia Grau
- IVF Laboratory, IVI-RMA-València, Valencia, Spain
| | - Raquel Tena
- Citogenomics Unit, Sistemas Genómicos, Paterna, Valencia, Spain
| | | | - Paloma Ferrer
- Citogenomics Unit, Sistemas Genómicos, Paterna, Valencia, Spain
| | - María-José Escribà
- IVF Laboratory, IVI-RMA-València, Valencia, Spain; IVI Foundation, Valencia, Spain; Instituto de Ciencia y Tecnología Animal, Universitat Politècnica de València, Valencia, Spain.
| | - Xavier Vendrell
- Reproductive Genetics Unit, Sistemas Genómicos, Paterna, Valencia, Spain
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Ishchuk MA, Malysheva OV, Komarova EM, Mekina ID, Lesik EA, Gzgzyan AM, Kogan IY, Baranov VS. Protamine 1 and 2 mRNA Abundance in Human Spermatozoa and Its Relation to Semen Quality and Sperm DNA Fragmentation among Fertility Clinic Patients. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421020058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Benn P. Uniparental disomy: Origin, frequency, and clinical significance. Prenat Diagn 2021; 41:564-572. [PMID: 33179335 DOI: 10.1002/pd.5837] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/28/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]
Abstract
Uniparental disomy (UPD) is defined as two copies of a whole chromosome derived from the same parent. There can be multiple mechanisms that lead to UPD; these are reviewed in the context of contemporary views on the mechanism leading to aneuploidy. Recent studies indicate that UPD is rare in an apparently healthy population and also rare in spontaneous abortion tissues. The most common type of UPD is a maternal heterodisomy (both maternal allele sets present). Isodisomy (a duplicated single set of alleles) or segmental loss of heterozygosity is sometimes encountered in SNP-based microarray referrals. Decisions regarding the most appropriate follow-up testing should consider the possibility of consanguinity (that will generally involve multiple regions), an imprinted gene disorder (chromosomes 6, 7, 11, 14, 15, 20), expression of an autosomal recessive disorder, and an occult aneuploid cell line that may be confined to the placenta. Upd(16)mat, per se, does not appear to be associated with an abnormal phenotype. UPD provides an insight into the history of early chromosome segregation error and understanding the rates and fate of these events are of key importance in the provision of fertility management and prenatal healthcare.
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Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA
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14
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Kohlrausch FB, Berteli TS, Wang F, Navarro PA, Keefe DL. Control of LINE-1 Expression Maintains Genome Integrity in Germline and Early Embryo Development. Reprod Sci 2021; 29:328-340. [PMID: 33481218 DOI: 10.1007/s43032-021-00461-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/06/2021] [Indexed: 11/28/2022]
Abstract
Maintenance of genome integrity in the germline and in preimplantation embryos is crucial for mammalian development. Epigenetic remodeling during primordial germ cell (PGC) and preimplantation embryo development may contribute to genomic instability in these cells, since DNA methylation is an important mechanism to silence retrotransposons. Long interspersed elements 1 (LINE-1 or L1) are the most common autonomous retrotransposons in mammals, corresponding to approximately 17% of the human genome. Retrotransposition events are more frequent in germ cells and in early stages of embryo development compared with somatic cells. It has been shown that L1 activation and expression occurs in germline and is essential for preimplantation development. In this review, we focus on the role of L1 retrotransposon in mouse and human germline and early embryo development and discuss the possible relationship between L1 expression and genomic instability during these stages. Although several studies have addressed L1 expression at different stages of development, the developmental consequences of this expression remain poorly understood. Future research is still needed to highlight the relationship between L1 retrotransposition events and genomic instability during germline and early embryo development.
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Affiliation(s)
- Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Thalita S Berteli
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA
| | - Paula A Navarro
- Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.
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15
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M'kacher R, Colicchio B, Marquet V, Borie C, Najar W, Hempel WM, Heidingsfelder L, Oudrhiri N, Al Jawhari M, Wilhelm-Murer N, Miguet M, Dieterlen A, Deschênes G, Tabet AC, Junker S, Grynberg M, Fenech M, Bennaceur-Griscelli A, Voisin P, Carde P, Jeandidier E, Yardin C. Telomere aberrations, including telomere loss, doublets, and extreme shortening, are increased in patients with infertility. Fertil Steril 2020; 115:164-173. [PMID: 33272625 DOI: 10.1016/j.fertnstert.2020.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To test the hypothesis that telomere shortening and/or loss are risk factors for infertility. DESIGN Retrospective analysis of the telomere status in patients with infertility using conventional cytogenetic data collected prospectively. SETTING Academic centers. PATIENT(S) Cytogenetic slides with cultured peripheral lymphocytes from 50 patients undergoing fertility treatment and 150 healthy donors, including 100 donors matched for age. INTERVENTION(S) Cytogenetic slides were used to detect chromosomal and telomere aberrations. MAIN OUTCOME MEASURE(S) Telomere length and telomere aberrations were analyzed after telomere and centromere staining. RESULT(S) The mean telomere length of patients consulting for infertility was significantly less than that of healthy donors of similar age. Moreover, patients with infertility showed significantly more extreme telomere loss and telomere doublet formation than healthy controls. Telomere shortening and/or telomere aberrations were more pronounced in patients with structural chromosomal aberrations. Dicentric chromosomes were identified in 6/13 patients, with constitutional chromosomal aberrations leading to chromosomal instability that correlated with chromosomal end-to-end fusions. CONCLUSION(S) Our findings demonstrate the feasibility of analyzing telomere aberrations in addition to chromosomal aberrations, using cytogenetic slides. Telomere attrition and/or dysfunction represent the main common cytogenetic characteristic of patients with infertility, leading to potential implications for fertility assessment. Pending further studies, these techniques that correlate the outcome of assisted reproduction and telomere integrity status may represent a novel and useful diagnostic and/or prognostic tool for medical care in this field.
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Affiliation(s)
- Radhia M'kacher
- Cell Environment, DNA Damage Research & Development, Paris, France.
| | - Bruno Colicchio
- Institut de Recherche en Informatique, Mathématiques, Automatique et Signal, Université de Haute-Alsace, Mulhouse, France
| | - Valentine Marquet
- Service de Cytogénétique, Génétique Médicale, et Biologie de la Reproduction Hôpital de la Mère et de l'Enfant, Centre hospitalo-universitaire Dupuytren, Limoges, France
| | - Claire Borie
- Assitance Pubique-Hopitaux de Paris (APHP)-Service d'hématologie-Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/INSERM 935, Villejuif, France
| | - Wala Najar
- Cell Environment, DNA Damage Research & Development, Paris, France; Faculté de médecine Paris Centre, Université de Paris, Paris, France
| | - William M Hempel
- Cell Environment, DNA Damage Research & Development, Paris, France
| | | | - Noufissa Oudrhiri
- Assitance Pubique-Hopitaux de Paris (APHP)-Service d'hématologie-Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/INSERM 935, Villejuif, France
| | | | - Nadège Wilhelm-Murer
- Service de génétique Groupe Hospitalier de la Région de Mulhouse et Sud Alsace, Mulhouse, France
| | - Marguerite Miguet
- Service de génétique Groupe Hospitalier de la Région de Mulhouse et Sud Alsace, Mulhouse, France
| | - Alain Dieterlen
- Institut de Recherche en Informatique, Mathématiques, Automatique et Signal, Université de Haute-Alsace, Mulhouse, France
| | | | | | - Steffen Junker
- Institute of Biomedicine, University of Aarhus, Aarhus, Denmark
| | - Michael Grynberg
- Department of Reproductive Medicine and Fertility Preservation, Hôpital Antoine Béclère, Clamart, France
| | - Michael Fenech
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia; Genome Health Foundation, North Brighton, South Australia, Australia
| | - Annelise Bennaceur-Griscelli
- Assitance Pubique-Hopitaux de Paris (APHP)-Service d'hématologie-Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/INSERM 935, Villejuif, France
| | - Philippe Voisin
- Cell Environment, DNA Damage Research & Development, Paris, France
| | - Patrice Carde
- Department of Hematology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Eric Jeandidier
- Service de génétique Groupe Hospitalier de la Région de Mulhouse et Sud Alsace, Mulhouse, France
| | - Catherine Yardin
- Service de Cytogénétique, Génétique Médicale, et Biologie de la Reproduction Hôpital de la Mère et de l'Enfant, Centre hospitalo-universitaire Dupuytren, Limoges, France; CNRS, XLIM, UMR 7252, University of Limoges, Limoges, France
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16
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Hattori A, Fukami M. Established and Novel Mechanisms Leading to de novo Genomic Rearrangements in the Human Germline. Cytogenet Genome Res 2020; 160:167-176. [DOI: 10.1159/000507837] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/31/2020] [Indexed: 01/05/2023] Open
Abstract
During gametogenesis, the human genome can acquire various de novo rearrangements. Most constitutional genomic rearrangements are created through 1 of the 4 well-known mechanisms, i.e., nonallelic homologous recombination, erroneous repair after double-strand DNA breaks, replication errors, and retrotransposition. However, recent studies have identified 2 types of extremely complex rearrangements that cannot be simply explained by these mechanisms. The first type consists of chaotic structural changes in 1 or a few chromosomes that result from “chromoanagenesis (an umbrella term that covers chromothripsis, chromoanasynthesis, and chromoplexy).” The other type is large independent rearrangements in multiple chromosomes indicative of “transient multifocal genomic crisis.” Germline chromoanagenesis (chromothripsis) likely occurs predominantly during spermatogenesis or postzygotic embryogenesis, while multifocal genomic crisis appears to be limited to a specific time window during oogenesis and early embryogenesis or during spermatogenesis. This review article introduces the current understanding of the molecular basis of de novo rearrangements in the germline.
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17
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Middelkamp S, van Tol HTA, Spierings DCJ, Boymans S, Guryev V, Roelen BAJ, Lansdorp PM, Cuppen E, Kuijk EW. Sperm DNA damage causes genomic instability in early embryonic development. SCIENCE ADVANCES 2020; 6:eaaz7602. [PMID: 32494621 PMCID: PMC7159919 DOI: 10.1126/sciadv.aaz7602] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/22/2020] [Indexed: 05/03/2023]
Abstract
Genomic instability is common in human embryos, but the underlying causes are largely unknown. Here, we examined the consequences of sperm DNA damage on the embryonic genome by single-cell whole-genome sequencing of individual blastomeres from bovine embryos produced with sperm damaged by γ-radiation. Sperm DNA damage primarily leads to fragmentation of the paternal chromosomes followed by random distribution of the chromosomal fragments over the two sister cells in the first cell division. An unexpected secondary effect of sperm DNA damage is the induction of direct unequal cleavages, which include the poorly understood heterogoneic cell divisions. As a result, chaotic mosaicism is common in embryos derived from fertilizations with damaged sperm. The mosaic aneuploidies, uniparental disomies, and de novo structural variation induced by sperm DNA damage may compromise fertility and lead to rare congenital disorders when embryos escape developmental arrest.
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Affiliation(s)
- Sjors Middelkamp
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
| | - Helena T. A. van Tol
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, Netherlands
| | - Diana C. J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Bernard A. J. Roelen
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, Netherlands
| | - Peter M. Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, Netherlands
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
- Hartwig Medical Foundation, Amsterdam, Netherlands
- Corresponding author.
| | - Ewart W. Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht 3584 CG, Netherlands
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18
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Pellestor F, Gatinois V. Chromoanagenesis: a piece of the macroevolution scenario. Mol Cytogenet 2020; 13:3. [PMID: 32010222 PMCID: PMC6988253 DOI: 10.1186/s13039-020-0470-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/05/2020] [Indexed: 01/04/2023] Open
Abstract
Over the last decade, new types of massive and complex chromosomal rearrangements based on the chaotic shattering and restructuring of chromosomes have been identified in cancer cells as well as in patients with congenital diseases and healthy individuals. These unanticipated phenomena are named chromothripsis, chromoanasynthesis and chromoplexy, and are grouped under the term of chromoanagenesis. As mechanisms for rapid and profound genome modifications in germlines and early development, these processes can be regarded as credible pathways for genomic evolution and speciation process. Their discovery confirms the importance of genome-centric investigations to fully understand organismal evolution. Because they oppose the model of progressive acquisition of driver mutations or rearrangements, these phenomena conceptually give support to the concept of macroevolution, known through the models of “Hopeful Monsters” and the “Punctuated Equilibrium”. In this review, we summarize mechanisms underlying chromoanagenesis processes and we show that numerous cases of chromosomal speciation and short-term adaptation could be correlated to chromoanagenesis-related mechanisms. In the frame of a modern and integrative analysis of eukaryote evolutionary processes, it seems important to consider the unexpected chromoanagenesis phenomena.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
| | - Vincent Gatinois
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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19
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Escribà MJ, Vendrell X, Peinado V. Segmental aneuploidy in human blastocysts: a qualitative and quantitative overview. Reprod Biol Endocrinol 2019; 17:76. [PMID: 31526391 PMCID: PMC6745804 DOI: 10.1186/s12958-019-0515-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Microarray-based and next generation sequencing (NGS) technologies have revealed that segmental aneuploidy is frequently present in human oocytes, cleavage-stage embryos and blastocysts. However, very little research has analyzed the type, size, chromosomal distribution and topography of the chromosomal segments at the different stages of development. METHODS This is a retrospective study of 822 PGT-A (preimplantation genetic test for aneuploidies) performed on trophectoderm samples from 3565 blastocysts biopsied between January 2016 and April 2017. The cycles in question had been initiated for varying clinical indications. Samples were analyzed by next generation sequencing-based technology. Segmental aneuploidies were evaluated when fragment size was > 5 Mb. Blastocysts presenting a single segmental aneuploidy (SSA), without any additional whole-chromosome gain/loss, were statistically analyzed for incidence, type, size and chromosomal emplacement. Segment sizes relative to the whole chromosome or arm (chromosome- and arm-ratios) were also studied. RESULTS 8.4% (299/3565) of blastocysts exhibited segmental aneuploidy for one or more chromosomes, some of which were associated with whole-chromosome aneuploidy while others were not. Nearly half of them (4.5%: 159/3565 of blastocysts) exhibited pure-SSA, meaning that a single chromosome was affected by a SSA. Segments were more frequent in medium-sized metacentric or submetacentric chromosomes and particularly in q-chrmosome arms, variables that were related to trophectoderm quality. SSA size was related to a greater extent to chromosome number and the arm affected than it was to SSA type. In absolute values (Mb), SSA size was larger in large chromosomes. However, the SSA:chromosome ratio was constant across all chromosomes and never exceeded 50% of the chromosome. CONCLUSIONS SSA frequency is chromosome- and topographically dependent, and its incidence is not related to clinical or embryological factors, but rather to trophectoderm quality. SSA might be originated by chromosome instability in response to chromothripsis, bias introduced by the biopsy and/or iatrogenic effects. TRIAL REGISTRATION Retrospectively registered.
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Affiliation(s)
| | - Xavier Vendrell
- Reproductive Genetics Unit, Sistemas Genómicos, Parque Tecnológico Paterna, 46980, Valencia, Spain
| | - Vanessa Peinado
- Igenomix, Parque Tecnológico Paterna, 46980, Valencia, Spain
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20
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Hattori A, Okamura K, Terada Y, Tanaka R, Katoh-Fukui Y, Matsubara Y, Matsubara K, Kagami M, Horikawa R, Fukami M. Transient multifocal genomic crisis creating chromothriptic and non-chromothriptic rearrangements in prezygotic testicular germ cells. BMC Med Genomics 2019; 12:77. [PMID: 31138192 PMCID: PMC6540402 DOI: 10.1186/s12920-019-0526-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/10/2019] [Indexed: 12/15/2022] Open
Abstract
Background The co-occurrence of multiple de novo copy number variations (CNVs) is a rare phenomenon in the human genome. Recently, an “organismal CNV mutator phenotype” has been reported to result in transient genomic instability introducing multiple de novo CNVs in primary oocytes and early-stage zygotes. These findings opened a new area of human genome research. Methods We performed genome-wide copy number analysis for ~ 2100 individuals with various congenital defects. Furthermore, extensive molecular analyses, including synthetic long-read whole-genome sequencing and haplotype-phasing, were carried out for an individual with multiple de novo CNVs. Results A boy was found to have de novo rearrangements on five chromosomes. The rearrangements comprised simple duplication and inversion as well as chaotic changes, all of which affected paternally derived chromosomes. Postzygotic genomic instability was ruled out. The duplicated regions on 6q and 13q contained both diallelic and triallelic loci, indicating that the genomic rearrangements were initially created during premeiotic mitosis and subsequently modified by physiological cross-over during meiosis I. Breakpoints of the rearrangements were indicative of non-homologous end joining, replication-based errors, and/or chromothripsis. The mutagenic event was independent of specific local DNA motifs or de novo point mutations, but may be driven by spermatogenesis-specific factors. Conclusions These results indicate that during spermatogenesis, a transient multifocal genomic crisis can introduce several chromothriptic and non-chromothriptic changes into the genome. These findings broaden the concept of the “organismal CNV mutator phenotype”. This study provides insights into mechanisms for altering the global chromosomal architecture of human embryos. Electronic supplementary material The online version of this article (10.1186/s12920-019-0526-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Atsushi Hattori
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.,Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, 157-8535, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Yumiko Terada
- Division of Endocrinology and Metabolism, National Medical Center for Children and Mothers, Tokyo, 157-8535, Japan
| | - Rika Tanaka
- Department of Neonatology, Aiiku Hospital, Tokyo, 105-8321, Japan
| | - Yuko Katoh-Fukui
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Yoichi Matsubara
- National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Reiko Horikawa
- Division of Endocrinology and Metabolism, National Medical Center for Children and Mothers, Tokyo, 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.
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21
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Inheritance of imbalances in recurrent chromosomal translocation t(11;22): clarification by PGT-SR and sperm-FISH analysis. Reprod Biomed Online 2019; 39:40-48. [PMID: 31097322 DOI: 10.1016/j.rbmo.2019.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/19/2019] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
Abstract
RESEARCH QUESTION To analyse why unbalanced viable offspring are derived mainly from the 3:1 segregation mode in t(11;22)(q23;q11.2) reciprocal translocation. DESIGN Retrospective analysis of 24 pre-implantation genetic testing for chromosomal structural re-arrangements (PGT-SR) cycles was performed on seven male and five female carriers of t(11;22) translocation. Sperm analysis was performed on each male carrier. These patients were directed to the study centre after several years of miscarriages and/or abortions, primary infertility for male carriers or birth of an affected child. RESULTS Twenty-four PGT-SR cycles were performed to exclude imbalances in both male and female carriers. The unbalanced embryos derived from the adjacent-1 segregation mode were the most represented in both male and female carriers (68.4% and 50%, respectively). These results were positively related with meiotic segregation analysis of reciprocal translocation in spermatozoa. A thorough analysis of the unbalanced embryo karyotypes determined that the expected viable +der22 karyotype resulting from 3:1 malsegregation was less represented at 5.3%. CONCLUSIONS These findings highlight the divergence that may exist between meiotic segregation and post-zygotic selection. Post-zygotic selection would be responsible for the elimination of unbalanced embryos derived from the adjacent-1 segregation mode. The combined action of several factors occurs at the beginning of post-zygotic selection. Genetic counselling must consider the risk of a birth related to the adjacent-1 segregation mode, irrespective of the sex of the translocation carrier. These results will allow deeper understanding of the PGT results of t(11;22) carriers, which often include a high number of aneuploid embryos.
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22
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Pellestor F, Gatinois V. Chromoanasynthesis: another way for the formation of complex chromosomal abnormalities in human reproduction. Hum Reprod 2019; 33:1381-1387. [PMID: 30325427 DOI: 10.1093/humrep/dey231] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Indexed: 12/24/2022] Open
Abstract
Chromoanasynthesis has been described as a novel cause of massive constitutional chromosomal rearrangements. Based on DNA replication machinery defects, chromoanasynthesis is characterized by the presence of chromosomal duplications and triplications locally clustered on one single chromosome, or a few chromosomes, associated with various other types of structural rearrangements. Two distinct mechanisms have been described for the formation of these chaotic genomic disorders, i.e. the fork stalling and template switching and the microhomology-mediated break-induced replication. Micronucleus-based processes have been evidenced as a causative mechanism, thus, highlighting the close connection between segregation errors and structural rearrangements. Accumulating data indicate that chromoanasynthesis is operating in human germline cells and during early embryonic development. The development of new tools for quantifying chromoanasynthesis events should provide further insight into the impact of this catastrophic cellular phenomenon in human reproduction.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, Montpellier, France
| | - Vincent Gatinois
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, Montpellier, France
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23
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Koltsova AS, Pendina AA, Efimova OA, Chiryaeva OG, Kuznetzova TV, Baranov VS. On the Complexity of Mechanisms and Consequences of Chromothripsis: An Update. Front Genet 2019; 10:393. [PMID: 31114609 PMCID: PMC6503150 DOI: 10.3389/fgene.2019.00393] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/11/2019] [Indexed: 12/28/2022] Open
Abstract
In the present review, we focus on the phenomenon of chromothripsis, a new type of complex chromosomal rearrangements. We discuss the challenges of chromothripsis detection and its distinction from other chromoanagenesis events. Along with already known causes and mechanisms, we introduce aberrant epigenetic regulation as a possible pathway to chromothripsis. We address the issue of chromothripsis characteristics in cancers and benign tumours, as well as chromothripsis inheritance in cases of its occurrence in germ cells, zygotes and early embryos. Summarising the presented data on different phenotypic effect of chromothripsis, we assume that its consequences are most likely determined not by the chromosome shattering and reassembly themselves, but by the genome regions involved in the rearrangement.
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Affiliation(s)
- Alla S Koltsova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Anna A Pendina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Olga A Efimova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Olga G Chiryaeva
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Tatyana V Kuznetzova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Vladislav S Baranov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
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24
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Garzo M, Catusi I, Colombo DM, De Grada L, Recalcati MP, Rodeschini O, Barone C, Beltrami N, Busuito R, Cappellani S, Ciaschini AM, Gulisano A, Malpezzi E, Pecile V, Pittalis MC, Romitti L, Stioui S, Larizza L, Giardino D. Ten new cases of Balanced Reciprocal Translocation Mosaicism (BRTM): Reproductive implications, frequency and mechanism. Eur J Med Genet 2019; 63:103639. [PMID: 30858057 DOI: 10.1016/j.ejmg.2019.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/27/2018] [Accepted: 03/05/2019] [Indexed: 12/14/2022]
Abstract
Chromosomal anomalies are well known to be an important cause of infertility, sterility and pregnancy loss. Balanced Reciprocal Translocation Mosaicism (BRTM) is an extremely rare phenomenon, mainly observed in subjects with a normal phenotype accompanied by reproductive failure. To date the mechanism of origin and the incidence of BRTM are poorly defined. Here we describe 10 new cases of BRTM. In 9 cases chromosome analysis revealed the presence of two different cell lines, one with a normal karyotype and the second with an apparently balanced reciprocal translocation. In the remaining case, both cell lines showed two different, but apparently balanced, reciprocal translocations. We document the clinical implications of BRTM, discuss its frequency in our referred population and suggest that carrier individuals might be more frequent than expected.
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Affiliation(s)
- Maria Garzo
- Istituto Auxologico Italiano, IRCCS, Lab. di Citogenetica Medica, Milano, Italy.
| | - Ilaria Catusi
- Istituto Auxologico Italiano, IRCCS, Lab. di Citogenetica Medica, Milano, Italy
| | | | - Laura De Grada
- Istituto Auxologico Italiano, IRCCS, Lab. di Citogenetica Medica, Milano, Italy
| | | | - Ornella Rodeschini
- Istituto Auxologico Italiano, IRCCS, Lab. di Citogenetica Medica, Milano, Italy
| | - Chiara Barone
- ARNAS Garibaldi Nesima, Catania, Italy; L.C. Laboratori Campisi srl, Avola, SR, Italy
| | | | - Rosa Busuito
- UOS Citogenetica Laboratorio Analisi ASST Ovest Milanese, Presidio Ospedaliero di Legnano, Italy
| | | | - Anna Maria Ciaschini
- Lab. di Genetica Medica SOS Malattie Rare, AOU Ospedali Riuniti Umberto I-G.M.Lancisi-G.Salesi, Ancona, Italy
| | | | - Elisabetta Malpezzi
- Policlinio S.Orsola-Malpighi, U.O.Ostetricia e Medicina dell'età Prenatale, Laboratorio di Citogenetica, Bologna, Italy
| | - Vanna Pecile
- Lab di Genetica Medica, IRCCS Burlo Garofolo, Trieste, Italy
| | - Maria Carla Pittalis
- Policlinio S.Orsola-Malpighi, U.O.Ostetricia e Medicina dell'età Prenatale, Laboratorio di Citogenetica, Bologna, Italy
| | - Lorenza Romitti
- ASST Grande Ospedale Metropolitano Niguarda,SC Anatomia Istologia Patologica e Citogenetica, Milano, Italy
| | - Sabine Stioui
- Lab di Citogenetica e Genetica Medica - Laboratorio Analisi Humanitas Research Hospital, Rozzano, MI, Italy
| | - Lidia Larizza
- Istituto Auxologico Italiano, IRCCS, Lab. di Citogenetica Medica, Milano, Italy
| | - Daniela Giardino
- Istituto Auxologico Italiano, IRCCS, Lab. di Citogenetica Medica, Milano, Italy
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25
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Casanovas A, Ribas-Maynou J, Lara-Cerrillo S, Jimenez-Macedo AR, Hortal O, Benet J, Carrera J, García-Peiró A. Double-stranded sperm DNA damage is a cause of delay in embryo development and can impair implantation rates. Fertil Steril 2019; 111:699-707.e1. [PMID: 30826116 DOI: 10.1016/j.fertnstert.2018.11.035] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To analyze the effect of single- and double-stranded sperm DNA fragmentation (ssSDF and dsSDF) on human embryo kinetics monitored under a time-lapse system. DESIGN Observational, double blind, prospective cohort study. SETTING University spin-off and private center. PATIENT(S) One hundred ninety-six embryos from 43 infertile couples were included prospectively. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) SsSDF and dsSDF were analyzed in the same semen sample used for intracytoplasmic sperm injection. Embryo kinetics was then monitored using time-lapse technology, and the timing of each embryo division was obtained. RESULT(S) When comparing embryos obtained from semen samples with low dsSDF and high dsSDF, splitting data using a statistically significant delay in high dsSDF was observed in second polar body extrusion, T4, T8, morula, and starting blastocyst and embryo implantation rates were impaired. Embryo kinetics and implantation rates are not significantly affected when high values of ssSDF are present. Different patterns of delay in embryo kinetics were observed for these different types of DNA damage: dsSDF caused a delay along all stages of embryo development; however, its major effect was observed at the second polar body extrusion and morula stages, coinciding with embryo DNA damage checkpoint activation as described before; ssSDF had its major effect at the pronucleus stage, but embryo kinetics was then restored at all following stages. The results show that dsSDF could be the main type of DNA damage that affects embryo development in intracytoplasmic sperm injection cycles, probably due to motility-based sperm selection in this assisted reproduction procedure. CONCLUSION(S) Double-stranded sperm DNA damage caused a delay in embryo development and impaired implantation, while single-stranded DNA damage did not significantly affect embryo kinetics and implantation.
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Affiliation(s)
| | - Jordi Ribas-Maynou
- Centro de Infertilidad Masculina y Análisis de Barcelona, Barcelona, Spain
| | | | | | - Olga Hortal
- Unitat d'Endocrinologia Ginecològica, Barcelona, Spain
| | - Jordi Benet
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Campus de la UAB, Barcelona, Spain
| | - Joan Carrera
- Unitat d'Endocrinologia Ginecològica, Barcelona, Spain
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Potential Role of Chromothripsis in the Genesis of Complex Chromosomal Rearrangements in Human Gametes and Preimplantation Embryo. Methods Mol Biol 2019; 1769:35-41. [PMID: 29564816 DOI: 10.1007/978-1-4939-7780-2_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
The discovery of a new class of massive chromosomal rearrangement, baptized chromothripsis, in different cancers and congenital disorders has deeply modified our understanding on the genesis of complex genomic rearrangements. Several mechanisms, involving abortive apoptosis, telomere erosion, mitotic errors, micronuclei formation, and p53 inactivation, might cause chromothripsis. The remarkable point is that all these plausible mechanisms have been identified in the field of human reproduction as causal factors for reproductive failures and chromosomal abnormality genesis. Specific features of gametogenesis and early embryonic development may contribute to the emergence of chromothripsis. Multiple lines of evidence support the assumption that chromothripsis may arise more frequently than previously thought in both gametogenesis and early human embryogenesis.
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27
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Pellestor F. Chromoanagenesis: cataclysms behind complex chromosomal rearrangements. Mol Cytogenet 2019; 12:6. [PMID: 30805029 PMCID: PMC6371609 DOI: 10.1186/s13039-019-0415-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background During the last decade, genome sequencing projects in cancer genomes as well as in patients with congenital diseases and healthy individuals have led to the identification of new types of massive chromosomal rearrangements arising during single chaotic cellular events. These unanticipated catastrophic phenomenon are termed chromothripsis, chromoanasynthesis and chromoplexis., and are grouped under the name of “chromoanagenesis”. Results For each process, several specific features have been described, allowing each phenomenon to be distinguished from each other and to understand its mechanism of formation and to better understand its aetiology. Thus, chromothripsis derives from chromosome shattering followed by the random restitching of chromosomal fragments with low copy-number change whereas chromoanasynthesis results from erroneous DNA replication of a chromosome through serial fork stalling and template switching with variable copy-number gains, and chromoplexy refers to the occurrence of multiple inter-and intra-chromosomal translocations and deletions with little or no copy-number alterations in prostate cancer. Cumulating data and experimental models have shown that chromothripsis and chromoanasynthesis may essentially result from lagging chromosome encapsulated in micronuclei or telomere attrition and end-to-end telomere fusion. Conclusion The concept of chromanagenesis has provided new insight into the aetiology of complex structural rearrangements, the connection between defective cell cycle progression and genomic instability, and the complexity of cancer evolution. Increasing reported chromoanagenesis events suggest that these chaotic mechanisms are probably much more frequent than anticipated.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371, avenue du Doyen Gaston Giraud, 34295 Montpellier cedex 5, France.,INSERM 1183 Unit «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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28
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Daughtry BL, Rosenkrantz JL, Lazar NH, Fei SS, Redmayne N, Torkenczy KA, Adey A, Yan M, Gao L, Park B, Nevonen KA, Carbone L, Chavez SL. Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion. Genome Res 2019; 29:367-382. [PMID: 30683754 PMCID: PMC6396419 DOI: 10.1101/gr.239830.118] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/22/2019] [Indexed: 12/12/2022]
Abstract
Aneuploidy that arises during meiosis and/or mitosis is a major contributor to early embryo loss. We previously showed that human preimplantation embryos encapsulate missegregated chromosomes into micronuclei while undergoing cellular fragmentation and that fragments can contain chromosomal material, but the source of this DNA was unknown. Here, we leveraged the use of a nonhuman primate model and single-cell DNA-sequencing (scDNA-seq) to examine the chromosomal content of 471 individual samples comprising 254 blastomeres, 42 polar bodies, and 175 cellular fragments from a large number (N = 50) of disassembled rhesus cleavage-stage embryos. Our analysis revealed that the aneuploidy and micronucleation frequency is conserved between humans and macaques, and that fragments encapsulate whole and/or partial chromosomes lost from blastomeres. Single-cell/fragment genotyping showed that these chromosome-containing cellular fragments (CCFs) can be maternally or paternally derived and display double-stranded DNA breaks. DNA breakage was further indicated by reciprocal subchromosomal losses/gains between blastomeres and large segmental errors primarily detected at the terminal ends of chromosomes. By combining time-lapse imaging with scDNA-seq, we determined that multipolar divisions at the zygote or two-cell stage were associated with CCFs and generated a random mixture of chromosomally normal and abnormal blastomeres with uniparental or biparental origins. Despite frequent chromosome missegregation at the cleavage-stage, we show that CCFs and nondividing aneuploid blastomeres showing extensive DNA damage are prevented from incorporation into blastocysts. These findings suggest that embryos respond to chromosomal errors by encapsulation into micronuclei, elimination via cellular fragmentation, and selection against highly aneuploid blastomeres to overcome chromosome instability during preimplantation development.
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Affiliation(s)
- Brittany L Daughtry
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Jimi L Rosenkrantz
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA.,Department of Molecular and Medical Genetics, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
| | - Nathan H Lazar
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
| | - Suzanne S Fei
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Nash Redmayne
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Kristof A Torkenczy
- Department of Molecular and Medical Genetics, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
| | - Andrew Adey
- Department of Molecular and Medical Genetics, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
| | - Melissa Yan
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Lina Gao
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Byung Park
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
| | - Lucia Carbone
- Department of Molecular and Medical Genetics, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA.,Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Division of Primate Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Shawn L Chavez
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA.,Department and Physiology and Pharmacology, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Department of Obstetrics and Gynecology, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Department of Biomedical Engineering, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
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29
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Abstract
Life starts with a zygote, which is formed by the fusion of a haploid sperm and egg. The formation of a blastomere by cleavage division (nuclear division without an increase in cell size) is the first step in embryogenesis, after the formation of the zygote. Blastomeres are responsible for reprogramming the parental genome as a new embryonic genome for generation of the pluripotent stem cells which then differentiate by Waddington's epigenetic landscape to create a new life. Multiple authors over the past 150 years have proposed that tumors arises from development gone awry at a point within Waddington's landscape. Recent discoveries showing that differentiated somatic cells can be reprogrammed into induced pluripotent stem cells, and that somatic cell nuclear transfer can be used to successfully clone animals, have fundamentally reshaped our understanding of tumor development and origin. Differentiated somatic cells are plastic and can be induced to dedifferentiate into pluripotent stem cells. Here, I review the evidence that suggests somatic cells may have a previously overlooked endogenous embryonic program that can be activated to dedifferentiate somatic cells into stem cells of various potencies for tumor initiation. Polyploid giant cancer cells (PGCCs) have long been observed in cancer and were thought originally to be nondividing. Contrary to this belief, recent findings show that stress-induced PGCCs divide by endoreplication, which may recapitulate the pattern of cleavage-like division in blastomeres and lead to dedifferentiation of somatic cells by a programmed process known as "the giant cell cycle", which comprise four distinct but overlapping phases: initiation, self-renewal, termination and stability. Depending on the intensity and type of stress, different levels of dedifferentiation result in the formation of tumors of different grades of malignancy. Based on these results, I propose a unified dualistic model to demonstrate the origin of human tumors. The tenet of this model includes four points, as follows. 1. Tumors originate from a stem cell at a specific developmental hierarchy, which can be achieved by dualistic origin: dedifferentiation of the zygote formed by two haploid gametes (sexual reproduction) via the blastomere during normal development, or transformation from damaged or aged mature somatic cells via a blastomere-like embryonic program (asexual reproduction). 2. Initiation of the tumor begins with a stem cell that has uncoupled the differentiation from the proliferation program which results in stem cell maturation arrest. 3. The developmental hierarchy at which stem cells arrest determines the degree of malignancy: the more primitive the level at which stem cells arrest, the greater the likelihood of the tumor being malignant. 4. Environmental factors and intrinsic genetic or epigenetic alterations represent the risk factors or stressors that facilitate stem cell arrest and somatic cell dedifferentiation. However, they, per se, are not the driving force of tumorigenesis. Thus, the birth of a tumor can be viewed as a triad that originates from a stem cell via dedifferentiation through a blastomere or blastomere-like program, which then differentiates along Waddington's landscape, and arrests at a developmental hierarchy. Blocking the PGCC-mediated dedifferentiation process and inducing their differentiation may represent a novel alternative approach to eliminate the tumor occurrence and therapeutic resistance.
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Affiliation(s)
- Jinsong Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030-4095, United States.
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30
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Guo X, Ni J, Liang Z, Xue J, Fenech MF, Wang X. The molecular origins and pathophysiological consequences of micronuclei: New insights into an age-old problem. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 779:1-35. [PMID: 31097147 DOI: 10.1016/j.mrrev.2018.11.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 02/07/2023]
Abstract
Micronuclei (MN), the small nucleus-like bodies separated from the primary nucleus, can exist in cells with numerical and/or structural chromosomal aberrations in apparently normal tissues and more so in tumors in humans. While MN have been observed for over 100 years, they were merely and constantly considered as passive indicators of chromosome instability (CIN) for a long time. Relatively little is known about the molecular origins and biological consequences of MN. Rapid technological advances are helping to close these gaps. Very recent studies provide exciting evidence that MN act as key platform for chromothripsis and a trigger of innate immune response, suggesting that MN could affect cellular functions by both genetic and nongenetic means. These previously unappreciated findings have reawakened widespread interests in MN. In this review, the diverse mechanisms leading to MN generation and the complex fate profiles of MN are discussed, together with the evidence for their contribution to CIN, inflammation, senescence and cell death. Moreover, we put this knowledge together into a speculative perspective on how MN may be responsible for cancer development and how their presence may influence the choice of treatment. We suggest that the heterogeneous responses to MN may function physiological to ensure the arrestment, elimination and immune clearance of damaged cells, but pathologically, may enable the survival and oncogenic transformation of cells bearing CIN. These insights not only underscore the complexity of MN biology, but also raise a host of new questions and provide fertile ground for future research.
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Affiliation(s)
- Xihan Guo
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Juan Ni
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Ziqing Liang
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Jinglun Xue
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Michael F Fenech
- University of South Australia, Adelaide, SA, 5000, Australia; Genome Health Foundation, North Brighton, SA, 5048, Australia.
| | - Xu Wang
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China.
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31
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Uryvaeva IV, Mikaelyan AS, Dashenkova NO, Marshak TL. Chromothripsis in Hepatocarcinogenesis: The Role of a Micronuclear Aberration and Polyploidy. BIOL BULL+ 2018. [DOI: 10.1134/s1062359018050163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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32
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Sabatini PJB, Ejaz R, Stavropoulos DJ, Mendoza-Londono R, Joseph-George AM. Stable transmission of an unbalanced chromosome 21 derived from chromoanasynthesis in a patient with a SYNGAP1 likely pathogenic variant. Mol Cytogenet 2018; 11:50. [PMID: 30181777 PMCID: PMC6114485 DOI: 10.1186/s13039-018-0394-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/06/2018] [Indexed: 11/30/2022] Open
Abstract
Background Complex genomic structural variations, involving chromoanagenesis, have been implicated in multiple congenital anomalies and abnormal neurodevelopment. Familial inheritance of complex chromosomal structural alteration resulting from germline chromoanagenesis-type mechanisms are limited. Case presentation We report a two-year eleven-month old male presenting with epilepsy, ataxia and dysmorphic features of unknown etiology. Chromosomal microarray identified a complex unbalanced rearrangement involving chromosome 21. G-banding and FISH for targeted regions of chromosome 21 revealed that the copy number imbalances were limited to gains dispersed throughout the long arm of chromosome 21, characteristic of a chromosome derived from chromoanagenesis. Family studies showed that the unbalanced chromosome had been stably inherited, as it was present in both his healthy mother and maternal grandfather. Further molecular testing for non-syndromic intellectual disability genes found a likely pathogenic mutation in SYNGAP1 (NM_006772.2:c.3722_3723del). Conclusions This study indicates that complex rearrangements involving an unbalanced chromosome derived from chromoanasynthesis can be familial and should be not be presumed pathogenic.
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Affiliation(s)
- Peter J B Sabatini
- 1Laboratory Medicine Program, Department of Pathology, University Health Network, 200 Elizabeth St, Toronto, ON M5G 2C4 Canada.,2Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Resham Ejaz
- 3Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Dimitri J Stavropoulos
- 2Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada.,4Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Roberto Mendoza-Londono
- 3Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Ann M Joseph-George
- 2Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada.,4Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
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33
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Pellestor F, Gatinois V. Chromothripsis, a credible chromosomal mechanism in evolutionary process. Chromosoma 2018; 128:1-6. [DOI: 10.1007/s00412-018-0679-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 01/17/2023]
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34
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Heng HH, Horne SD, Chaudhry S, Regan SM, Liu G, Abdallah BY, Ye CJ. A Postgenomic Perspective on Molecular Cytogenetics. Curr Genomics 2018; 19:227-239. [PMID: 29606910 PMCID: PMC5850511 DOI: 10.2174/1389202918666170717145716] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/29/2017] [Accepted: 02/03/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The postgenomic era is featured by massive data collection and analyses from various large scale-omics studies. Despite the promising capability of systems biology and bioinformatics to handle large data sets, data interpretation, especially the translation of -omics data into clinical implications, has been challenging. DISCUSSION In this perspective, some important conceptual and technological limitations of current systems biology are discussed in the context of the ultimate importance of the genome beyond the collection of all genes. Following a brief summary of the contributions of molecular cytogenetics/cytogenomics in the pre- and post-genomic eras, new challenges for postgenomic research are discussed. Such discussion leads to a call to search for a new conceptual framework and holistic methodologies. CONCLUSION Throughout this synthesis, the genome theory of somatic cell evolution is highlighted in contrast to gene theory, which ignores the karyotype-mediated higher level of genetic information. Since "system inheritance" is defined by the genome context (gene content and genomic topology) while "parts inheritance" is defined by genes/epigenes, molecular cytogenetics and cytogenomics (which directly study genome structure, function, alteration and evolution) will play important roles in this postgenomic era.
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Affiliation(s)
- Henry H. Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Steven D. Horne
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sophia Chaudhry
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sarah M. Regan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Guo Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Batoul Y. Abdallah
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Christine J. Ye
- The Division of Hematology/Oncology, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA
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35
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Slamova Z, Nazaryan-Petersen L, Mehrjouy MM, Drabova J, Hancarova M, Marikova T, Novotna D, Vlckova M, Vlckova Z, Bak M, Zemanova Z, Tommerup N, Sedlacek Z. Very short DNA segments can be detected and handled by the repair machinery during germline chromothriptic chromosome reassembly. Hum Mutat 2018; 39:709-716. [DOI: 10.1002/humu.23408] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Zuzana Slamova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Lusine Nazaryan-Petersen
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Mana M. Mehrjouy
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Jana Drabova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Tatana Marikova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Drahuse Novotna
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - Marketa Vlckova
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | | | - Mads Bak
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Zuzana Zemanova
- Institute of Medical Biochemistry and Laboratory Diagnostics; General University Hospital and Charles University 1st Faculty of Medicine; Prague Czech Republic
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen Denmark
| | - Zdenek Sedlacek
- Department of Biology and Medical Genetics; Charles University 2nd Faculty of Medicine and University Hospital Motol; Prague Czech Republic
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36
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Abstract
Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations." To advance this exciting field, we need an effective experimental system to induce and characterize the karyotype reorganization process. In this chapter, an experimental protocol to induce chaotic genomes is described, following a brief discussion of the mechanism and implication of genome chaos in cancer evolution.
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Affiliation(s)
- Christine J Ye
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Guo Liu
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Henry H Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, USA.
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA.
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37
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Abstract
The highly complex structural genome variations chromothripsis, chromoanasynthesis, and chromoplexy are subsumed under the term chromoanagenesis, which means chromosome rebirth. Precipitated by numerous DNA double-strand breaks, they differ in number of and distances between breakpoints, associated copy number variations, order and orientation of segments, and flanking sequences at joining points. Results from patients with the autosomal dominant cancer susceptibility disorder Li-Fraumeni syndrome implicated somatic TP53 mutations in chromothripsis. TP53 participates in the G2/M phase checkpoint, halting cell cycling after premature chromosome compaction during the second half of the S phase, thus preventing chromosome shattering. By experimental TP53 ablation and micronucleus induction, one or a few isolated chromosomes underwent desynchronized replication and chromothripsis. Secondly, chromothripsis occurred after experimental induction of telomere crisis after which dicentric chromosomes sustained TREX1-mediated resolution of chromosome bridges and kataegis. Third, DNA polymerase Polθ-dependent chromothripsis has been documented. Finally, a family with chromothripsis after L1 element-dependent retrotransposition and Alu/Alu homologous recombination has been reported. Human chromosomal instability syndromes share defects in responses to DNA double-strand breaks, characteristic cell cycle perturbations, elevated rates of micronucleus formation, premature chromosome compaction, and apoptosis. They are also associated with elevated susceptibility to malignant disease, such as medulloblastomas and gliomas in ataxia-telangiectasia, leukemia and lymphoma in Bloom syndrome, and osteosarcoma and soft tissue sarcoma in Werner syndrome. The latter syndrome is characterized by a premature aging-like progressive decline of mesenchymal tissues. In all thus far studied cases, constitutional chromothripsis occurred in the male germline and male patients with defects in the double-strand break response genes ATM, MRE11, BLM, LIG4, WRN, and Ku70 show impaired fertility. Conceivably, chromothripsis may, in a stochastic rather than deterministic way, be implicated in germline structural variation, malignant disease, premature aging, genome mosaicism in somatic tissues, and male infertility.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany.
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38
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Abstract
Chromothripsis, or chromosome shattering, occurs after chromosomes missegregate, are pulverized and subsequently repaired erroneously, leading to highly complex structural rearrangements. In plants, chromothripsis has been observed as a result of mitotic malfunction connected with the incomplete loss of haploid inducer chromosomes during uniparental genome elimination. Uniparental genome elimination, a process that results in haploid induction, is a phenomenon that typically results in the loss of an entire parental chromosome set in early embryos, resulting in haploid plants. In Arabidopsis thaliana, genome elimination can be achieved via the manipulation of the centromere-specific histone H3 variant, CENH3. Genomic characterization of F1 progeny resulting from CENH3-mediated genome elimination crosses in Arabidopsis revealed haploids (~39%), diploids (~25%), and aneuploids (~37%). Within the aneuploid class, ~11% show evidence for chromothripsis. Here, we present a protocol to identify Arabidopsis aneuploids that have inherited chromothriptic chromosomes during genome elimination crosses and describe in detail how to perform in silico reconstructions for individuals with chromothripsis using the somatic mutation finder (SMuFin) tool.
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Affiliation(s)
- Isabelle M Henry
- Genome Center & Department of Plant Biology, University of California, Davis, CA, USA
| | - Luca Comai
- Genome Center & Department of Plant Biology, University of California, Davis, CA, USA.
| | - Ek Han Tan
- School of Biology and Ecology, University of Maine, Orono, ME, USA.
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Fukami M, Kurahashi H. Clinical Consequences of Chromothripsis and Other Catastrophic Cellular Events. Methods Mol Biol 2018; 1769:21-33. [PMID: 29564815 DOI: 10.1007/978-1-4939-7780-2_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Chromothripsis was initially described as a novel cause of chromosomal rearrangements in cancer cells and was subsequently implicated in the development of gross chromosomal rearrangements in the germline. Other catastrophic cellular events such as chromoanasynthesis and chromoplexy have also been observed in human cells. Such events have been associated with various phenotypes including mental retardation and congenital malformations. Here, we introduce representative cases of human disorders arising from somatic or germline chromothripsis or similar catastrophic events. In this chapter, we use the term "chromoanagenesis" to indicate all catastrophic events including chromothripsis.
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Affiliation(s)
- Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan.
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40
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Daughtry BL, Chavez SL. Time-Lapse Imaging for the Detection of Chromosomal Abnormalities in Primate Preimplantation Embryos. Methods Mol Biol 2018; 1769:293-317. [PMID: 29564832 DOI: 10.1007/978-1-4939-7780-2_19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The use of time-lapse microscopic imaging has proven to be a powerful tool for the study of mitotic divisions and other cellular processes across diverse species and cell types. Although time-lapse monitoring (TLM) of human preimplantation development was first introduced to the in vitro fertilization (IVF) community several decades ago, it was not until relatively recently that TLM systems were commercialized for clinical embryology purposes. Traditionally, human IVF embryos are assessed by successful progression and morphology under a stereomicroscope at distinct time points prior to selection for transfer. Due to the high frequency of aneuploidy, embryos may also be biopsied at the cleavage or blastocyst stage for preimplantation genetic screening (PGS) of whole and/or partial chromosomal abnormalities. However, embryo biopsy is invasive and can hinder subsequent development, and there are additional concerns over chromosomal mosaicism and resolution with PGS. Moreover, embryos are typically outside of the incubator in suboptimal culture conditions for extended periods of time during these procedures. With TLM systems, embryos remain in the stable microenvironment of an incubator and are simultaneously imaged for noninvasive embryo evaluation using a fraction of the light exposure as compared to a stereomicroscope. Each image is then compiled into a time-lapse movie, the information from which can be extrapolated to correlate morphological, spatial, and temporal parameters with embryo quality and copy number status. Here, we describe the various TLM systems available for clinical and/or research use in detail and provide step-by-step instructions on how the measurement of specific timing intervals and certain morphological criteria can be implemented into IVF protocols to enhance embryo assessment and avoid the selection of aneuploid embryos. We also discuss the biological significance of processes unique to mitotically dividing embryos and the likelihood that complex chromosomal events such as chromothripsis occur during preimplantation development in humans and other mammals, particularly nonhuman primates.
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Affiliation(s)
- Brittany L Daughtry
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University School of Medicine, Portland, OR, USA.,Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Shawn L Chavez
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR, USA. .,Department and Physiology and Pharmacology, Oregon Health and Science University School of Medicine, Portland, OR, USA. .,Department of Obstetrics and Gynecology, Oregon Health and Science University School of Medicine, Portland, OR, USA.
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41
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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42
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Poot M. The Age of the Father. Mol Syndromol 2017; 8:169-171. [PMID: 28690481 DOI: 10.1159/000471776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2017] [Indexed: 11/19/2022] Open
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43
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Collins RL, Brand H, Redin CE, Hanscom C, Antolik C, Stone MR, Glessner JT, Mason T, Pregno G, Dorrani N, Mandrile G, Giachino D, Perrin D, Walsh C, Cipicchio M, Costello M, Stortchevoi A, An JY, Currall BB, Seabra CM, Ragavendran A, Margolin L, Martinez-Agosto JA, Lucente D, Levy B, Sanders SJ, Wapner RJ, Quintero-Rivera F, Kloosterman W, Talkowski ME. Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome. Genome Biol 2017; 18:36. [PMID: 28260531 PMCID: PMC5338099 DOI: 10.1186/s13059-017-1158-6] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/20/2017] [Indexed: 12/13/2022] Open
Abstract
Background Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies. Results We sequenced 689 participants with autism spectrum disorder (ASD) and other developmental abnormalities to construct a genome-wide map of large SV. Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution. Our results encompass 11,735 distinct large SV sites, 38.1% of which are novel and 16.8% of which are balanced or complex. We characterize 16 recurrent subclasses of complex SV (cxSV), revealing that: (1) cxSV are larger and rarer than canonical SV; (2) each genome harbors 14 large cxSV on average; (3) 84.4% of large cxSVs involve inversion; and (4) most large cxSV (93.8%) have not been delineated in previous studies. Rare SVs are more likely to disrupt coding and regulatory non-coding loci, particularly when truncating constrained and disease-associated genes. We also identify multiple cases of catastrophic chromosomal rearrangements known as chromoanagenesis, including somatic chromoanasynthesis, and extreme balanced germline chromothripsis events involving up to 65 breakpoints and 60.6 Mb across four chromosomes, further defining rare categories of extreme cxSV. Conclusions These data provide a foundational map of large SV in the morbid human genome and demonstrate a previously underappreciated abundance and diversity of cxSV that should be considered in genomic studies of human disease. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1158-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryan L Collins
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, 02115, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Harrison Brand
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Claire E Redin
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Carrie Hanscom
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Caroline Antolik
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Matthew R Stone
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Joseph T Glessner
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Tamara Mason
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Giulia Pregno
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Naghmeh Dorrani
- Department of Pathology & Laboratory Medicine and UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, UCLA, Los Angeles, CA, 90095, USA
| | - Giorgia Mandrile
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Danielle Perrin
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Cole Walsh
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Michelle Cipicchio
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Maura Costello
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Alexei Stortchevoi
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Joon-Yong An
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, 94103, USA
| | - Benjamin B Currall
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Catarina M Seabra
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA.,GABBA Program, University of Porto, Porto, 4099-002, Portugal
| | - Ashok Ragavendran
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Lauren Margolin
- Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Julian A Martinez-Agosto
- Department of Pathology & Laboratory Medicine and UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, UCLA, Los Angeles, CA, 90095, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Brynn Levy
- Department of Pathology, Columbia University, New York, NY, 10032, USA
| | - Stephan J Sanders
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, 94103, USA
| | - Ronald J Wapner
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology & Laboratory Medicine and UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, UCLA, Los Angeles, CA, 90095, USA
| | - Wigard Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, 3584CG, The Netherlands
| | - Michael E Talkowski
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA. .,Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, 02115, USA. .,Program in Population and Medical Genetics and Genomics Platform, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA.
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Fukami M, Shima H, Suzuki E, Ogata T, Matsubara K, Kamimaki T. Catastrophic cellular events leading to complex chromosomal rearrangements in the germline. Clin Genet 2017; 91:653-660. [PMID: 27888607 DOI: 10.1111/cge.12928] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 12/28/2022]
Abstract
Although complex chromosomal rearrangements were thought to reflect the accumulation of DNA damage over time, recent studies have shown that such rearrangements frequently arise from 'all-at-once' catastrophic cellular events. These events, designated chromothripsis, chromoanasynthesis, and chromoanagenesis, were first documented in the cancer genome and subsequently observed in the germline. These events likely result from micronucleus-mediated chromosomal shattering and subsequent random reassembly of DNA fragments, although several other mechanisms have also been proposed. Typically, only one or a few chromosomes of paternal origin are affected per event. These events can produce intrachromosomal deletions, duplications, inversions, and translocations, as well as interchromosomal translocations. Germline complex rearrangements of autosomes often result in developmental delay and dysmorphic features, whereas X chromosomal rearrangements are usually associated with relatively mild clinical manifestations. The concept of these catastrophic events provides novel insights into the etiology of human genomic disorders. This review introduces the molecular characteristics and phenotypic outcomes of catastrophic cellular events in the germline.
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Affiliation(s)
- M Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - H Shima
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - E Suzuki
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - T Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - K Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - T Kamimaki
- Department of Pediatrics, Shizuoka City Shimizu Hospital, Shizuoka, Japan
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45
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Poot M. Of Simple and Complex Genome Rearrangements, Chromothripsis, Chromoanasynthesis, and Chromosome Chaos. Mol Syndromol 2017; 8:115-117. [PMID: 28588432 DOI: 10.1159/000454964] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2016] [Indexed: 01/23/2023] Open
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46
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Del Rey J, Santos M, González-Meneses A, Milà M, Fuster C. Heterogeneity of a Constitutional Complex Chromosomal Rearrangement in 2q. Cytogenet Genome Res 2016; 148:156-64. [PMID: 27216161 DOI: 10.1159/000445859] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2016] [Indexed: 11/19/2022] Open
Abstract
Complex chromosome rearrangements (CCRs) are unusual structural chromosome alterations found in humans, and to date only a few have been characterized molecularly. New mechanisms, such as chromothripsis, have been proposed to explain the presence of the CCRs in cancer cells and in patients with congenital disorders and/or mental retardation. The aim of the present study was the molecular characterization of a constitutional CCR in a girl with multiple congenital disorders and intellectual disability in order to determine the genotype-phenotype relation and to clarify whether the CCR could have been caused by chromosomal catastrophic events. The present CCR was characterized by G-banding, high-resolution CGH, multiplex ligation-dependent probe amplification and subtelomeric 2q-FISH analyses. Preliminary results indicate that the de novo CCR is unbalanced showing a 2q37.3 deletion and 2q34q37.2 partial trisomy. Our patient shows some of the typical traits and intellectual disability described in patients with 2q37 deletion and also in carriers of 2q34q37.2 partial trisomy; thus, the clinical disorders could be explained by additional effects of both chromosome alterations (deletions and duplications). A posterior, sequential FISH study using BAC probes revealed the unexpected presence of at least 17 different reorganizations affecting 2q34q37.2, suggesting the existence of chromosome instability in this region. The present CCR is the first case described in the literature of heterogeneity of unbalanced CCRs affecting a small region of 2q, indicating that the mechanisms involved in constitutional chromosome rearrangement may be more complex than previously thought.
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Affiliation(s)
- Javier Del Rey
- Unitat de Biologia Celx00B7;lular i Genx00E8;tica Mx00E8;dica, Facultat de Medicina, Universitat Autx00F2;noma de Barcelona, Barcelona, Spain
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47
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Mapping Breakpoints of Complex Chromosome Rearrangements Involving a Partial Trisomy 15q23.1-q26.2 Revealed by Next Generation Sequencing and Conventional Techniques. PLoS One 2016; 11:e0154574. [PMID: 27218255 PMCID: PMC4878739 DOI: 10.1371/journal.pone.0154574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/16/2016] [Indexed: 11/25/2022] Open
Abstract
Complex chromosome rearrangements (CCRs), which are rather rare in the whole population, may be associated with aberrant phenotypes. Next-generation sequencing (NGS) and conventional techniques, could be used to reveal specific CCRs for better genetic counseling. We report the CCRs of a girl and her mother, which were identified using a combination of NGS and conventional techniques including G-banding, fluorescence in situ hybridization (FISH) and PCR. The girl demonstrated CCRs involving chromosomes 3 and 8, while the CCRs of her mother involved chromosomes 3, 5, 8, 11 and 15. HumanCytoSNP-12 Chip analysis identified a 35.4 Mb duplication on chromosome 15q21.3-q26.2 in the proband and a 1.6 Mb microdeletion at chromosome 15q21.3 in her mother. The proband inherited the rearranged chromosomes 3 and 8 from her mother, and the duplicated region on chromosome 15 of the proband was inherited from the mother. Approximately one hundred genes were identified in the 15q21.3-q26.2 duplicated region of the proband. In particular, TPM1, SMAD6, SMAD3, and HCN4 may be associated with her heart defects, and HEXA, KIF7, and IDH2 are responsible for her developmental and mental retardation. In addition, we suggest that a microdeletion on the 15q21.3 region of the mother, which involved TCF2, TCF12, ADMA10 and AQP9, might be associated with mental retardation. We delineate the precise structures of the derivative chromosomes, chromosome duplication origin and possible molecular mechanisms for aberrant phenotypes by combining NGS data with conventional techniques.
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48
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Poot M. Chromothripsis after Stumbling through DNA Replication. Mol Syndromol 2016; 6:207-9. [PMID: 26997940 DOI: 10.1159/000441081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2015] [Indexed: 11/19/2022] Open
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49
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Daughtry BL, Chavez SL. Chromosomal instability in mammalian pre-implantation embryos: potential causes, detection methods, and clinical consequences. Cell Tissue Res 2016; 363:201-225. [PMID: 26590822 PMCID: PMC5621482 DOI: 10.1007/s00441-015-2305-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 09/24/2015] [Indexed: 01/08/2023]
Abstract
Formation of a totipotent blastocyst capable of implantation is one of the first major milestones in early mammalian embryogenesis, but less than half of in vitro fertilized embryos from most mammals will progress to this stage of development. Whole chromosomal abnormalities, or aneuploidy, are key determinants of whether human embryos will arrest or reach the blastocyst stage. Depending on the type of chromosomal abnormality, however, certain embryos still form blastocysts and may be morphologically indistinguishable from chromosomally normal embryos. Despite the implementation of pre-implantation genetic screening and other advanced in vitro fertilization (IVF) techniques, the identification of aneuploid embryos remains complicated by high rates of mosaicism, atypical cell division, cellular fragmentation, sub-chromosomal instability, and micro-/multi-nucleation. Moreover, several of these processes occur in vivo following natural human conception, suggesting that they are not simply a consequence of culture conditions. Recent technological achievements in genetic, epigenetic, chromosomal, and non-invasive imaging have provided additional embryo assessment approaches, particularly at the single-cell level, and clinical trials investigating their efficacy are continuing to emerge. In this review, we summarize the potential mechanisms by which aneuploidy may arise, the various detection methods, and the technical advances (such as time-lapse imaging, "-omic" profiling, and next-generation sequencing) that have assisted in obtaining this data. We also discuss the possibility of aneuploidy resolution in embryos via various corrective mechanisms, including multi-polar divisions, fragment resorption, endoreduplication, and blastomere exclusion, and conclude by examining the potential implications of these findings for IVF success and human fecundity.
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Affiliation(s)
- Brittany L Daughtry
- Department of Cell, Developmental & Cancer Biology, Graduate Program in Molecular & Cellular Biosciences, Oregon Health & Science University School of Medicine, Portland, Ore., USA
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Shawn L Chavez
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006, USA.
- Physiology & Pharmacology, Oregon Health & Science University School of Medicine, Portland, Ore., USA.
- Department of Obstetrics & Gynecology, Oregon Health & Science University School of Medicine, Portland, Ore., USA.
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50
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Carbone L, Chavez SL. Mammalian pre-implantation chromosomal instability: species comparison, evolutionary considerations, and pathological correlations. Syst Biol Reprod Med 2015; 61:321-35. [PMID: 26366555 DOI: 10.3109/19396368.2015.1073406] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Pre-implantation embryo development in mammals begins at fertilization with the migration and fusion of the maternal and paternal pro-nuclei, followed by the degradation of inherited factors involved in germ cell specification and the activation of embryonic genes required for subsequent cell divisions, compaction, and blastulation. The majority of studies on early embryogenesis have been conducted in the mouse or non-mammalian species, often requiring extrapolation of the findings to human development. Given both conserved similarities and species-specific differences, however, even comparison between closely related mammalian species may be challenging as certain aspects, including susceptibility to chromosomal aberrations, varies considerably across mammals. Moreover, most human embryo studies are limited to patient samples obtained from in vitro fertilization (IVF) clinics and donated for research, which are generally of poorer quality and produced with germ cells that may be sub-optimal. Recent technical advances in genetic, epigenetic, chromosomal, and time-lapse imaging analyses of high quality whole human embryos have greatly improved our understanding of early human embryogenesis, particularly at the single embryo and cell level. This review summarizes the major characteristics of mammalian pre-implantation development from a chromosomal perspective, in addition to discussing the technological achievements that have recently been developed to obtain this data. We also discuss potential translation to clinical applications in reproductive medicine and conclude by examining the broader implications of these findings for the evolution of mammalian species and cancer pathology in somatic cells.
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Affiliation(s)
- Lucia Carbone
- a Division of Neuroscience , Oregon National Primate Research Center .,b Department of Behavioral Neuroscience .,c Department of Molecular & Medical Genetics .,d Bioinformatics & Computational Biology, Oregon Health & Science University
| | - Shawn L Chavez
- e Division of Reproductive & Developmental Sciences , Oregon National Primate Research Center .,f Department of Obstetrics & Gynecology , and.,g Department of Physiology & Pharmacology , Oregon Health & Science University , Portland , Oregon , USA
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