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Nath N, Hagenau L, Weiss S, Tzvetkova A, Jensen LR, Kaderali L, Port M, Scherthan H, Kuss AW. Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts. Int J Mol Sci 2020; 21:E5778. [PMID: 32806598 PMCID: PMC7460866 DOI: 10.3390/ijms21165778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023] Open
Abstract
While ionizing radiation (IR) is a powerful tool in medical diagnostics, nuclear medicine, and radiology, it also is a serious threat to the integrity of genetic material. Mutagenic effects of IR to the human genome have long been the subject of research, yet still comparatively little is known about the genome-wide effects of IR exposure on the DNA-sequence level. In this study, we employed high throughput sequencing technologies to investigate IR-induced DNA alterations in human gingiva fibroblasts (HGF) that were acutely exposed to 0.5, 2, and 10 Gy of 240 kV X-radiation followed by repair times of 16 h or 7 days before whole-genome sequencing (WGS). Our analysis of the obtained WGS datasets revealed patterns of IR-induced variant (SNV and InDel) accumulation across the genome, within chromosomes as well as around the borders of topologically associating domains (TADs). Chromosome 19 consistently accumulated the highest SNVs and InDels events. Translocations showed variable patterns but with recurrent chromosomes of origin (e.g., Chr7 and Chr16). IR-induced InDels showed a relative increase in number relative to SNVs and a characteristic signature with respect to the frequency of triplet deletions in areas without repetitive or microhomology features. Overall experimental conditions and datasets the majority of SNVs per genome had no or little predicted functional impact with a maximum of 62, showing damaging potential. A dose-dependent effect of IR was surprisingly not apparent. We also observed a significant reduction in transition/transversion (Ti/Tv) ratios for IR-dependent SNVs, which could point to a contribution of the mismatch repair (MMR) system that strongly favors the repair of transitions over transversions, to the IR-induced DNA-damage response in human cells. Taken together, our results show the presence of distinguishable characteristic patterns of IR-induced DNA-alterations on a genome-wide level and implicate DNA-repair mechanisms in the formation of these signatures.
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Affiliation(s)
- Neetika Nath
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Lisa Hagenau
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
| | - Stefan Weiss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
| | - Ana Tzvetkova
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Lars R. Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Matthias Port
- Bundeswehr Institute for Radiobiology Affiliated to the University of Ulm, 80937 München, Germany; (M.P.); (H.S.)
| | - Harry Scherthan
- Bundeswehr Institute for Radiobiology Affiliated to the University of Ulm, 80937 München, Germany; (M.P.); (H.S.)
| | - Andreas W. Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
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2
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Li F, Xu Y, Liu B, Singh PK, Zhao W, Jin J, Han G, Scott AW, Dong X, Huo L, Ma L, Pizzi MP, Wang Y, Li Y, Harada K, Xie M, Skinner HD, Ding S, Wang L, Krishnan S, Johnson RL, Song S, Ajani JA. YAP1-Mediated CDK6 Activation Confers Radiation Resistance in Esophageal Cancer - Rationale for the Combination of YAP1 and CDK4/6 Inhibitors in Esophageal Cancer. Clin Cancer Res 2018; 25:2264-2277. [PMID: 30563933 DOI: 10.1158/1078-0432.ccr-18-1029] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 08/16/2018] [Accepted: 12/14/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Esophageal cancer is a lethal disease that is often resistant to therapy. Alterations of YAP1 and CDK6 are frequent in esophageal cancer. Deregulation of both molecules may be responsible for therapy resistance. EXPERIMENTAL DESIGN Expressions of YAP1 and CDK6 were examined in esophageal cancer cells and tissues using immunoblotting and immunohistochemistry. YAP1 expression was induced in esophageal cancer cells to examine YAP1-mediated CDK6 activation and its association with radiation resistance. Pharmacologic and genetic inhibitions of YAP1 and CDK6 were performed to dissect the mechanisms and assess the antitumor effects in vitro and in vivo. RESULTS YAP1 expression was positively associated with CDK6 expression in resistant esophageal cancer tissues and cell lines. YAP1 overexpression upregulated CDK6 expression and transcription, and promoted radiation resistance, whereas treatment with the YAP1 inhibitor, CA3, strongly suppressed YAP1 and CDK6 overexpression, reduced Rb phosphorylation, as well as sensitized radiation-resistant/YAP1high esophageal cancer cells to irradiation. CDK4/6 inhibitor, LEE011, and knock down of CDK6 dramatically inhibited expression of YAP1 and sensitized resistant esophageal cancer cells to irradiation indicating a positive feed-forward regulation of YAP1 by CDK6. In addition, suppression of both the YAP1 and CDK6 pathways by the combination of CA3 and LEE011 significantly reduced esophageal cancer cell growth and cancer stem cell population (ALDH1 + and CD133 + ), sensitized cells to irradiation, and showed a strong antitumor effect in vivo against radiation-resistant esophageal cancer cells. CONCLUSIONS Our results document that a positive crosstalk between the YAP1 and CDK6 pathways plays an important role in conferring radiation resistance to esophageal cancer cells. Targeting both YAP1 and CDK6 pathways could be a novel therapeutic strategy to overcome resistance in esophageal cancer.
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Affiliation(s)
- Fan Li
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas.,Department of General Surgery, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Yan Xu
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Bovey Liu
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Pankaj Kumar Singh
- Department of Radiation Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Wei Zhao
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Jiankang Jin
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Guangchun Han
- Department of Genomic Medicine, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Ailing W Scott
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Xiaochuan Dong
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Longfei Huo
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Lang Ma
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Melissa Pool Pizzi
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Ying Wang
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Yuan Li
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Kazuto Harada
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Min Xie
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Heath D Skinner
- Department of Radiation Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Sheng Ding
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Linghua Wang
- Department of Genomic Medicine, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Sunil Krishnan
- Department of Radiation Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Randy L Johnson
- Department of Cancer Biology, U.T.MD. Anderson Cancer Center, Houston, Texas
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas.
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, U.T.MD. Anderson Cancer Center, Houston, Texas.
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3
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Ravi M, Lal AS, Begum SK. Prophasing interphase chromatin for assessing genetic damages-The evolution, applications and the future prospects. Mutat Res 2018; 810:19-32. [PMID: 29906650 DOI: 10.1016/j.mrfmmm.2018.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/30/2018] [Accepted: 06/07/2018] [Indexed: 11/18/2022]
Abstract
Premature chromosome condensation (PCC) involves induction of near-chromosome-like morphology to interphase chromatin. Experimental induction of PCC was achieved by somatic cell hybridization (SCH), an approach which evolved into a chemical-induction process. PCC presents most probably the only way in which cytogenetic assessment of damages can be analyzed in special situations such as availability of limited numbers of sample cells and for cells which have lost their ability to divide. Initial experiments on PCC were reported in late 1960s and the technique has evolved into one with wide range of applications owing to its increased efficiency in detecting primary DNA damages. Biodosimetry remains as the primary area which utilizes PCC technique to the maximum efficiency with several multiple-groups participating in collaborative exercises for biodosimetric applications. However, in spite of the advantages that the technique offers, it is yet to reach its full potential. This is due to the inherent limitations of the manner in which PCC is induced currently; by the somatic cell hybridization and chemical-induction processes. An approach which combines these two would sure help in taking PCC to its highest potential as the preferred technique for assessment of primary DNA damages. We present the chronological events of evolution of the PCC technique along with its applications. Also, the limitations of the technique along with the suggestions for further refinement of the PCC technique are discussed.
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Affiliation(s)
- Maddaly Ravi
- Department of Human Genetics, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Medical College and Research Institute, Porur, Chennai 600116, India.
| | - Aswathy S Lal
- Department of Human Genetics, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Medical College and Research Institute, Porur, Chennai 600116, India
| | - S Kauser Begum
- Department of Human Genetics, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Medical College and Research Institute, Porur, Chennai 600116, India
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4
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Venkatesan S, Natarajan AT, Hande MP. Chromosomal instability--mechanisms and consequences. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 793:176-84. [PMID: 26520388 DOI: 10.1016/j.mrgentox.2015.08.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 01/08/2023]
Abstract
Chromosomal instability is defined as a state of numerical and/or structural chromosomal anomalies in cells. Numerous studies have documented the incidence of chromosomal instability, which acutely or chronically may lead to accelerated ageing (tissue-wide or even organismal), cancer or other genetic disorders. Potential mechanisms leading to the generation of chromosome-genome instability include erroneous/inefficient DNA repair, chromosome segregation defects, spindle assembly defects, DNA replication stress, telomere shortening/dysfunction - to name a few. Understanding the cellular and molecular mechanisms for chromosomal instability in various human cells and tissues will be useful in elucidating the cause for many age associated diseases including cancer. This approach holds a great promise for the cytogenetic assays not only for prognosis but also for diagnostic purposes in clinical settings. In this review, a multi-dimensional approach has been attempted to portray the complexity behind the incidence of chromosome-genome instability including evolutionary implications at the species level for some of the mechanisms of chromosomal instability.
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Affiliation(s)
- Shriram Venkatesan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597
| | - Adayapalam T Natarajan
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy
| | - M Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597; Tembusu College, National University of Singapore, Singapore, 138597.
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5
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Dutta B, Ren Y, Hao P, Sim KH, Cheow E, Adav S, Tam JP, Sze SK. Profiling of the Chromatin-associated Proteome Identifies HP1BP3 as a Novel Regulator of Cell Cycle Progression. Mol Cell Proteomics 2014; 13:2183-97. [PMID: 24830416 DOI: 10.1074/mcp.m113.034975] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Indexed: 12/31/2022] Open
Abstract
The chromatin-associated proteome (chromatome) regulates cellular gene expression by restricting access of transcriptional machinery to template DNA, and dynamic re-modeling of chromatin structure is required to regulate critical cell functions including growth and replication, DNA repair and recombination, and oncogenic transformation in progression to cancer. Central to the control of these processes is efficient regulation of the host cell cycle, which is maintained by rapid changes in chromatin conformation during normal cycle progression. A global overview of chromatin protein organization is therefore essential to fully understand cell cycle regulation, but the influence of the chromatome and chromatin binding topology on host cell cycle progression remains poorly defined. Here we used partial MNase digestion together with iTRAQ-based high-throughput quantitative proteomics to quantify chromatin-associated proteins during interphase progression. We identified a total of 481 proteins with high confidence that were involved in chromatin-dependent events including transcriptional regulation, chromatin re-organization, and DNA replication and repair, whereas the quantitative data revealed the temporal interactions of these proteins with chromatin during interphase progression. When combined with biochemical and functional assays, these data revealed a strikingly dynamic association of protein HP1BP3 with the chromatin complex during different stages of interphase, and uncovered a novel regulatory role for this molecule in transcriptional regulation. We report that HP1BP3 protein maintains heterochromatin integrity during G1-S progression and regulates the duration of G1 phase to critically influence cell proliferative capacity.
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Affiliation(s)
- Bamaprasad Dutta
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Yan Ren
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Piliang Hao
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Kae Hwan Sim
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Esther Cheow
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Sunil Adav
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - James P Tam
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Siu Kwan Sze
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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6
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Song W, Liu Y, Liu Y, Zhang C, Yuan B, Zhang L, Sun S. Increased p16 DNA methylation in mouse thymic lymphoma induced by irradiation. PLoS One 2014; 9:e93850. [PMID: 24747802 PMCID: PMC3991568 DOI: 10.1371/journal.pone.0093850] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 03/07/2014] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is an important part of epigenetics. In this study, we examined the methylation state of two CpG islands in the promoter of the p16 gene in radiation-induced thymic lymphoma samples. The mRNA and protein levels of P16 were significantly reduced in radiation-induced thymic lymphoma tissue samples. Twenty-three CpG sites of the CpG islands in the p16 promoter region were detected, and the methylation percentages of −71, −63, −239, −29, −38, −40, −23, 46 CpG sites were significantly higher in radiation-induced thymic lymphoma tissue samples than those in matched non-irradiated thymus tissue samples. This study provides new evidence for the methylation state of p16 in the radiation-induced thymic lymphoma samples, which suggests that the methylation of these CpG sites in the p16 promoter may reduce its expression in the thymic lymphoma after irradiation.
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Affiliation(s)
| | - Yongzhe Liu
- Department of Toxicology, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Ying Liu
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Cong Zhang
- Ministry of Health, Key Laboratory of Radiobiology, Jilin University, Changchun, China, National Laboratory of Medical Molecular Biology, Tsinghua University, Beijing, PR China
| | - Bao Yuan
- College of Animal Sciences, Jilin University, Changchun, China
| | - Lianbo Zhang
- Department of Plastic and Reconstructive Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
- * E-mail:
| | - Shilong Sun
- Ministry of Health, Key Laboratory of Radiobiology, Jilin University, Changchun, China, National Laboratory of Medical Molecular Biology, Tsinghua University, Beijing, PR China
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7
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Bond CE, Nancarrow DJ, Wockner LF, Wallace L, Montgomery GW, Leggett BA, Whitehall VLJ. Microsatellite stable colorectal cancers stratified by the BRAF V600E mutation show distinct patterns of chromosomal instability. PLoS One 2014; 9:e91739. [PMID: 24651849 PMCID: PMC3961279 DOI: 10.1371/journal.pone.0091739] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/13/2014] [Indexed: 02/07/2023] Open
Abstract
The BRAF (V600E) mutation in colorectal cancers that are microsatellite stable (MSS) confers a poor patient prognosis, whereas BRAF mutant microsatellite-unstable (MSI) colorectal cancers have an excellent prognosis. BRAF wild type cancers are typically MSS and display chromosomal instability (CIN). CIN has not been extensively studied on a genome-wide basis in relation to BRAF mutational status in colorectal cancer. BRAF mutant/MSS (BRAFmut/MSS) cancers (n = 33) and BRAF mutant/MSI (BRAFmut/MSI) cancers (n = 30) were compared for presence of copy number aberrations (CNAs) indicative of CIN, with BRAF wild type/MSS (BRAFwt/MSS) cancers (n = 18) using Illumina CytoSNP-12 arrays. BRAFmut/MSS and BRAFwt/MSS cancers showed comparable numbers of CNAs/cancer at 32.8 and 29.8 respectively. However, there were differences in patterns of CNA length between MSS cohorts, with BRAFmut/MSS cancers having significantly greater proportions of focal CNAs compared to BRAFwt/MSS cancers (p<0.0001); whereas whole chromosomal arm CNAs were more common in BRAFwt/MSS cancers (p<0.0001). This related to a reduced average CNA length in BRAFmut/MSS compared to BRAFwt/MSS cancers (20.7 Mb vs 33.4 Mb;p<0.0001); and a smaller average percent of CIN affected genomes in BRAFmut/MSS compared to BRAFwt/MSS cancers (23.9% vs 34.9% respectively). BRAFmut/MSI cancers were confirmed to have low CNA rates (5.4/cancer) and minimal CIN-affected genomes (average of 4.5%) compared to MSS cohorts (p<0.0001). BRAFmut/MSS cancers had more frequent deletion CNAs compared to BRAFwt/MSS cancers on 6p and 17q at loci not typically correlated with colorectal cancer, and greater amplification CNAs on 8q and 18q compared to BRAFwt/MSS cancers. These results indicate that comparable rates of CIN occur between MSS subgroups, however significant differences in their patterns of instability exist, with BRAFmut/MSS cancers showing a ‘focal pattern’ and BRAFwt/MSS cancers having a ‘whole arm pattern’ of CIN. This and the genomic loci more frequently affected in BRAFmut/MSS cancers provides further evidence of the biological distinctions of this important cancer subgroup.
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Affiliation(s)
- Catherine E. Bond
- Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
| | - Derek J. Nancarrow
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Leesa F. Wockner
- Cancer and Population Studies Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Leanne Wallace
- Molecular Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Grant W. Montgomery
- Molecular Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Barbara A. Leggett
- Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Vicki L. J. Whitehall
- Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Pathology Queensland, Brisbane, Queensland, Australia
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Lavelle C, Foray N. Chromatin structure and radiation-induced DNA damage: from structural biology to radiobiology. Int J Biochem Cell Biol 2014; 49:84-97. [PMID: 24486235 DOI: 10.1016/j.biocel.2014.01.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 01/13/2014] [Accepted: 01/18/2014] [Indexed: 10/25/2022]
Abstract
Genomic DNA in eukaryotic cells is basically divided into chromosomes, each consisting of a single huge nucleosomal fiber. It is now clear that chromatin structure and dynamics play a critical role in all processes involved in DNA metabolism, e.g. replication, transcription, repair and recombination. Radiation is a useful tool to study the biological effects of chromatin alterations. Conversely, radiotherapy and radiodiagnosis raise questions about the influence of chromatin integrity on clinical features and secondary effects. This review focuses on the link between DNA damage and chromatin structure at different scales, showing how a comprehensive multiscale vision is required to understand better the effect of radiations on DNA. Clinical aspects related to high- and low-dose of radiation and chromosomal instability will be discussed. At the same time, we will show that the analysis of the radiation-induced DNA damage distribution provides good insight on chromatin structure. Hence, we argue that chromatin "structuralists" and radiobiological "clinicians" would each benefit from more collaboration with the other. We hope that this focused review will help in this regard.
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Affiliation(s)
- Christophe Lavelle
- Genome Structure and Instability, National Museum of Natural History, Paris, France; CNRS UMR7196, Paris, France; INSERM U1154, Paris, France; Nuclear Architecture and Dynamics, CNRS GDR 3536, Paris, France.
| | - Nicolas Foray
- Nuclear Architecture and Dynamics, CNRS GDR 3536, Paris, France; INSERM, UMR1052, Radiobiology Group, Cancer Research Centre of Lyon, Lyon, France
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9
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Modulation of DNA base excision repair during neuronal differentiation. Neurobiol Aging 2013; 34:1717-27. [PMID: 23375654 DOI: 10.1016/j.neurobiolaging.2012.12.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 12/21/2012] [Accepted: 12/22/2012] [Indexed: 11/22/2022]
Abstract
Neurons are terminally differentiated cells with a high rate of metabolism and multiple biological properties distinct from their undifferentiated precursors. Previous studies showed that nucleotide excision DNA repair is downregulated in postmitotic muscle cells and neurons. Here, we characterize DNA damage susceptibility and base excision DNA repair (BER) capacity in undifferentiated and differentiated human neural cells. The results show that undifferentiated human SH-SY5Y neuroblastoma cells are less sensitive to oxidative damage than their differentiated counterparts, in part because they have robust BER capacity, which is heavily attenuated in postmitotic neurons. The reduction in BER activity in differentiated cells correlates with diminished protein levels of key long patch BER components, flap endonuclease-1, proliferating cell nuclear antigen, and ligase I. Thus, because of their higher BER capacity, proliferative neural progenitor cells are more efficient at repairing DNA damage compared with their neuronally differentiated progeny.
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10
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Fluorescence in situ hybridization on electrophoresed cells to detect sequence specific DNA damage. Methods Mol Biol 2013; 1054:219-35. [PMID: 23913296 DOI: 10.1007/978-1-62703-565-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Fluorescence in situ hybridization (FISH) to label fragments of DNA with probes which can specifically locate a genomic region of interest, combined with the single cell electrophoresis (Comet) assay, also termed Comet-FISH, allows the quantification of DNA damage and repair at a specific genomic locus. While the Comet assay alone quantifies only the overall DNA damage of an individual cell, subsequent FISH on the electrophoresed single cell genome enables the coincidental localization of fluorescently labelled sequences (i.e., probes) to the respective damaged or undamaged genes or specific genomic regions of interest. In that way sequence specific DNA damage, global genomic and transcription coupled repair or the three dimensional ultrastructure of cells from any tissue can be comparatively investigated. This protocol provides a detailed description of the principles and basic methodology of a standard Comet-FISH experiment to study interphase cells of any tissue. Also important variations of the protocol (e.g., neutral conditions to detect double strand breaks) as well as the production of fluorochrome-labelled DNA probes via random priming are described.
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11
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Eidelman YA, Slanina SV, Salnikov IV, Andreev SG. Mechanistic modelling allows to assess pathways of DNA lesion interactions underlying chromosome aberration formation. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412120022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Kwasniewska J, Grabowska M, Kwasniewski M, Kolano B. Comet-FISH with rDNA probes for the analysis of mutagen-induced DNA damage in plant cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:369-375. [PMID: 22556029 DOI: 10.1002/em.21699] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 04/03/2012] [Accepted: 04/05/2012] [Indexed: 05/31/2023]
Abstract
We used comet-fluorescence in situ hybridization (FISH) in the model plant species Crepis capillaris following exposure of seedlings to maleic hydrazide (MH). FISH with 5S and 25S rDNA probes was applied to comets obtained under alkaline conditions to establish whether these DNA regions were preferentially involved in comet tail formation. MH treatment induced significant fragmentation of nuclear DNA and of rDNA loci. A 24-h post-treatment recovery period allowed a partial reversibility of MH-induced damage on nuclear and rDNA regions. Analyses of FISH signals demonstrated that rDNA sequences were always involved in tail formation and that 5S rDNA was more frequently present in the tail than 25S rDNA, regardless of treatment. The involvement of 25S rDNA in nucleolus formation and differences in chromatin structure between the two loci may explain the different susceptibility of the 25S and 5S rDNA regions to migrate into the tail. This work is the first report on the application of FISH to comet preparations from plants to analyze the distribution and repair of DNA damage within specific genomic regions after mutagenic treatment. Moreover, our work suggests that comet-FISH in plants may be a useful tool for environmental monitoring assessment.
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Affiliation(s)
- Jolanta Kwasniewska
- Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
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Seidel C, Lautenschläger C, Dunst J, Müller AC. Factors influencing heterogeneity of radiation-induced DNA-damage measured by the alkaline comet assay. Radiat Oncol 2012; 7:61. [PMID: 22520045 PMCID: PMC3424130 DOI: 10.1186/1748-717x-7-61] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 04/11/2012] [Indexed: 11/30/2022] Open
Abstract
Background To investigate whether different conditions of DNA structure and radiation treatment could modify heterogeneity of response. Additionally to study variance as a potential parameter of heterogeneity for radiosensitivity testing. Methods Two-hundred leukocytes per sample of healthy donors were split into four groups. I: Intact chromatin structure; II: Nucleoids of histone-depleted DNA; III: Nucleoids of histone-depleted DNA with 90 mM DMSO as antioxidant. Response to single (I-III) and twice (IV) irradiation with 4 Gy and repair kinetics were evaluated using %Tail-DNA. Heterogeneity of DNA damage was determined by calculation of variance of DNA-damage (V) and mean variance (Mvar), mutual comparisons were done by one-way analysis of variance (ANOVA). Results Heterogeneity of initial DNA-damage (I, 0 min repair) increased without histones (II). Absence of histones was balanced by addition of antioxidants (III). Repair reduced heterogeneity of all samples (with and without irradiation). However double irradiation plus repair led to a higher level of heterogeneity distinguishable from single irradiation and repair in intact cells. Increase of mean DNA damage was associated with a similarly elevated variance of DNA damage (r = +0.88). Conclusions Heterogeneity of DNA-damage can be modified by histone level, antioxidant concentration, repair and radiation dose and was positively correlated with DNA damage. Experimental conditions might be optimized by reducing scatter of comet assay data by repair and antioxidants, potentially allowing better discrimination of small differences. Amount of heterogeneity measured by variance might be an additional useful parameter to characterize radiosensitivity.
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Affiliation(s)
- Clemens Seidel
- Department of General Psychiatry I, PZN-Wiesloch, Teaching Hospital of Ruprecht-Karls-University Heidelberg, Heidelberger Str. 1a, Wiesloch 69168, Germany
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Hertel-Aas T, Oughton DH, Jaworska A, Brunborg G. Induction and repair of DNA strand breaks and oxidised bases in somatic and spermatogenic cells from the earthworm Eisenia fetida after exposure to ionising radiation. Mutagenesis 2011; 26:783-93. [DOI: 10.1093/mutage/ger048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Terzoudi GI, Hatzi VI, Donta-Bakoyianni C, Pantelias GE. Chromatin dynamics during cell cycle mediate conversion of DNA damage into chromatid breaks and affect formation of chromosomal aberrations: biological and clinical significance. Mutat Res 2011; 711:174-186. [PMID: 21185845 DOI: 10.1016/j.mrfmmm.2010.12.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 11/30/2010] [Accepted: 12/17/2010] [Indexed: 05/30/2023]
Abstract
The formation of diverse chromosomal aberrations following irradiation and the variability in radiosensitivity at different cell-cycle stages remain a long standing controversy, probably because most of the studies have focused on elucidating the enzymatic mechanisms involved using simple DNA substrates. Yet, recognition, processing and repair of DNA damage occur within the nucleoprotein complex of chromatin which is dynamic in nature, capable of rapid unfolding, disassembling, assembling and refolding. The present work reviews experimental work designed to investigate the impact of chromatin dynamics and chromosome conformation changes during cell-cycle in the formation of chromosomal aberrations. Using conventional cytogenetics and premature chromosome condensation to visualize interphase chromatin, the data presented support the hypothesis that chromatin dynamic changes during cell-cycle are important determinants in the conversion of sub-microscopic DNA lesions into chromatid breaks. Consequently, the type and yield of radiation-induced chromosomal aberrations at a given cell-cycle-stage depends on the combined effect of DNA repair processes and chromatin dynamics, which is cell-cycle-regulated and subject to up- or down-regulation following radiation exposure or genetic alterations. This new hypothesis is used to explain the variability in radiosensitivity observed at various cell-cycle-stages, among mutant cells and cells of different origin, or among different individuals, and to revisit unresolved issues and unanswered questions. In addition, it is used to better understand hypersensitivity of AT cells and to provide an improved predictive G2-assay for evaluating radiosensitivity at individual level. Finally, experimental data at single cell level obtained using hybrid cells suggest that the proposed hypothesis applies only to the irradiated component of the hybrid.
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Affiliation(s)
- Georgia I Terzoudi
- Institute of Radioisotopes and Radiodiagnostic Products, National Centre for Scientific Research "Demokritos", 15310 Ag. Paraskevi Attikis, Athens, Greece
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Johnson SM, Torrice CD, Bell JF, Monahan KB, Jiang Q, Wang Y, Ramsey MR, Jin J, Wong KK, Su L, Zhou D, Sharpless NE. Mitigation of hematologic radiation toxicity in mice through pharmacological quiescence induced by CDK4/6 inhibition. J Clin Invest 2010; 120:2528-36. [PMID: 20577054 DOI: 10.1172/jci41402] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 04/28/2010] [Indexed: 01/28/2023] Open
Abstract
Total body irradiation (TBI) can induce lethal myelosuppression, due to the sensitivity of proliferating hematopoietic stem/progenitor cells (HSPCs) to ionizing radiation (IR). No effective therapy exists to mitigate the hematologic toxicities of TBI. Here, using selective and structurally distinct small molecule inhibitors of cyclin-dependent kinase 4 (CDK4) and CDK6, we have demonstrated that selective cellular quiescence increases radioresistance of human cell lines in vitro and mice in vivo. Cell lines dependent on CDK4/6 were resistant to IR and other DNA-damaging agents when treated with CDK4/6 inhibitors. In contrast, CDK4/6 inhibitors did not protect cell lines that proliferated independently of CDK4/6 activity. Treatment of wild-type mice with CDK4/6 inhibitors induced reversible pharmacological quiescence (PQ) of early HSPCs but not most other cycling cells in the bone marrow or other tissues. Selective PQ of HSPCs decreased the hematopoietic toxicity of TBI, even when the CDK4/6 inhibitor was administered several hours after TBI. Moreover, PQ at the time of administration of therapeutic IR to mice harboring autochthonous cancers reduced treatment toxicity without compromising the therapeutic tumor response. These results demonstrate an effective method to mitigate the hematopoietic toxicity of IR in mammals, which may be potentially useful after radiological disaster or as an adjuvant to anticancer therapy.
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Affiliation(s)
- Søren M Johnson
- Department of Genetics, The Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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