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Raimer Young HM, Hou PC, Bartosik AR, Atkin ND, Wang L, Wang Z, Ratan A, Zang C, Wang YH. DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity. Nucleic Acids Res 2024; 52:3837-3855. [PMID: 38452213 DOI: 10.1093/nar/gkae164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/03/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
CCCTC-binding factor (CTCF) binding sites are hotspots of genome instability. Although many factors have been associated with CTCF binding site fragility, no study has integrated all fragility-related factors to understand the mechanism(s) of how they work together. Using an unbiased, genome-wide approach, we found that DNA double-strand breaks (DSBs) are enriched at strong, but not weak, CTCF binding sites in five human cell types. Energetically favorable alternative DNA secondary structures underlie strong CTCF binding sites. These structures coincided with the location of topoisomerase II (TOP2) cleavage complex, suggesting that DNA secondary structure acts as a recognition sequence for TOP2 binding and cleavage at CTCF binding sites. Furthermore, CTCF knockdown significantly increased DSBs at strong CTCF binding sites and at CTCF sites that are located at topologically associated domain (TAD) boundaries. TAD boundary-associated CTCF sites that lost CTCF upon knockdown displayed increased DSBs when compared to the gained sites, and those lost sites are overrepresented with G-quadruplexes, suggesting that the structures act as boundary insulators in the absence of CTCF, and contribute to increased DSBs. These results model how alternative DNA secondary structures facilitate recruitment of TOP2 to CTCF binding sites, providing mechanistic insight into DNA fragility at CTCF binding sites.
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Affiliation(s)
- Heather M Raimer Young
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Pei-Chi Hou
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Anna R Bartosik
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Lixin Wang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
| | - Aakrosh Ratan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Chongzhi Zang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
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Soheili-Nezhad S, Ibáñez-Solé O, Izeta A, Hoeijmakers JHJ, Stoeger T. Time is ticking faster for long genes in aging. Trends Genet 2024; 40:299-312. [PMID: 38519330 PMCID: PMC11003850 DOI: 10.1016/j.tig.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 03/24/2024]
Abstract
Recent studies of aging organisms have identified a systematic phenomenon, characterized by a negative correlation between gene length and their expression in various cell types, species, and diseases. We term this phenomenon gene-length-dependent transcription decline (GLTD) and suggest that it may represent a bottleneck in the transcription machinery and thereby significantly contribute to aging as an etiological factor. We review potential links between GLTD and key aging processes such as DNA damage and explore their potential in identifying disease modification targets. Notably, in Alzheimer's disease, GLTD spotlights extremely long synaptic genes at chromosomal fragile sites (CFSs) and their vulnerability to postmitotic DNA damage. We suggest that GLTD is an integral element of biological aging.
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Affiliation(s)
- Sourena Soheili-Nezhad
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Olga Ibáñez-Solé
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Ander Izeta
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Tecnun-University of Navarra, 20018 Donostia-San Sebastian, Spain.
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands; University of Cologne, Faculty of Medicine, Cluster of Excellence for Aging Research, Institute for Genome Stability in Ageing and Disease, Cologne, Germany; Princess Maxima Center for Pediatric Oncology, Oncode Institute, Utrecht, The Netherlands.
| | - Thomas Stoeger
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL, USA; Potocsnak Longevity Institute, Northwestern University, Chicago, IL, USA; Simpson Querrey Lung Institute for Translational Science, Chicago, IL, USA.
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Mirceta M, Shum N, Schmidt MHM, Pearson CE. Fragile sites, chromosomal lesions, tandem repeats, and disease. Front Genet 2022; 13:985975. [PMID: 36468036 PMCID: PMC9714581 DOI: 10.3389/fgene.2022.985975] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/02/2022] [Indexed: 09/16/2023] Open
Abstract
Expanded tandem repeat DNAs are associated with various unusual chromosomal lesions, despiralizations, multi-branched inter-chromosomal associations, and fragile sites. Fragile sites cytogenetically manifest as localized gaps or discontinuities in chromosome structure and are an important genetic, biological, and health-related phenomena. Common fragile sites (∼230), present in most individuals, are induced by aphidicolin and can be associated with cancer; of the 27 molecularly-mapped common sites, none are associated with a particular DNA sequence motif. Rare fragile sites ( ≳ 40 known), ≤ 5% of the population (may be as few as a single individual), can be associated with neurodevelopmental disease. All 10 molecularly-mapped folate-sensitive fragile sites, the largest category of rare fragile sites, are caused by gene-specific CGG/CCG tandem repeat expansions that are aberrantly CpG methylated and include FRAXA, FRAXE, FRAXF, FRA2A, FRA7A, FRA10A, FRA11A, FRA11B, FRA12A, and FRA16A. The minisatellite-associated rare fragile sites, FRA10B, FRA16B, can be induced by AT-rich DNA-ligands or nucleotide analogs. Despiralized lesions and multi-branched inter-chromosomal associations at the heterochromatic satellite repeats of chromosomes 1, 9, 16 are inducible by de-methylating agents like 5-azadeoxycytidine and can spontaneously arise in patients with ICF syndrome (Immunodeficiency Centromeric instability and Facial anomalies) with mutations in genes regulating DNA methylation. ICF individuals have hypomethylated satellites I-III, alpha-satellites, and subtelomeric repeats. Ribosomal repeats and subtelomeric D4Z4 megasatellites/macrosatellites, are associated with chromosome location, fragility, and disease. Telomere repeats can also assume fragile sites. Dietary deficiencies of folate or vitamin B12, or drug insults are associated with megaloblastic and/or pernicious anemia, that display chromosomes with fragile sites. The recent discovery of many new tandem repeat expansion loci, with varied repeat motifs, where motif lengths can range from mono-nucleotides to megabase units, could be the molecular cause of new fragile sites, or other chromosomal lesions. This review focuses on repeat-associated fragility, covering their induction, cytogenetics, epigenetics, cell type specificity, genetic instability (repeat instability, micronuclei, deletions/rearrangements, and sister chromatid exchange), unusual heritability, disease association, and penetrance. Understanding tandem repeat-associated chromosomal fragile sites provides insight to chromosome structure, genome packaging, genetic instability, and disease.
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Affiliation(s)
- Mila Mirceta
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Natalie Shum
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Monika H. M. Schmidt
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Abstract
The enormous diversity of antibodies is a key element to combat infections. Antibodies containing pathogen receptors were a surprising discovery that contrasted antibody diversification through classic recombination events. However, such insert-containing antibodies were thus far exclusively detected in African individuals exposed to malaria parasites and were identified as screening byproducts or through hypothesis-driven search. The prevalence and complexity of insertion events remained elusive. In this study, we devise an unbiased, systematic approach to identify inserts in the human antibody repertoire. We show that inserts from distant genomic regions occur in the majority of donors and are independent of Plasmodium falciparum preexposure. Our findings suggest that four distinct classes of insertion events contribute diversity to the human antibody repertoire. Recombination of antibody genes in B cells can involve distant genomic loci and contribute a foreign antigen-binding element to form hybrid antibodies with broad reactivity for Plasmodium falciparum. So far, antibodies containing the extracellular domain of the LAIR1 and LILRB1 receptors represent unique examples of cross-chromosomal antibody diversification. Here, we devise a technique to profile non-VDJ elements from distant genes in antibody transcripts. Independent of the preexposure of donors to malaria parasites, non-VDJ inserts were detected in 80% of individuals at frequencies of 1 in 104 to 105 B cells. We detected insertions in heavy, but not in light chain or T cell receptor transcripts. We classify the insertions into four types depending on the insert origin and destination: 1) mitochondrial and 2) nuclear DNA inserts integrated at VDJ junctions; 3) inserts originating from telomere proximal genes; and 4) fragile sites incorporated between J-to-constant junctions. The latter class of inserts was exclusively found in memory and in in vitro activated B cells, while all other classes were already detected in naïve B cells. More than 10% of inserts preserved the reading frame, including transcripts with signs of antigen-driven affinity maturation. Collectively, our study unravels a mechanism of antibody diversification that is layered on the classical V(D)J and switch recombination.
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Alvarez S, da Silva Almeida AC, Albero R, Biswas M, Barreto-Galvez A, Gunning TS, Shaikh A, Aparicio T, Wendorff A, Piovan E, Van Vlierberghe P, Gygi S, Gautier J, Madireddy A, A Ferrando A. Functional mapping of PHF6 complexes in chromatin remodeling, replication dynamics, and DNA repair. Blood 2022; 139:3418-3429. [PMID: 35338774 PMCID: PMC9185155 DOI: 10.1182/blood.2021014103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/27/2022] [Indexed: 01/05/2023] Open
Abstract
The Plant Homeodomain 6 gene (PHF6) encodes a nucleolar and chromatin-associated leukemia tumor suppressor with proposed roles in transcription regulation. However, specific molecular mechanisms controlled by PHF6 remain rudimentarily understood. Here we show that PHF6 engages multiple nucleosome remodeling protein complexes, including nucleosome remodeling and deacetylase, SWI/SNF and ISWI factors, the replication machinery and DNA repair proteins. Moreover, after DNA damage, PHF6 localizes to sites of DNA injury, and its loss impairs the resolution of DNA breaks, with consequent accumulation of single- and double-strand DNA lesions. Native chromatin immunoprecipitation sequencing analyses show that PHF6 specifically associates with difficult-to-replicate heterochromatin at satellite DNA regions enriched in histone H3 lysine 9 trimethyl marks, and single-molecule locus-specific analyses identify PHF6 as an important regulator of genomic stability at fragile sites. These results extend our understanding of the molecular mechanisms controlling hematopoietic stem cell homeostasis and leukemia transformation by placing PHF6 at the crossroads of chromatin remodeling, replicative fork dynamics, and DNA repair.
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Affiliation(s)
- Silvia Alvarez
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Robert Albero
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Mayukh Biswas
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Thomas S Gunning
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Anam Shaikh
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | - Tomas Aparicio
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Erich Piovan
- UOC Immunologia e Diagnostica Molecolare Oncologica, Istituto Oncologico Veneto-Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Padova, Italy
- Dipartimento di Scienze Chirurgiche, Oncologiche e Gastroenterologiche, Sezione di Oncologia, Università di Padova, Padova, Italy
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Steven Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Genetics and Development, College of Physicians and Surgeons, and
| | | | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Systems Biology, Columbia University, New York, NY; and
- Department of Pediatrics and
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
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Shale C, Cameron DL, Baber J, Wong M, Cowley MJ, Papenfuss AT, Cuppen E, Priestley P. Unscrambling cancer genomes via integrated analysis of structural variation and copy number. CELL GENOMICS 2022; 2:100112. [PMID: 36776527 PMCID: PMC9903802 DOI: 10.1016/j.xgen.2022.100112] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 09/29/2021] [Accepted: 02/25/2022] [Indexed: 11/17/2022]
Abstract
Complex somatic genomic rearrangements and copy number alterations are hallmarks of nearly all cancers. We have developed an algorithm, LINX, to aid interpretation of structural variant and copy number data derived from short-read, whole-genome sequencing. LINX classifies raw structural variant calls into distinct events and predicts their effect on the local structure of the derivative chromosome and the functional impact on affected genes. Visualizations facilitate further investigation of complex rearrangements. LINX allows insights into a diverse range of structural variation events and can reliably detect pathogenic rearrangements, including gene fusions, immunoglobulin enhancer rearrangements, intragenic deletions, and duplications. Uniquely, LINX also predicts chained fusions that we demonstrate account for 13% of clinically relevant oncogenic fusions. LINX also reports a class of inactivation events that we term homozygous disruptions that may be a driver mutation in up to 9% of tumors and may frequently affect PTEN, TP53, and RB1.
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Affiliation(s)
- Charles Shale
- Hartwig Medical Foundation Australia, Sydney, NSW, Australia
- Hartwig Medical Foundation, Science Park 408, Amsterdam, the Netherlands
| | - Daniel L. Cameron
- Hartwig Medical Foundation Australia, Sydney, NSW, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jonathan Baber
- Hartwig Medical Foundation Australia, Sydney, NSW, Australia
- Hartwig Medical Foundation, Science Park 408, Amsterdam, the Netherlands
| | - Marie Wong
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Kensington, NSW, Australia
| | - Mark J. Cowley
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Kensington, NSW, Australia
| | - Anthony T. Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Edwin Cuppen
- Hartwig Medical Foundation, Science Park 408, Amsterdam, the Netherlands
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, the Netherlands
| | - Peter Priestley
- Hartwig Medical Foundation Australia, Sydney, NSW, Australia
- Hartwig Medical Foundation, Science Park 408, Amsterdam, the Netherlands
- Corresponding author
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Kuchta-Gładysz M, Wójcik E, Grzesiakowska A, Rymuza K, Szeleszczuk O. Chromosomal Instability at Fragile Sites in Blue Foxes, Silver Foxes, and Their Interspecific Hybrids. Animals (Basel) 2021; 11:ani11061743. [PMID: 34207981 PMCID: PMC8230692 DOI: 10.3390/ani11061743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary The paper describes the karyotypes of blue and silver foxes and their hybrids, in terms of the numbers of A and B chromosomes and the frequency of fragile sites on chromosomes. Genome stability in these species is affected by Robertson translocations in the karyotype of the blue fox and by B chromosomes in the silver fox. The fragile sites assay was used as a biomarker to assess genome stability in foxes. This test enables the identification of breaks, chromatid gaps, and deletions. In healthy individuals, the number of these instabilities remains low. The test can be used to select individuals with the most stable genome for breeding of blue and silver foxes. The fewer an individual’s susceptible sites, the more likely it is to have good reproductive performance. This factor is extremely important in the case of blue foxes, which are an endangered species. Abstract A cytogenetic assay based on fragile sites (FS) enables the identification of breaks, chromatid gaps, and deletions. In healthy individuals, the number of these instabilities remains low. Genome stability in these species is affected by Robertsonian translocations in the karyotype of the blue fox and by B chromosomes in the silver fox. The aims of the study were to characterise the karyotype of blue foxes, silver foxes, and their hybrids and to identify chromosomal fragile sites used to evaluate genome stability. The diploid number of A chromosomes in blue foxes ranged from 48 to 50, while the number of B chromosomes in silver foxes varied from one to four, with a constant number of A chromosomes (2n = 34). In interspecific hybrids, both types of karyotypic variation were identified, with the diploid number of A chromosomes ranging from 40 to 44 and the number of B chromosomes varying from 0 to 3. The mean frequency of FS in foxes was 4.06 ± 0.19: 4.61 ± 0.37 in blue foxes, 3.46 ± 0.28 in silver foxes, and 4.12 ± 0.22 in hybrids. A relationship was identified between an increased number of A chromosomes in the karyotype of the hybrids and the frequency of chromosomal breaks. The FS assay was used as a biomarker for the evaluation of genomic stability in the animals in the study.
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Affiliation(s)
- Marta Kuchta-Gładysz
- Department of Animal Reproduction, Anatomy and Genomics, Faculty of Animal Sciences, University of Agriculture in Krakow, ul. Mickiewicza 24/28, 30-059 Kraków, Poland; (M.K.-G.); (A.G.); (O.S.)
| | - Ewa Wójcik
- Institute of Animal Science and Fisheries, Faculty of Agrobioengineering and Animal Husbandry, Siedlce University of Natural Sciences and Humanities, ul. Prusa 14, 08-110 Siedlce, Poland
- Correspondence:
| | - Anna Grzesiakowska
- Department of Animal Reproduction, Anatomy and Genomics, Faculty of Animal Sciences, University of Agriculture in Krakow, ul. Mickiewicza 24/28, 30-059 Kraków, Poland; (M.K.-G.); (A.G.); (O.S.)
| | - Katarzyna Rymuza
- Institute of Agriculture and Horticulture, Faculty of Agrobioengineering and Animal Husbandry, Siedlce University of Natural Sciences and Humanities, ul. Prusa 14, 08-110 Siedlce, Poland;
| | - Olga Szeleszczuk
- Department of Animal Reproduction, Anatomy and Genomics, Faculty of Animal Sciences, University of Agriculture in Krakow, ul. Mickiewicza 24/28, 30-059 Kraków, Poland; (M.K.-G.); (A.G.); (O.S.)
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Finocchi F, Pelloni M, Balercia G, Pallotti F, Radicioni AF, Lenzi A, Lombardo F, Paoli D. Seminal plasma miRNAs in Klinefelter syndrome and in obstructive and non-obstructive azoospermia. Mol Biol Rep 2020; 47:4373-4382. [DOI: 10.1007/s11033-020-05552-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/23/2020] [Indexed: 02/08/2023]
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Abstract
Chromosome instability adversely affects animal fertility and reproduction. Analysis of instability can be a valuable diagnostic tool. Helpful tests for assessment of instabilities include the sister chromatid exchange assay, identification of fragile sites, the bleomycin assay and the comet assay. These techniques can be used to assess and compare the chromosome stability of individual breeds of animals. The aim of the study was to assess chromosome stability in boars: Duroc, Duroc x Pietrain and Pietrain x Duroc crossbreds, Polish Large White, and the Neckar, P76 and PIC lines. The study assessed the chromosome stability of boars. The distribution of instabilities in individual breeds was varied. The average frequency of chromatid exchange was 4.8 ± 1.5, while that of fragile sites was 3.9 ± 1.4. The mean level of DNA damage (% tail DNA) was 9.4 ± 8.3, while in the bleomycin assay b/c and %AM were 0.6 ± 0.7 and 44.4 ± 4.1. A higher rate of instability was found in older individuals than in younger ones. The cytogenetic assays used to identify various forms of chromosome instability can be used to evaluate boars intended for breeding.
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Affiliation(s)
- Ewa Wójcik
- Institute of Animal Science and Fisheries, Siedlce University of Natural Sciences and Humanities, Siedlce, Poland
- * E-mail:
| | - Agnieszka Sokół
- Institute of Animal Science and Fisheries, Siedlce University of Natural Sciences and Humanities, Siedlce, Poland
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MiRNAs Targeting Double Strand DNA Repair Pathways Lurk in Genomically Unstable Rare Fragile Sites and Determine Cancer Outcomes. Cancers (Basel) 2020; 12:cancers12040876. [PMID: 32260317 PMCID: PMC7226545 DOI: 10.3390/cancers12040876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/12/2022] Open
Abstract
Double strand break (DSB) repair mechanisms guard genome integrity and their deterioration causes genomic instability. Common and rare fragile sites (CFS and RFS, respectively) are particularly vulnerable to instability, and there is an inverse correlation between fragile site (FS) expression and DSB repair protein levels. Upon DSB repair dysfunction, genes residing at these sites are at greater risk of deregulation compared to genes located at non-FS. In this regard, it remains enigmatic why the incidence of miRNA genes at FS is higher compared to non-FS. Herein, using bioinformatics, we examined whether miRNA genes localized at FS inhibit components of DSB repair pathways and assessed their effects on cancer. We show that such miRNAs over-accumulate in RFS, and that FRAXA, which is expressed in Fragile X syndrome, is a conserved hotspot for miRNAs inhibiting DSB repair. Axes of FRAXA-residing miRNAs/DSB repair targets affect survival in a cancer type-specific manner. Moreover, copy number variations in the region encompassing these miRNA genes discriminate survival between male and female patients. Given that, thus far, only CFS have been considered relevant for carcinogenesis, our data are the first to associate RFS with cancer, through the impairment of DSB repair by the FRAXA-residing miRNAs.
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Lyu X, Chastain M, Chai W. Genome-wide mapping and profiling of γH2AX binding hotspots in response to different replication stress inducers. BMC Genomics 2019; 20:579. [PMID: 31299901 PMCID: PMC6625122 DOI: 10.1186/s12864-019-5934-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Replication stress (RS) gives rise to DNA damage that threatens genome stability. RS can originate from different sources that stall replication by diverse mechanisms. However, the mechanism underlying how different types of RS contribute to genome instability is unclear, in part due to the poor understanding of the distribution and characteristics of damage sites induced by different RS mechanisms. RESULTS We use ChIP-seq to map γH2AX binding sites genome-wide caused by aphidicolin (APH), hydroxyurea (HU), and methyl methanesulfonate (MMS) treatments in human lymphocyte cells. Mapping of γH2AX ChIP-seq reveals that APH, HU, and MMS treatments induce non-random γH2AX chromatin binding at discrete regions, suggesting that there are γH2AX binding hotspots in the genome. Characterization of the distribution and sequence/epigenetic features of γH2AX binding sites reveals that the three treatments induce γH2AX binding at largely non-overlapping regions, suggesting that RS may cause damage at specific genomic loci in a manner dependent on the fork stalling mechanism. Nonetheless, γH2AX binding sites induced by the three treatments share common features including compact chromatin, coinciding with larger-than-average genes, and depletion of CpG islands and transcription start sites. Moreover, we observe significant enrichment of SINEs in γH2AX sites in all treatments, indicating that SINEs may be a common barrier for replication polymerases. CONCLUSIONS Our results identify the location and common features of genome instability hotspots induced by different types of RS, and help in deciphering the mechanisms underlying RS-induced genetic diseases and carcinogenesis.
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Affiliation(s)
- Xinxing Lyu
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Megan Chastain
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Weihang Chai
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA.
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12
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Lin H, Zhang Z, Iomini C, Dutcher SK. Identifying RNA splicing factors using IFT genes in Chlamydomonas reinhardtii. Open Biol 2019. [PMID: 29514868 PMCID: PMC5881031 DOI: 10.1098/rsob.170211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Intraflagellar transport moves proteins in and out of flagella/cilia and it is essential for the assembly of these organelles. Using whole-genome sequencing, we identified splice site mutations in two IFT genes, IFT81 (fla9) and IFT121 (ift121-2), which lead to flagellar assembly defects in the unicellular green alga Chlamydomonas reinhardtii. The splicing defects in these ift mutants are partially corrected by mutations in two conserved spliceosome proteins, DGR14 and FRA10. We identified a dgr14 deletion mutant, which suppresses the 3′ splice site mutation in IFT81, and a frameshift mutant of FRA10, which suppresses the 5′ splice site mutation in IFT121. Surprisingly, we found dgr14-1 and fra10 mutations suppress both splice site mutations. We suggest these two proteins are involved in facilitating splice site recognition/interaction; in their absence some splice site mutations are tolerated. Nonsense mutations in SMG1, which is involved in nonsense-mediated decay, lead to accumulation of aberrant transcripts and partial restoration of flagellar assembly in the ift mutants. The high density of introns and the conservation of noncore splicing factors, together with the ease of scoring the ift mutant phenotype, make Chlamydomonas an attractive organism to identify new proteins involved in splicing through suppressor screening.
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Affiliation(s)
- Huawen Lin
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Zhengyan Zhang
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Carlo Iomini
- Department of Ophthalmology, Mount Sinai School of Medicine, New York, NY, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
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13
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Azenha D, Lopes MC, Martins TC. Claspin: From replication stress and DNA damage responses to cancer therapy. DNA Repair (Amst) 2019; 115:203-246. [DOI: 10.1016/bs.apcsb.2018.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Zheglo D, Brueckner LM, Sepman O, Wecht EM, Kuligina E, Suspitsin E, Imyanitov E, Savelyeva L. The FRA14B
common fragile site maps to a region prone to somatic and germline rearrangements within the large GPHN
gene. Genes Chromosomes Cancer 2018; 58:284-294. [DOI: 10.1002/gcc.22706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 01/27/2023] Open
Affiliation(s)
- Diana Zheglo
- FSBI Research Centre for Medical Genetics; Moscow Russia
| | - Lena M. Brueckner
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Olga Sepman
- Klinik fuer Allgemein-, Viszeral-, Thorax- und minimal-invasive Chirurgie; Pforzheim Germany
| | - Elisa M. Wecht
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | | | - Evgenij Suspitsin
- Petrov Institute of Oncology; St Petersburg Russia
- St. Petersburg Pediatric Medical University; Sankt-Peterburg Russia
| | - Evgenij Imyanitov
- Petrov Institute of Oncology; St Petersburg Russia
- Mechnikov North-Western Medical University; Saint Petersburg Russia
| | - Larissa Savelyeva
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
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15
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Wang H, Li S, Zhang H, Wang Y, Hao S, Wu X. BLM prevents instability of structure-forming DNA sequences at common fragile sites. PLoS Genet 2018; 14:e1007816. [PMID: 30496191 PMCID: PMC6289451 DOI: 10.1371/journal.pgen.1007816] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/11/2018] [Accepted: 11/07/2018] [Indexed: 01/04/2023] Open
Abstract
Genome instability often arises at common fragile sites (CFSs) leading to cancer-associated chromosomal rearrangements. However, the underlying mechanisms of how CFS protection is achieved is not well understood. We demonstrate that BLM plays an important role in the maintenance of genome stability of structure-forming AT-rich sequences derived from CFSs (CFS-AT). BLM deficiency leads to increased DSB formation and hyper mitotic recombination at CFS-AT and induces instability of the plasmids containing CFS-AT. We further showed that BLM is required for suppression of CFS breakage upon oncogene expression. Both helicase activity and ATR-mediated phosphorylation of BLM are important for preventing genetic instability at CFS-AT sequences. Furthermore, the role of BLM in protecting CFS-AT is not epistatic to that of FANCM, a translocase that is involved in preserving CFS stability. Loss of BLM helicase activity leads to drastic decrease of cell viability in FANCM deficient cells. We propose that BLM and FANCM utilize different mechanisms to remove DNA secondary structures forming at CFS-AT on replication forks, thereby preventing DSB formation and maintaining CFS stability. Common fragile sites (CFSs) are large chromosomal regions which are more prone to breakage than other places in the genome. They are a part of normal chromosome structure and are present in all human beings, but are also hotspots for chromosomal rearrangement during oncogenesis. Understanding how CFSs are protected to prevent genome instability is thus extremely important for revealing the mechanism underlying cancer development. We found that Bloom syndrome protein BLM is involved in resolving DNA secondary structures that arise at AT-rich sequences in CFSs, suggesting a critical function of BLM in protecting CFSs. We also found that this BLM function is distinct from the role of Fanconi anemia protein FANCM in protecting CFSs, and loss of both BLM and FANCM activities leads to cell death. These studies reveal important mechanisms of the maintenance of CFS stability in mammalian cells.
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Affiliation(s)
- Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Shibo Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Huimin Zhang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ya Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Shuailin Hao
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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16
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Tsao WC, Eckert KA. Detours to Replication: Functions of Specialized DNA Polymerases during Oncogene-induced Replication Stress. Int J Mol Sci 2018; 19:ijms19103255. [PMID: 30347795 PMCID: PMC6214091 DOI: 10.3390/ijms19103255] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 01/10/2023] Open
Abstract
Incomplete and low-fidelity genome duplication contribute to genomic instability and cancer development. Difficult-to-Replicate Sequences, or DiToRS, are natural impediments in the genome that require specialized DNA polymerases and repair pathways to complete and maintain faithful DNA synthesis. DiToRS include non B-DNA secondary structures formed by repetitive sequences, for example within chromosomal fragile sites and telomeres, which inhibit DNA replication under endogenous stress conditions. Oncogene activation alters DNA replication dynamics and creates oncogenic replication stress, resulting in persistent activation of the DNA damage and replication stress responses, cell cycle arrest, and cell death. The response to oncogenic replication stress is highly complex and must be tightly regulated to prevent mutations and tumorigenesis. In this review, we summarize types of known DiToRS and the experimental evidence supporting replication inhibition, with a focus on the specialized DNA polymerases utilized to cope with these obstacles. In addition, we discuss different causes of oncogenic replication stress and its impact on DiToRS stability. We highlight recent findings regarding the regulation of DNA polymerases during oncogenic replication stress and the implications for cancer development.
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Affiliation(s)
- Wei-Chung Tsao
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
| | - Kristin A Eckert
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
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17
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Pan-Cancer Analysis Reveals Differential Susceptibility of Bidirectional Gene Promoters to DNA Methylation, Somatic Mutations, and Copy Number Alterations. Int J Mol Sci 2018; 19:ijms19082296. [PMID: 30081598 PMCID: PMC6121907 DOI: 10.3390/ijms19082296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/26/2018] [Accepted: 08/02/2018] [Indexed: 12/12/2022] Open
Abstract
Bidirectional gene promoters affect the transcription of two genes, leading to the hypothesis that they should exhibit protection against genetic or epigenetic changes in cancer. Therefore, they provide an excellent opportunity to learn about promoter susceptibility to somatic alteration in tumors. We tested this hypothesis using data from genome-scale DNA methylation (14 cancer types), simple somatic mutation (10 cancer types), and copy number variation profiling (14 cancer types). For DNA methylation, the difference in rank differential methylation between tumor and tumor-adjacent normal matched samples based on promoter type was tested by the Wilcoxon rank sum test. Logistic regression was used to compare differences in simple somatic mutations. For copy number alteration, a mixed effects logistic regression model was used. The change in methylation between non-diseased tissues and their tumor counterparts was significantly greater in single compared to bidirectional promoters across all 14 cancer types examined. Similarly, the extent of copy number alteration was greater in single gene compared to bidirectional promoters for all 14 cancer types. Furthermore, among 10 cancer types with available simple somatic mutation data, bidirectional promoters were slightly more susceptible. These results suggest that selective pressures related with specific functional impacts during carcinogenesis drive the susceptibility of promoter regions to somatic alteration.
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18
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Foss EJ, Lao U, Bedalov A. G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome. J Vis Exp 2018. [PMID: 29630039 DOI: 10.3791/56286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Numerous techniques have been developed to follow the progress of DNA replication through the S phase of the cell cycle. Most of these techniques have been directed toward elucidation of the location and timing of initiation of genome duplication rather than its completion. However, it is critical that we understand regions of the genome that are last to complete replication, because these regions suffer elevated levels of chromosomal breakage and mutation, and they have been associated with both disease and aging. Here we describe how we have extended a technique that has been used to monitor replication initiation to instead identify those regions of the genome last to complete replication. This approach is based on a combination of flow cytometry and high throughput sequencing. Although this report focuses on the application of this technique to yeast, the approach can be used with any cells that can be sorted in a flow cytometer according to DNA content.
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Affiliation(s)
- Eric J Foss
- Division of Clinical Research, Fred Hutchinson Cancer Research Center
| | - Uyen Lao
- Division of Clinical Research, Fred Hutchinson Cancer Research Center
| | - Antonio Bedalov
- Division of Clinical Research, Fred Hutchinson Cancer Research Center; Departments of Medicine and Biochemistry, University of Washington;
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19
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Majka J, Zwierzykowski Z, Majka M, Kosmala A. Karyotype reshufflings of Festuca pratensis × Lolium perenne hybrids. PROTOPLASMA 2018; 255:451-458. [PMID: 28884345 PMCID: PMC5830480 DOI: 10.1007/s00709-017-1161-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
Many different processes have an impact on the shape of plant karyotype. Recently, cytogenetic examination of Lolium species has revealed the occurrence of spontaneous fragile sites (FSs) associated with 35S rDNA regions. The FSs are defined as the chromosomal regions that are sensitive to forming gaps or breaks on chromosomes. The shape of karyotype can also be determined by interstitial telomeric sequences (ITSs), what was recognized for the first time in this paper in chromosomes of Festuca pratensis × Lolium perenne hybrids. Both FSs and ITSs can contribute to genome instabilities and chromosome rearrangements. To evaluate whether these cytogenetic phenomena have an impact on karyotype reshuffling observed in Festuca × Lolium hybrids, we examined F1 F. pratensis × L. perenne plants and generated F2-F9 progeny by fluorescent in situ hybridization (FISH) using rDNA sequences, telomere and centromere probes, as well as by genomic in situ hybridization (GISH). Analyses using a combination of FISH and GISH revealed that intergenomic rearrangements did not correspond to FSs but overlapped with ITSs for several analyzed genotypes. It suggests that internal telomeric repeats can affect the shape of F. pratensis × L. perenne karyotypes. However, other factors that are involved in rearrangements and have a more crucial impact could exist, but they are still unknown.
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Affiliation(s)
- Joanna Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Zbigniew Zwierzykowski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Maciej Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Arkadiusz Kosmala
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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20
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The incidence and origin of segmental aneuploidy in human oocytes and preimplantation embryos. Hum Reprod 2017; 32:2549-2560. [DOI: 10.1093/humrep/dex324] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/03/2017] [Indexed: 11/14/2022] Open
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21
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Azenha D, Lopes MC, Martins TC. Claspin functions in cell homeostasis-A link to cancer? DNA Repair (Amst) 2017; 59:27-33. [PMID: 28942358 DOI: 10.1016/j.dnarep.2017.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 10/18/2022]
Abstract
Cancer remains one of the leading causes of mortality worldwide. Most cancers present high degrees of genomic instability. DNA damage and replication checkpoints function as barriers to halt cell cycle progression until damage is resolved, preventing the perpetuation of errors. Activation of these checkpoints is critically dependent on Claspin, an adaptor protein that mediates the phosphorylation of the effector kinase Chk1 by ATR. However, Claspin also performs other roles related to the protection and maintenance of cell and genome integrity. For instance, following DNA damage and checkpoint activation, Claspin bridges checkpoint responses to DNA repair or to apoptosis. During DNA replication, Claspin acts a sensor and couples DNA unwinding to strand polymerization, and may also indirectly regulate replication initiation at firing origins. As Claspin participates in several processes that are vital to maintenance of cell homeostasis, its function is tightly regulated at multiple levels. Nevertheless, little is known about its role in cancer. Accumulating evidence suggests that Claspin inactivation could be an essential event during carcinogenesis, indicating that Claspin may function as a tumour suppressor. In this review, we will examine the functions of Claspin and how its deregulation may contribute to cancer initiation and progression. To conclude, we will discuss means by which Claspin can be targeted for cancer therapy.
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Affiliation(s)
- Diana Azenha
- Faculdade de Farmácia da Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal; Centro de Neurociências e Biologia Celular, Universidade de Coimbra, Rua Larga, Faculdade de Medicina, Pólo I, 1º andar, 3004-504 Coimbra, Portugal; Instituto Português de Oncologia de Coimbra de Francisco Gentil, Av. Bissaya Barreto 98, Apartado 2005, 3000-651, Coimbra, Portugal.
| | - Maria Celeste Lopes
- Faculdade de Farmácia da Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal; Centro de Neurociências e Biologia Celular, Universidade de Coimbra, Rua Larga, Faculdade de Medicina, Pólo I, 1º andar, 3004-504 Coimbra, Portugal.
| | - Teresa C Martins
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, Rua Larga, Faculdade de Medicina, Pólo I, 1º andar, 3004-504 Coimbra, Portugal; Instituto Português de Oncologia de Coimbra de Francisco Gentil, Av. Bissaya Barreto 98, Apartado 2005, 3000-651, Coimbra, Portugal.
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22
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Handa H, Sasaki Y, Hattori H, Alkebsi L, Kasamatsu T, Saitoh T, Mitsui T, Yokohama A, Tsukamoto N, Matsumoto M, Murakami H. Recurrent alterations of the WW domain containing oxidoreductase gene spanning the common fragile site FRA16D in multiple myeloma and monoclonal gammopathy of undetermined significance. Oncol Lett 2017; 14:4372-4378. [PMID: 28943951 DOI: 10.3892/ol.2017.6672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 03/03/2017] [Indexed: 11/05/2022] Open
Abstract
The putative tumor suppressor gene WW domain containing oxidoreductase (WWOX) spans a common fragile site (CFS) on chromosome 16q23.3. CFSs are regions of profound genomic instability and sites for genomic deletions in cancer cells. Therefore, WWOX is structurally altered in diverse nonhematological cancer types. However, the function of WWOX in hematological tumor types, including multiple myeloma (MM) and monoclonal gammopathy of undetermined significance (MGUS) remains unclear. WWOX expression and methylation in patients with MM, MGUS, or noninvasive lymphoma (control) were analyzed using reverse transcription- and methylation specific-polymerase chain reaction analysis. Variant WWOX transcripts were detected in 65 and 50% of patients with MM and MGUS, respectively, compared with 10% of controls. WWOX expression was higher in patients with MM, and WWOX promoter methylation was detected in 35% of patients with MM compared with 5% of patients with MGUS and 4% of controls. WWOX promoter methylation was significantly associated with shorter overall survival time of patients, in particular those with MM who were never treated with novel agents. Genomic alterations, including deletions and promoter methylation that affect WWOX expression occur early and may be involved in the pathogenesis, progression, and prognosis of MM.
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Affiliation(s)
- Hiroshi Handa
- Department of Medicine and Clinical Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Yoshiko Sasaki
- Department of Laboratory Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Hikaru Hattori
- Department of Laboratory Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Lobna Alkebsi
- Department of Laboratory Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Tetsuhiro Kasamatsu
- Department of Laboratory Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Takayuki Saitoh
- Department of Laboratory Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Takeki Mitsui
- Department of Medicine and Clinical Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Akihiko Yokohama
- Blood Transfusion Service, Gunma University Hospital, Maebashi, Gunma 371-8511, Japan
| | - Norifumi Tsukamoto
- Oncology Center, Gunma University Hospital, Maebashi, Gunma 371-8511, Japan
| | - Morio Matsumoto
- Department of Hematology, National Hospital Organization Shibukawa Medical Center, Shibukawa, Gunma 377-0280, Japan
| | - Hirokazu Murakami
- Department of Laboratory Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
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23
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Bhowmick R, Hickson ID. The "enemies within": regions of the genome that are inherently difficult to replicate. F1000Res 2017; 6:666. [PMID: 28620461 PMCID: PMC5461909 DOI: 10.12688/f1000research.11024.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/11/2017] [Indexed: 12/23/2022] Open
Abstract
An unusual feature of many eukaryotic genomes is the presence of regions that appear intrinsically difficult to copy during the process of DNA replication. Curiously, the location of these difficult-to-replicate regions is often conserved between species, implying a valuable role in some aspect of genome organization or maintenance. The most prominent class of these regions in mammalian cells is defined as chromosome fragile sites, which acquired their name because of a propensity to form visible gaps/breaks on otherwise-condensed chromosomes in mitosis. This fragility is particularly apparent following perturbation of DNA replication-a phenomenon often referred to as "replication stress". Here, we review recent data on the molecular basis for chromosome fragility and the role of fragile sites in the etiology of cancer. In particular, we highlight how studies on fragile sites have provided unexpected insights into how the DNA repair machinery assists in the completion of DNA replication.
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Affiliation(s)
- Rahul Bhowmick
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
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24
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Jahid S, Sun J, Gelincik O, Blecua P, Edelmann W, Kucherlapati R, Zhou K, Jasin M, Gümüş ZH, Lipkin SM. Inhibition of colorectal cancer genomic copy number alterations and chromosomal fragile site tumor suppressor FHIT and WWOX deletions by DNA mismatch repair. Oncotarget 2017; 8:71574-71586. [PMID: 29069730 PMCID: PMC5641073 DOI: 10.18632/oncotarget.17776] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/24/2017] [Indexed: 01/15/2023] Open
Abstract
Homologous recombination (HR) enables precise DNA repair after DNA double strand breaks (DSBs) using identical sequence templates, whereas homeologous recombination (HeR) uses only partially homologous sequences. Homeologous recombination introduces mutations through gene conversion and genomic deletions through single-strand annealing (SSA). DNA mismatch repair (MMR) inhibits HeR, but the roles of mammalian MMR MutL homologues (MLH1, PMS2 and MLH3) proteins in HeR suppression are poorly characterized. Here, we demonstrate that mouse embryonic fibroblasts (MEFs) carrying Mlh1, Pms2, and Mlh3 mutations have higher HeR rates, by using 7,863 uniquely mapping paired direct repeat sequences (DRs) in the mouse genome as endogenous gene conversion and SSA reporters. Additionally, when DSBs are induced by gamma-radiation, Mlh1, Pms2 and Mlh3 mutant MEFs have higher DR copy number alterations (CNAs), including DR CNA hotspots previously identified in mouse MMR-deficient colorectal cancer (dMMR CRC). Analysis of The Cancer Genome Atlas CRC data revealed that dMMR CRCs have higher genome-wide DR HeR rates than MMR proficient CRCs, and that dMMR CRCs have deletion hotspots in tumor suppressors FHIT/WWOX at chromosomal fragile sites FRA3B and FRA16D (which have elevated DSB rates) flanked by paired homologous DRs and inverted repeats (IR). Overall, these data provide novel insights into the MMR-dependent HeR inhibition mechanism and its role in tumor suppression.
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Affiliation(s)
- Sohail Jahid
- Departments of Medicine and Genetic Medicine, Weill Cornell Medicine, 10021, NY, USA
| | - Jian Sun
- Departments of Medicine and Genetic Medicine, Weill Cornell Medicine, 10021, NY, USA
| | - Ozkan Gelincik
- Departments of Medicine and Genetic Medicine, Weill Cornell Medicine, 10021, NY, USA
| | - Pedro Blecua
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, 10065, NY, USA
| | - Winfried Edelmann
- Department of Cell Biology and Department of Genetics, Albert Einstein College of Medicine of Yeshiva University, 10461, NY, USA
| | - Raju Kucherlapati
- Department of Genetics, Harvard Medical School, 02115, Boston, MA, USA
| | - Kathy Zhou
- Department of Biostatistics and Epidemiology, Weill Cornell Medical College, 10021, NY, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 10065, NY, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 10029, NY, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 10029, NY, USA
| | - Steven M Lipkin
- Departments of Medicine and Genetic Medicine, Weill Cornell Medicine, 10021, NY, USA
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25
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Wang W, Mani AM, Wu ZH. DNA damage-induced nuclear factor-kappa B activation and its roles in cancer progression. JOURNAL OF CANCER METASTASIS AND TREATMENT 2017; 3:45-59. [PMID: 28626800 PMCID: PMC5472228 DOI: 10.20517/2394-4722.2017.03] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA damage is a vital challenge to cell homeostasis. Cellular responses to DNA damage (DDR) play essential roles in maintaining genomic stability and survival, whose failure could lead to detrimental consequences such as cancer development and aging. Nuclear factor-kappa B (NF-κB) is a family of transcription factors that plays critical roles in cellular stress response. Along with p53, NF-κB modulates transactivation of a large number of genes which participate in various cellular processes involved in DDR. Here the authors summarize the recent progress in understanding DNA damage response and NF-κB signaling pathways. This study particularly focuses on DNA damage-induced NF-κB signaling cascade and its physiological and pathological significance in B cell development and cancer therapeutic resistance. The authors also discuss promising strategies for selectively targeting this genotoxic NF-κB signaling aiming to antagonize acquired resistance and resensitize refractory cancer cells to cytotoxic treatments.
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Affiliation(s)
- Wei Wang
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Arul M. Mani
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Zhao-Hui Wu
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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26
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Villacis RAR, Basso TR, Canto LM, Nóbrega AF, Achatz MI, Rogatto SR. Germline large genomic alterations on 7q in patients with multiple primary cancers. Sci Rep 2017; 7:41677. [PMID: 28139749 PMCID: PMC5282589 DOI: 10.1038/srep41677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 12/29/2016] [Indexed: 11/11/2022] Open
Abstract
Patients with multiple primary cancers (MPCs) are suspected to have a hereditary cancer syndrome. However, only a small proportion may be explained by mutations in high-penetrance genes. We investigate two unrelated MPC patients that met Hereditary Breast and Ovaria Cancer criteria, both presenting triple negative breast tumors and no mutations in BRCA1, BRCA2 and TP53 genes. Germline rearrangements on chromosome 7q, involving over 40 Mb of the same region, were found in both patients: one with mosaic loss (80% of cells) and the other with cnLOH (copy-neutral loss of heterozygosity) secondary to maternal allele duplication. Five children tested had no alterations on 7q. The patients shared 330 genes in common on 7q22.1-q34, including several tumor suppressor genes (TSGs) previously related to breast cancer risk and imprinted genes. The analysis of the triple negative BC from one patient revealed a mosaic gain of 7q translated for over-expressed cancer-related genes. The involvement of TSGs and imprinted genes, mapped on 7q, has the potential of being associated to MPC risk, as well as cancer progression. To our knowledge, this is the first description of patients with MPCs that harbor constitutive large alterations on 7q.
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Affiliation(s)
- R. A. R. Villacis
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília - UnB, Brasília, DF, Brazil
| | - T. R. Basso
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - L. M. Canto
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - A. F. Nóbrega
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - M. I. Achatz
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - S. R. Rogatto
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
- Department of Clinical Genetics, Vejle Hospital, DK and University of Southern Denmark, Denmark
- Department of Urology, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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Wang X, Zhang S, Zheng R, Yue F, Lin SHS, Rahmeh AA, Lee EYC, Zhang Z, Lee MYWT. PDIP46 (DNA polymerase δ interacting protein 46) is an activating factor for human DNA polymerase δ. Oncotarget 2017; 7:6294-313. [PMID: 26819372 PMCID: PMC4868757 DOI: 10.18632/oncotarget.7034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/25/2016] [Indexed: 02/07/2023] Open
Abstract
PDIP46 (SKAR, POLDIP3) was discovered through its interaction with the p50 subunit of human DNA polymerase δ (Pol δ). Its functions in DNA replication are unknown. PDIP46 associates with Pol δ in cell extracts both by immunochemical and protein separation methods, as well as by ChIP analyses. PDIP46 also interacts with PCNA via multiple copies of a novel PCNA binding motif, the APIMs (AlkB homologue-2 PCNA-Interacting Motif). Sites for both p50 and PCNA binding were mapped to the N-terminal region containing the APIMs. Functional assays for the effects of PDIP46 on Pol δ activity on singly primed ssM13 DNA templates revealed that it is a novel and potent activator of Pol δ. The effects of PDIP46 on Pol δ in primer extension, strand displacement and synthesis through simple hairpin structures reveal a mechanism where PDIP46 facilitates Pol δ4 synthesis through regions of secondary structure on complex templates. In addition, evidence was obtained that PDIP46 is also capable of exerting its effects by a direct interaction with Pol δ, independent of PCNA. Mutation of the Pol δ and PCNA binding region resulted in a loss of PDIP46 functions. These studies support the view that PDIP46 is a novel accessory protein for Pol δ that is involved in cellular DNA replication. This raises the possibility that altered expression of PDIP46 or its mutation may affect Pol δ functions in vivo, and thereby be a nexus for altered genomic stability.
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Affiliation(s)
- Xiaoxiao Wang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, USA
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, USA
| | - Rong Zheng
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, USA
| | - Fu Yue
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, USA
| | - Szu Hua Sharon Lin
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, USA
| | - Amal A Rahmeh
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, USA
| | - Ernest Y C Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, USA
| | - Zhongtao Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, USA
| | - Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, USA
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Madireddy A, Gerhardt J. Replication Through Repetitive DNA Elements and Their Role in Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:549-581. [PMID: 29357073 DOI: 10.1007/978-981-10-6955-0_23] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human cells contain various repetitive DNA sequences, which can be a challenge for the DNA replication machinery to travel through and replicate correctly. Repetitive DNA sequence can adopt non-B DNA structures, which could block the DNA replication. Prolonged stalling of the replication fork at the endogenous repeats in human cells can have severe consequences such as genome instability that includes repeat expansions, contractions, and chromosome fragility. Several neurological and muscular diseases are caused by a repeat expansion. Furthermore genome instability is the major cause of cancer. This chapter describes some of the important classes of repetitive DNA sequences in the mammalian genome, their ability to form secondary DNA structures, their contribution to replication fork stalling, and models for repeat expansion as well as chromosomal fragility. Included in this chapter are also some of the strategies currently employed to detect changes in DNA replication and proteins that could prevent the repeat-mediated disruption of DNA replication in human cells. Additionally summarized are the consequences of repeat-associated perturbation of the DNA replication, which could lead to specific human diseases.
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29
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Feng W, Chakraborty A. Fragility Extraordinaire: Unsolved Mysteries of Chromosome Fragile Sites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:489-526. [PMID: 29357071 DOI: 10.1007/978-981-10-6955-0_21] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chromosome fragile sites are a fascinating cytogenetic phenomenon now widely implicated in a slew of human diseases ranging from neurological disorders to cancer. Yet, the paths leading to these revelations were far from direct, and the number of fragile sites that have been molecularly cloned with known disease-associated genes remains modest. Moreover, as more fragile sites were being discovered, research interests in some of the earliest discovered fragile sites ebbed away, leaving a number of unsolved mysteries in chromosome biology. In this review we attempt to recount some of the early discoveries of fragile sites and highlight those phenomena that have eluded intense scrutiny but remain extremely relevant in our understanding of the mechanisms of chromosome fragility. We then survey the literature for disease association for a comprehensive list of fragile sites. We also review recent studies addressing the underlying cause of chromosome fragility while highlighting some ongoing debates. We report an observed enrichment for R-loop forming sequences in fragile site-associated genes than genomic average. Finally, we will leave the reader with some lingering questions to provoke discussion and inspire further scientific inquiries.
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Affiliation(s)
- Wenyi Feng
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
| | - Arijita Chakraborty
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
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30
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The Causes and Consequences of Topological Stress during DNA Replication. Genes (Basel) 2016; 7:genes7120134. [PMID: 28009828 PMCID: PMC5192510 DOI: 10.3390/genes7120134] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/11/2016] [Accepted: 12/14/2016] [Indexed: 01/08/2023] Open
Abstract
The faithful replication of sister chromatids is essential for genomic integrity in every cell division. The replication machinery must overcome numerous difficulties in every round of replication, including DNA topological stress. Topological stress arises due to the double-stranded helical nature of DNA. When the strands are pulled apart for replication to occur, the intertwining of the double helix must also be resolved or topological stress will arise. This intrinsic problem is exacerbated by specific chromosomal contexts encountered during DNA replication. The convergence of two replicons during termination, the presence of stable protein-DNA complexes and active transcription can all lead to topological stresses being imposed upon DNA replication. Here we describe how replication forks respond to topological stress by replication fork rotation and fork reversal. We also discuss the genomic contexts where topological stress is likely to occur in eukaryotes, focusing on the contribution of transcription. Finally, we describe how topological stress, and the ways forks respond to it, may contribute to genomic instability in cells.
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31
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Mandrioli M, Rivi V, Nardelli A, Manicardi GC. Genomic and Cytogenetic Localization of the Carotenoid Genes in the Aphid Genome. Cytogenet Genome Res 2016; 149:207-217. [PMID: 27585067 DOI: 10.1159/000448669] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2016] [Indexed: 11/19/2022] Open
Abstract
Data published in the scientific literature suggests a possible link between chromosomal rearrangements involving autosomes 1 and 3 and the presence of red morphs in the peach-potato aphid Myzus persicae (Sulzer). In order to begin a study of this relationship, we analysed the genomic and chromosomal location of genes involved in carotenoid biosynthesis in M. persicae and the pea aphid, Acyrthosiphon pisum (Harris), since carotenoids are the basis of the colour in many aphid species. Genomic analysis identified a DNA sequence containing carotenoid genes in synteny between the 2 species. According to the results obtained using in situ PCR, carotenoid genes were located in a subterminal portion of autosome 1 in both species. The same localization has also been observed in the onion aphid Neotoxoptera formosana Takahashi that, as M. persicae and A. pisum, belongs to the tribe Macrosiphini, thereby suggesting a synteny of this chromosomal region in aphids. In situ PCR experiments performed on 2 M. persicae asexual lineages bearing heterozygous translocations involving autosomes 1 and 3 revealed that carotenoid genes were located within chromosomal portions involved in recurrent rearrangements. We also verified by bioinformatics analyses the presence of fragile sites that could explain these recurrent rearrangements in M. persicae.
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Affiliation(s)
- Mauro Mandrioli
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
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Kovtun IV, Murphy SJ, Johnson SH, Cheville JC, Vasmatzis G. Chromosomal catastrophe is a frequent event in clinically insignificant prostate cancer. Oncotarget 2016; 6:29087-96. [PMID: 26337081 PMCID: PMC4745713 DOI: 10.18632/oncotarget.4900] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/11/2015] [Indexed: 11/27/2022] Open
Abstract
Massive genomic rearrangements, a result of single catastrophic event termed chromothrispsis or chromosomal catastrophe, have been identified in a variety of human cancers. In a few cancer types, chromothripsis was found to be associated with poor prognosis. We performed mate-pair sequencing and analysis of structural rearrangements in 132 prostate cancer cases which included clinically insignificant Gleason score 6 tumors, clinically significant tumors of higher grade (7+) and high grade prostatic intraepithelial neoplasia. Chromothripsis was observed at least 30 per cent of the samples across different grades. Surprisingly, it was frequently observed in clinically insignificant Gleason score 6 tumors, indicating that chromothripsis does not define more aggressive phenotype. The degree of chromothripsis did not increase significantly in tumors of advanced grades and did not appear to contribute to tumor progression. Our data showed that distribution of chromothriptic rearrangements differed from that of fragile sites but correlated with the size of chromosomes. We also provided evidence that rearrangements resulting from chromothripsis were present in the cells of neighboring Gleason patterns of the same tumor. Our data suggest that that chromothripsis plays role in prostate cancer initiation.
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Affiliation(s)
- Irina V Kovtun
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA.,Department of Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen J Murphy
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah H Johnson
- Department of Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - John C Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.,Department of Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Marczok S, Bortz B, Wang C, Pospisil H. Comprehensive Analysis of Genome Rearrangements in Eight Human Malignant Tumor Tissues. PLoS One 2016; 11:e0158995. [PMID: 27391163 PMCID: PMC4938598 DOI: 10.1371/journal.pone.0158995] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 06/25/2016] [Indexed: 11/19/2022] Open
Abstract
Carcinogenesis is a complex multifactorial, multistage process, but the precise mechanisms are not well understood. In this study, we performed a genome-wide analysis of the copy number variation (CNV), breakpoint region (BPR) and fragile sites in 2,737 tumor samples from eight tumor entities and in 432 normal samples. CNV detection and BPR identification revealed that BPRs tended to accumulate in specific genomic regions in tumor samples whereas being dispersed genome-wide in the normal samples. Hotspots were observed, at which segments with similar alteration in copy number were overlapped along with BPRs adjacently clustered. Evaluation of BPR occurrence frequency showed that at least one was detected in about and more than 15% of samples for each tumor entity while BPRs were maximal in 12% of the normal samples. 127 of 2,716 tumor-relevant BPRs (termed 'common BPRs') exhibited also a noticeable occurrence frequency in the normal samples. Colocalization assessment identified 20,077 CNV-affecting genes and 169 of these being known tumor-related genes. The most noteworthy genes are KIAA0513 important for immunologic, synaptic and apoptotic signal pathways, intergenic non-coding RNA RP11-115C21.2 possibly acting as oncogene or tumor suppressor by changing the structure of chromatin, and ADAM32 likely importance in cancer cell proliferation and progression by ectodomain-shedding of diverse growth factors, and the well-known tumor suppressor gene p53. The BPR distributions indicate that CNV mutations are likely non-random in tumor genomes. The marked recurrence of BPRs at specific regions supports common progression mechanisms in tumors. The presence of hotspots together with common BPRs, despite its small group size, imply a relation between fragile sites and cancer-gene alteration. Our data further suggest that both protein-coding and non-coding genes possessing a range of biological functions might play a causative or functional role in tumor biology. This research enhances our understanding of the mechanisms for tumorigenesis and progression.
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Affiliation(s)
- Stefanie Marczok
- University of Applied Sciences Wildau, High Performance Computing in Life Sciences, Institute for Applied Biosciences, Wildau, Germany
| | - Birgit Bortz
- University of Applied Sciences Wildau, High Performance Computing in Life Sciences, Institute for Applied Biosciences, Wildau, Germany
| | - Chong Wang
- University of Applied Sciences Wildau, High Performance Computing in Life Sciences, Institute for Applied Biosciences, Wildau, Germany
| | - Heike Pospisil
- University of Applied Sciences Wildau, High Performance Computing in Life Sciences, Institute for Applied Biosciences, Wildau, Germany
- * E-mail:
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PMS2 inactivation by a complex rearrangement involving an HERV retroelement and the inverted 100-kb duplicon on 7p22.1. Eur J Hum Genet 2016; 24:1598-1604. [PMID: 27329736 DOI: 10.1038/ejhg.2016.75] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/12/2016] [Accepted: 05/26/2016] [Indexed: 11/08/2022] Open
Abstract
Biallelic PMS2 mutations are responsible for more than half of all cases of constitutional mismatch repair deficiency (CMMRD), a recessively inherited childhood cancer predisposition syndrome. The mismatch repair gene PMS2 is partly embedded within one copy of an inverted 100-kb low-copy repeat (LCR) on 7p22.1. In an individual with CMMRD syndrome, PMS2 was found to be homozygously inactivated by a complex chromosomal rearrangement, which separates the 5'-part from the 3'-part of the gene. The rearrangement involves sequences of the inverted 100-kb LCR and a human endogenous retrovirus element and may be associated with an inversion that is indistinguishable from the known inversion polymorphism affecting the ~0.7-Mb sequence intervening the LCR. Its formation is best explained by a replication-based mechanism (RBM) such as fork stalling and template switching/microhomology-mediated break-induced replication (FoSTeS/MMBIR). This finding supports the hypothesis that the inverted LCR can not only facilitate the formation of the non-allelic homologous recombination-mediated inversion polymorphism but it also promotes the occurrence of more complex rearrangements that can be associated with a large inversion, as well, but are mediated by a RBM. This further suggests that among the inversion polymorphism on 7p22.1, more complex rearrangements might be hidden. Furthermore, as the locus is embedded in a common fragile site (CFS) region, this rearrangement also supports the recently raised hypothesis that CFS sequence motifs may facilitate replication-based rearrangement mechanisms.
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35
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Villalba-Campos M, Chuaire-Noack L, Sánchez-Corredor MC, Rondón-Lagos M. High chromosomal instability in workers occupationally exposed to solvents and paint removers. Mol Cytogenet 2016; 9:46. [PMID: 27325915 PMCID: PMC4913430 DOI: 10.1186/s13039-016-0256-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/09/2016] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Painters are exposed to an extensive variety of harmful substances like aromatic hydrocarbons used as solvents and paint removers, some of which have shown clastogenic activity. These substances constitute a complex mixture of chemicals which contain well-known genotoxicants, such as Benzene, Toluene and Xylene. Thus, chronic occupational exposure to such substances may be considered to possess genotoxic risk. In Colombia the information available around the genotoxic damage (Chromosomal and DNA damage) in car paint shop workers is limited and the knowledge of this damage could contribute not only to a better understanding of the carcinogenic effect of this kind of substances but also could be used as biomarkers of occupational exposure to genotoxic agents. RESULTS In this study, the genotoxic effect of aromatic hydrocarbons was assessed in peripheral blood lymphocytes of 24 workers occupationally exposed and 24 unexposed donors, by using Cytogenetic analysis and comet assay. A high frequency of Chromosomal alterations was found in the exposed group in comparison with those observed in the unexposed group. Among the total of CAs observed in the exposed group, fragilities were most frequently found (100 %), followed by chromosomal breaks (58 %), structural (41.2 %) and numerical chromosomal alterations (21 %). Numerical chromosomal alterations, fragilities and chromosomal breaks showed significant differences between exposed and unexposed groups. Among the fragilities, fra(9)(q12) was the most frequently observed. DNA damage index was also significantly higher in the exposed group compared to the unexposed group (p < 0.000). CONCLUSIONS Our results revealed that occupational exposure to aromatic hydrocarbons is significantly associated with Chromosomal and DNA damage in car paint shops workers and are also indicative of high chromosomal instability. The high frequency of both Chromosomal Alterations and DNA Damage Index observed in this study indicates an urgent need of intervention not only to prevent the increased risk of developing cancer but also to the application of strict health control and motivation to the use of appropriate protecting devices during work.
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Affiliation(s)
- Mónica Villalba-Campos
- />Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, DC Colombia
| | - Lilian Chuaire-Noack
- />Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, DC Colombia
| | | | - Milena Rondón-Lagos
- />Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, DC Colombia
- />Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy
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36
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Hernández AF, Menéndez P. Linking Pesticide Exposure with Pediatric Leukemia: Potential Underlying Mechanisms. Int J Mol Sci 2016; 17:461. [PMID: 27043530 PMCID: PMC4848917 DOI: 10.3390/ijms17040461] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/15/2016] [Accepted: 03/23/2016] [Indexed: 01/01/2023] Open
Abstract
Leukemia is the most common cancer in children, representing 30% of all childhood cancers. The disease arises from recurrent genetic insults that block differentiation of hematopoietic stem and/or progenitor cells (HSPCs) and drives uncontrolled proliferation and survival of the differentiation-blocked clone. Pediatric leukemia is phenotypically and genetically heterogeneous with an obscure etiology. The interaction between genetic factors and environmental agents represents a potential etiological driver. Although information is limited, the principal toxic mechanisms of potential leukemogenic agents (e.g., etoposide, benzene metabolites, bioflavonoids and some pesticides) include topoisomerase II inhibition and/or excessive generation of free radicals, which may induce DNA single- and double-strand breaks (DNA-DSBs) in early HSPCs. Chromosomal rearrangements (duplications, deletions and translocations) may occur if these lesions are not properly repaired. The initiating hit usually occurs in utero and commonly leads to the expression of oncogenic fusion proteins. Subsequent cooperating hits define the disease latency and occur after birth and may be of a genetic, epigenetic or immune nature (i.e., delayed infection-mediated immune deregulation). Here, we review the available experimental and epidemiological evidence linking pesticide exposure to infant and childhood leukemia and provide a mechanistic basis to support the association, focusing on early initiating molecular events.
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Affiliation(s)
- Antonio F Hernández
- Department of Legal Medicine and Toxicology, University of Granada School of Medicine, Granada 18016, Spain.
| | - Pablo Menéndez
- Department of Biomedicine, Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Barcelona 08036, Spain.
- Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
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Mutations in TP53 increase the risk of SOX2 copy number alterations and silencing of TP53 reduces SOX2 expression in non-small cell lung cancer. BMC Cancer 2016; 16:28. [PMID: 26780934 PMCID: PMC4717590 DOI: 10.1186/s12885-016-2061-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 01/10/2016] [Indexed: 12/25/2022] Open
Abstract
Background Amplifications of the transcription factor, SRY (sex determining region Y)-box 2 (SOX2), are common in non-small cell lung cancer (NSCLC). SOX2 signaling is important in maintaining the stem cell-like phenotype of cancer cells and contributes to the pathogenesis of lung cancer. TP53 is known to inhibit gene amplifications and to repress many stem cell-associated genes following DNA damage. The aim of this study was to investigate if TP53 mutational status affected SOX2 copy number variation and gene expression in early-stage NSCLC patients; moreover, to assess if TP53 regulates SOX2 expression in human lung cancer cells. Methods 258 early-stage lung cancer patients were included in the study. Exons 4–9 in the TP53 gene were sequenced for mutations in tumor tissues. SOX2 copy number as well as TP53 and SOX2 gene expression were analyzed in tumor and in adjacent non-tumorous tissues by qPCR. TP53 and SOX2 were silenced using gene-specific siRNAs in human lung adenocarcinoma A427 cells, and the expression of TP53, SOX2 and subset of selected miRNAs was analyzed by qPCR. The odds ratios (ORs) for associations between copy number variation and lung cancer were estimated by conditional logistic regression, and the correlation between gene status and clinicopathological characteristics was assessed by Chi-square or Fisher’s exact test. Gene expression data was analyzed using nonparametric Mann–Whitney test. Results TP53 mutations were associated with an increased risk of acquiring a SOX2 copy number alteration (OR = 2.08, 95 % CI: 1.14–3.79, p = 0.017), which was more frequently occurring in tumor tissues (34 %) than in adjacent non-tumorous tissues (3 %). Moreover, SOX2 and TP53 expression levels were strongly correlated in tumor tissues. In vitro studies showed that a reduction in TP53 was associated with decreased SOX2 expression in A427 cells. Furthermore, TP53 knockdown reduced the miRNA hsa-miR-145, which has previously been shown to regulate SOX2 expression. Conclusions TP53 signaling may be important in the regulation of SOX2 copy number and expression in NSCLC tumors, and the miRNA hsa-miR-145-5p may be one potential driver. This prompts for further studies on the mechanisms behind the TP53-induced regulation of SOX2 expression and the possible importance of hsa-miR-145 in lung cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2061-3) contains supplementary material, which is available to authorized users.
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38
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Xu J, Liu P, Meng X, Bai J, Fu S, Guan R, Sun W. Association between sister chromatid exchange and double minute chromosomes in human tumor cells. Mol Cytogenet 2015; 8:91. [PMID: 26594241 PMCID: PMC4653931 DOI: 10.1186/s13039-015-0192-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/04/2015] [Indexed: 11/10/2022] Open
Abstract
Background Double minute chromosomes (DMs) are the cytogenetic hallmark of extra-chromosomal genomic amplification. They can well represent the advanced stage of malignancy. However, the mechanisms of DM generation are still not fully understood. Here, the sister chromatid exchange (SCE) was used to determine whether the occurrence of DMs was related to the high genomic instability in human carcinoma cells. We analyzed SCE frequencies in two groups of cell lines: the first group contained DM-positive cell lines such as UACC-1598, SK-PN-DW, and NCI-N87 carcinomas, while the second group comprised DM-negative cell lines including HO-8910, U251, and MGC-803. Results The data showed that SCE was significantly increased in the DM-positive cells as compared to the DM-negative cells. In addition, there was a positive correlation between the incidence of DMs and the SCE frequency in the UACC-1598, SK-PN-DW, and NCI-N87 carcinoma cells. Conclusions Because SCE can reflect general genome instability, it is suggested that the DMs are likely to be closely associated with genomic instability in carcinoma cells. Meanwhile, SCE may be involved in the malignant progression of DM-positive cancers.
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Affiliation(s)
- Jie Xu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Peng Liu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Xiangning Meng
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jing Bai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Medical Genetics, Heilongjiang Higher Education Institutions, Harbin Medical University, Harbin, China
| | - Rongwei Guan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
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Thys RG, Lehman CE, Pierce LCT, Wang YH. Environmental and chemotherapeutic agents induce breakage at genes involved in leukemia-causing gene rearrangements in human hematopoietic stem/progenitor cells. Mutat Res 2015; 779:86-95. [PMID: 26163765 PMCID: PMC4808301 DOI: 10.1016/j.mrfmmm.2015.06.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/27/2015] [Accepted: 06/23/2015] [Indexed: 01/27/2023]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) give rise to all of the cells that make up the hematopoietic system in the human body, making their stability and resilience especially important. Damage to these cells can severely impact cell development and has the potential to cause diseases, such as leukemia. Leukemia-causing chromosomal rearrangements have largely been studied in the context of radiation exposure and are formed by a multi-step process, including an initial DNA breakage and fusion of the free DNA ends. However, the mechanism for DNA breakage in patients without previous radiation exposure is unclear. Here, we investigate the role of non-cytotoxic levels of environmental factors, benzene, and diethylnitrosamine (DEN), and chemotherapeutic agents, etoposide, and doxorubicin, in generating DNA breakage at the patient breakpoint hotspots of the MLL and CBFB genes in human HSPCs. These conditions represent exposure to chemicals encountered daily or residual doses from chemotherapeutic drugs. Exposure of HSPCs to non-cytotoxic levels of environmental chemicals or chemotherapeutic agents causes DNA breakage at preferential sites in the human genome, including the leukemia-related genes MLL and CBFB. Though benzene, etoposide, and doxorubicin have previously been linked to leukemia formation, this is the first study to demonstrate a role for DEN in the generation of DNA breakage at leukemia-specific sites. These chemical-induced DNA breakpoints coincide with sites of predicted topoisomerase II cleavage. The distribution of breakpoints by exposure to non-cytotoxic levels of chemicals showed a similar pattern to fusion breakpoints in leukemia patients. Our findings demonstrate that HSPCs exposed to non-cytotoxic levels of environmental chemicals and chemotherapeutic agents are prone to topoisomerase II-mediated DNA damage at the leukemia-associated genes MLL and CBFB. These data suggest a role for long-term environmental chemical or residual chemotherapeutic drug exposure in generation of DNA breakage at sites with a propensity to form leukemia-causing gene rearrangements.
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Affiliation(s)
- Ryan G Thys
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157-1016, USA.
| | - Christine E Lehman
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157-1016, USA.
| | | | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908-0733, USA.
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Manicardi GC, Nardelli A, Mandrioli M. Fast chromosomal evolution and karyotype instability: recurrent chromosomal rearrangements in the peach potato aphidMyzus persicae(Hemiptera: Aphididae). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12621] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Gian Carlo Manicardi
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 213/d 41125 Modena Italy
| | - Andrea Nardelli
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 213/d 41125 Modena Italy
| | - Mauro Mandrioli
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 213/d 41125 Modena Italy
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Thys RG, Lehman CE, Pierce LCT, Wang YH. DNA secondary structure at chromosomal fragile sites in human disease. Curr Genomics 2015; 16:60-70. [PMID: 25937814 PMCID: PMC4412965 DOI: 10.2174/1389202916666150114223205] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/09/2015] [Accepted: 01/14/2015] [Indexed: 11/22/2022] Open
Abstract
DNA has the ability to form a variety of secondary structures that can interfere with normal cellular processes, and many of these structures have been associated with neurological diseases and cancer. Secondary structure-forming sequences are often found at chromosomal fragile sites, which are hotspots for sister chromatid exchange, chromosomal translocations, and deletions. Structures formed at fragile sites can lead to instability by disrupting normal cellular processes such as DNA replication and transcription. The instability caused by disruption of replication and transcription can lead to DNA breakage, resulting in gene rearrangements and deletions that cause disease. In this review, we discuss the role of DNA secondary structure at fragile sites in human disease.
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Affiliation(s)
- Ryan G Thys
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Christine E Lehman
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | | | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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Brečević L, Rinčić M, Krsnik Ž, Sedmak G, Hamid AB, Kosyakova N, Galić I, Liehr T, Borovečki F. Association of new deletion/duplication region at chromosome 1p21 with intellectual disability, severe speech deficit and autism spectrum disorder-like behavior: an all-in approach to solving the DPYD enigma. Transl Neurosci 2015; 6:59-86. [PMID: 28123791 PMCID: PMC4936614 DOI: 10.1515/tnsci-2015-0007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/29/2014] [Indexed: 12/14/2022] Open
Abstract
We describe an as yet unreported neocentric small supernumerary marker chromosome (sSMC) derived from chromosome 1p21.3p21.2. It was present in 80% of the lymphocytes in a male patient with intellectual disability, severe speech deficit, mild dysmorphic features, and hyperactivity with elements of autism spectrum disorder (ASD). Several important neurodevelopmental genes are affected by the 3.56 Mb copy number gain of 1p21.3p21.2, which may be considered reciprocal in gene content to the recently recognized 1p21.3 microdeletion syndrome. Both 1p21.3 deletions and the presented duplication display overlapping symptoms, fitting the same disorder category. Contribution of coding and non-coding genes to the phenotype is discussed in the light of cellular and intercellular homeostasis disequilibrium. In line with this the presented 1p21.3p21.2 copy number gain correlated to 1p21.3 microdeletion syndrome verifies the hypothesis of a cumulative effect of the number of deregulated genes - homeostasis disequilibrium leading to overlapping phenotypes between microdeletion and microduplication syndromes. Although miR-137 appears to be the major player in the 1p21.3p21.2 region, deregulation of the DPYD (dihydropyrimidine dehydrogenase) gene may potentially affect neighboring genes underlying the overlapping symptoms present in both the copy number loss and copy number gain of 1p21. Namely, the all-in approach revealed that DPYD is a complex gene whose expression is epigenetically regulated by long non-coding RNAs (lncRNAs) within the locus. Furthermore, the long interspersed nuclear element-1 (LINE-1) L1MC1 transposon inserted in DPYD intronic transcript 1 (DPYD-IT1) lncRNA with its parasites, TcMAR-Tigger5b and pair of Alu repeats appears to be the “weakest link” within the DPYD gene liable to break. Identification of the precise mechanism through which DPYD is epigenetically regulated, and underlying reasons why exactly the break (FRA1E) happens, will consequently pave the way toward preventing severe toxicity to the antineoplastic drug 5-fluorouracil (5-FU) and development of the causative therapy for the dihydropyrimidine dehydrogenase deficiency.
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Affiliation(s)
- Lukrecija Brečević
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
- E-mail: ;
| | - Martina Rinčić
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Željka Krsnik
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
| | - Goran Sedmak
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
| | - Ahmed B. Hamid
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Ivan Galić
- Center for Rehabilitation Stančić, Stančić bb, 10370 Stančić, Croatia
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Fran Borovečki
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
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Li J, Liu J, Ren Y, Liu P. Roles of the WWOX in pathogenesis and endocrine therapy of breast cancer. Exp Biol Med (Maywood) 2015; 240:324-8. [PMID: 25476151 PMCID: PMC4935229 DOI: 10.1177/1535370214561587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Breast cancer is one of the most common malignancies, often with complicated etiology and poor clinical outcome. In recent years, a critical role has emerged for the WW domain-containing oxidoreductase (WWOX) in breast cancer. WWOX is a tumor suppressor; it is deleted or attenuated in 29-63.2% of breast cancer tissues and is associated with a poor prognosis of breast cancer patients. WWOX heterozygous knockout mice show a higher incidence of mammary tumors and impaired branching morphogenesis. At the molecular level, WWOX interacts with AP2γ, ErbB4, SMAD3, and WBP2 suppressing their transcription activities in breast cancer cell lines. This review provides comprehensive insights into the current knowledge of WWOX activities in the pathogenesis and endocrine therapy of breast cancer.
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Affiliation(s)
- Juan Li
- Center for Translational Medicine, The First Affiliated Hospital, Xian Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China
| | - Jie Liu
- Center for Translational Medicine, The First Affiliated Hospital, Xian Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China
| | - Yu Ren
- Department of Surgical Oncology, The First Affiliated Hospital, Xian Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China
| | - Peijun Liu
- Center for Translational Medicine, The First Affiliated Hospital, Xian Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China
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Savelyeva L, Brueckner LM. Molecular characterization of common fragile sites as a strategy to discover cancer susceptibility genes. Cell Mol Life Sci 2014; 71:4561-75. [PMID: 25231336 PMCID: PMC11114050 DOI: 10.1007/s00018-014-1723-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 12/19/2022]
Abstract
The cytogenetic hypothesis that common fragile sites (cFSs) are hotspots of cancer breakpoints is increasingly supported by recent data from whole-genome profiles of different cancers. cFSs are components of the normal chromosome structure that are particularly prone to breakage under conditions of replication stress. In recent years, cFSs have become of increasing interest in cancer research, as they not only appear to be frequent targets of genomic alterations in progressive tumors, but also already in precancerous lesions. Despite growing evidence of their importance in disease development, most cFSs have not been investigated at the molecular level and most cFS genes have not been identified. In this review, we summarize the current data on molecularly characterized cFSs, their genetic and epigenetic characteristics, and put emphasis on less-studied cFS genes as potential contributors to cancer development.
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Affiliation(s)
- Larissa Savelyeva
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany,
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45
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Franchitto A, Pichierri P. Replication fork recovery and regulation of common fragile sites stability. Cell Mol Life Sci 2014; 71:4507-17. [PMID: 25216703 PMCID: PMC11113654 DOI: 10.1007/s00018-014-1718-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
Abstract
The acquisition of genomic instability is a triggering factor in cancer development, and common fragile sites (CFS) are the preferential target of chromosomal instability under conditions of replicative stress in the human genome. Although the mechanisms leading to CFS expression and the cellular factors required to suppress CFS instability remain largely undefined, it is clear that DNA becomes more susceptible to breakage when replication is impaired. The models proposed so far to explain how CFS instability arises imply that replication fork progression along these regions is perturbed due to intrinsic features of fragile sites and events that directly affect DNA replication. The observation that proteins implicated in the safe recovery of stalled forks or in engaging recombination at collapsed forks increase CFS expression when downregulated or mutated suggests that the stabilization and recovery of perturbed replication forks are crucial to guarantee CFS integrity.
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Affiliation(s)
- Annapaola Franchitto
- Section of Molecular Epidemiology, Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy,
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Georgakilas AG, Tsantoulis P, Kotsinas A, Michalopoulos I, Townsend P, Gorgoulis VG. Are common fragile sites merely structural domains or highly organized "functional" units susceptible to oncogenic stress? Cell Mol Life Sci 2014; 71:4519-44. [PMID: 25238782 PMCID: PMC4232749 DOI: 10.1007/s00018-014-1717-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 01/07/2023]
Abstract
Common fragile sites (CFSs) are regions of the genome with a predisposition to DNA double-strand breaks in response to intrinsic (oncogenic) or extrinsic replication stress. CFS breakage is a common feature in carcinogenesis from its earliest stages. Given that a number of oncogenes and tumor suppressors are located within CFSs, a question that emerges is whether fragility in these regions is only a structural “passive” incident or an event with a profound biological effect. Furthermore, there is sparse evidence that other elements, like non-coding RNAs, are positioned with them. By analyzing data from various libraries, like miRbase and ENCODE, we show a prevalence of various cancer-related genes, miRNAs, and regulatory binding sites, such as CTCF within CFSs. We propose that CFSs are not only susceptible structural domains, but highly organized “functional” entities that when targeted, severe repercussion for cell homeostasis occurs.
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Affiliation(s)
- Alexandros G Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780, Athens, Greece
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47
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Alternative lengthening of telomeres: recurrent cytogenetic aberrations and chromosome stability under extreme telomere dysfunction. Neoplasia 2014; 15:1301-13. [PMID: 24339742 DOI: 10.1593/neo.131574] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/17/2013] [Accepted: 10/21/2013] [Indexed: 12/23/2022] Open
Abstract
Human tumors using the alternative lengthening of telomeres (ALT) exert high rates of telomere dysfunction. Numerical chromosomal aberrations are very frequent, and structural rearrangements are widely scattered among the genome. This challenging context allows the study of telomere dysfunction-driven chromosomal instability in neoplasia (CIN) in a massive scale. We used molecular cytogenetics to achieve detailed karyotyping in 10 human ALT neoplastic cell lines. We identified 518 clonal recombinant chromosomes affected by 649 structural rearrangements. While all human chromosomes were involved in random or clonal, terminal, or pericentromeric rearrangements and were capable to undergo telomere healing at broken ends, a differential recombinatorial propensity of specific genomic regions was noted. We show that ALT cells undergo epigenetic modifications rendering polycentric chromosomes functionally monocentric, and because of increased terminal recombinogenicity, they generate clonal recombinant chromosomes with interstitial telomeric repeats. Losses of chromosomes 13, X, and 22, gains of 2, 3, 5, and 20, and translocation/deletion events involving several common chromosomal fragile sites (CFSs) were recurrent. Long-term reconstitution of telomerase activity in ALT cells reduced significantly the rates of random ongoing telomeric and pericentromeric CIN. However, the contribution of CFS in overall CIN remained unaffected, suggesting that in ALT cells whole-genome replication stress is not suppressed by telomerase activation. Our results provide novel insights into ALT-driven CIN, unveiling in parallel specific genomic sites that may harbor genes critical for ALT cancerous cell growth.
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48
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Heterochromatin controls γH2A localization in Neurospora crassa. EUKARYOTIC CELL 2014; 13:990-1000. [PMID: 24879124 DOI: 10.1128/ec.00117-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In response to genotoxic stress, ATR and ATM kinases phosphorylate H2A in fungi and H2AX in animals on a C-terminal serine. The resulting modified histone, called γH2A, recruits chromatin-binding proteins that stabilize stalled replication forks or promote DNA double-strand-break repair. To identify genomic loci that might be prone to replication fork stalling or DNA breakage in Neurospora crassa, we performed chromatin immunoprecipitation (ChIP) of γH2A followed by next-generation sequencing (ChIP-seq). γH2A-containing nucleosomes are enriched in Neurospora heterochromatin domains. These domains are comprised of A·T-rich repetitive DNA sequences associated with histone H3 methylated at lysine-9 (H3K9me), the H3K9me-binding protein heterochromatin protein 1 (HP1), and DNA cytosine methylation. H3K9 methylation, catalyzed by DIM-5, is required for normal γH2A localization. In contrast, γH2A is not required for H3K9 methylation or DNA methylation. Normal γH2A localization also depends on HP1 and a histone deacetylase, HDA-1, but is independent of the DNA methyltransferase DIM-2. γH2A is globally induced in dim-5 mutants under normal growth conditions, suggesting that the DNA damage response is activated in these mutants in the absence of exogenous DNA damage. Together, these data suggest that heterochromatin formation is essential for normal DNA replication or repair.
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Li J, Liu J, Ren Y, Yang J, Liu P. Common Chromosomal Fragile Site Gene WWOX in Metabolic Disorders and Tumors. Int J Biol Sci 2014; 10:142-8. [PMID: 24520212 PMCID: PMC3920169 DOI: 10.7150/ijbs.7727] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 11/14/2013] [Indexed: 11/14/2022] Open
Abstract
WWOX, a gene that spans the second most common chromosomal fragile site (FRA16D), often exhibits homozygous deletions and translocation breakpoints under multiple cellular stresses induced by extrinsic or intrinsic factors, such as hypoxia, UV, and DNA damage regents. Loss of WWOX is closely related to genomic instability, tumorigenesis, cancer progression and therapy resistance. WWOX heterozygous knockout mice show an increased incidence of spontaneous or induced tumors. WWOX can interact via the WW domain with proteins that possess proline PPxY motifs and is involved in a variety of cellular processes. Accumulating evidence has shown that WWOX that contains a short-chain dehydrogenase/reductase (SDR) domain is involved in steroid metabolism and bone development. Reduced or lost expression of WWOX will lead to development of metabolic disease. In this review, we focus on the roles of WWOX in metabolic disorders and tumors.
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Affiliation(s)
- Juan Li
- 1. Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University College of Medicine
| | - Jie Liu
- 1. Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University College of Medicine
| | - Yu Ren
- 2. Department of Surgical Oncology, The First Affiliated Hospital of Xian Jiaotong University College of Medicine
| | - Jin Yang
- 3. Department of Oncology, The First Affiliated Hospital of Xian Jiaotong University College of Medicine
| | - Peijun Liu
- 1. Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University College of Medicine
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50
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Monyarch G, de Castro Reis F, Zock JP, Giraldo J, Pozo-Rodríguez F, Espinosa A, Rodríguez-Trigo G, Verea H, Castaño-Vinyals G, Gómez FP, Antó JM, Coll MD, Barberà JA, Fuster C. Chromosomal bands affected by acute oil exposure and DNA repair errors. PLoS One 2013; 8:e81276. [PMID: 24303039 PMCID: PMC3841120 DOI: 10.1371/journal.pone.0081276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/21/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In a previous study, we showed that individuals who had participated in oil clean-up tasks after the wreckage of the Prestige presented an increase of structural chromosomal alterations two years after the acute exposure had occurred. Other studies have also reported the presence of DNA damage during acute oil exposure, but little is known about the long term persistence of chromosomal alterations, which can be considered as a marker of cancer risk. OBJECTIVES We analyzed whether the breakpoints involved in chromosomal damage can help to assess the risk of cancer as well as to investigate their possible association with DNA repair efficiency. METHODS Cytogenetic analyses were carried out on the same individuals of our previous study and DNA repair errors were assessed in cultures with aphidicolin. RESULTS Three chromosomal bands, 2q21, 3q27 and 5q31, were most affected by acute oil exposure. The dysfunction in DNA repair mechanisms, expressed as chromosomal damage, was significantly higher in exposed-oil participants than in those not exposed (p= 0.016). CONCLUSION The present study shows that breaks in 2q21, 3q27 and 5q31 chromosomal bands, which are commonly involved in hematological cancer, could be considered useful genotoxic oil biomarkers. Moreover, breakages in these bands could induce chromosomal instability, which can explain the increased risk of cancer (leukemia and lymphomas) reported in chronically benzene-exposed individuals. In addition, it has been determined that the individuals who participated in clean-up of the oil spill presented an alteration of their DNA repair mechanisms two years after exposure.
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Affiliation(s)
- Gemma Monyarch
- Unitat de Biologia Cel·lular i Genètica Mèdica, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Fernanda de Castro Reis
- Unitat de Biologia Cel·lular i Genètica Mèdica, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Jan-Paul Zock
- Centre de Recerca en Epidemiologia Ambiental (CREAL), Barcelona, Spain
- Institut de Recerca Hospital del Mar (IMIM), Barcelona, Spain
- CIBER Epidemiologia i Salut Pública (CIBERESP), Barcelona, Spain
| | - Jesús Giraldo
- Unitat de Bioestadística and Institut de Neurociències, Facultat de Medicina, UAB, Bellaterra, Spain
| | - Francisco Pozo-Rodríguez
- Departamento de Medicina Respiratoria, Unidad Epidemiologia Clínica, Hospital 12 de Octubre, Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Mallorca, Spain
| | - Ana Espinosa
- Centre de Recerca en Epidemiologia Ambiental (CREAL), Barcelona, Spain
- Institut de Recerca Hospital del Mar (IMIM), Barcelona, Spain
- CIBER Epidemiologia i Salut Pública (CIBERESP), Barcelona, Spain
| | - Gema Rodríguez-Trigo
- CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Mallorca, Spain
- Departamento de Medicina Respiratoria, Hospital Clínico San Carlos, Madrid, Spain
| | - Hector Verea
- Departamento de Medicina Respiratoria, Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Gemma Castaño-Vinyals
- Centre de Recerca en Epidemiologia Ambiental (CREAL), Barcelona, Spain
- Institut de Recerca Hospital del Mar (IMIM), Barcelona, Spain
- CIBER Epidemiologia i Salut Pública (CIBERESP), Barcelona, Spain
| | - Federico P. Gómez
- CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Mallorca, Spain
- Departament de Medicina Respiratòria, Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Josep M. Antó
- Centre de Recerca en Epidemiologia Ambiental (CREAL), Barcelona, Spain
- Institut de Recerca Hospital del Mar (IMIM), Barcelona, Spain
- CIBER Epidemiologia i Salut Pública (CIBERESP), Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Maria Dolors Coll
- Unitat de Biologia Cel·lular, Facultat de Ciències, UAB, Bellaterra, Spain
| | - Joan Albert Barberà
- CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Mallorca, Spain
- Departament de Medicina Respiratòria, Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Carme Fuster
- Unitat de Biologia Cel·lular i Genètica Mèdica, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
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