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Cho E, Swartz CD, Williams A, V Rivas M, Recio L, Witt KL, Schmidt EK, Yaplee J, Smith TH, Van P, Lo FY, Valentine CC, Salk JJ, Marchetti F, Smith-Roe SL, Yauk CL. Error-corrected duplex sequencing enables direct detection and quantification of mutations in human TK6 cells with strong inter-laboratory consistency. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 889:503649. [PMID: 37491114 PMCID: PMC10395007 DOI: 10.1016/j.mrgentox.2023.503649] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 07/27/2023]
Abstract
Error-corrected duplex sequencing (DS) enables direct quantification of low-frequency mutations and offers tremendous potential for chemical mutagenicity assessment. We investigated the utility of DS to quantify induced mutation frequency (MF) and spectrum in human lymphoblastoid TK6 cells exposed to a prototypical DNA alkylating agent, N-ethyl-N-nitrosourea (ENU). Furthermore, we explored appropriate experimental parameters for this application, and assessed inter-laboratory reproducibility. In two independent experiments in two laboratories, TK6 cells were exposed to ENU (25-200 µM) and DNA was sequenced 48, 72, and 96 h post-exposure. A DS mutagenicity panel targeting twenty 2.4-kb regions distributed across the genome was used to sample diverse, genome-representative sequence contexts. A significant increase in MF that was unaffected by time was observed in both laboratories. Concentration-response in the MF from the two laboratories was strongly positively correlated (r = 0.97). C:G>T:A, T:A>C:G, T:A>A:T, and T:A>G:C mutations increased in consistent, concentration-dependent manners in both laboratories, with high proportions of C:G>T:A at all time points. The consistent results across the three time points suggest that 48 h may be sufficient for mutation analysis post-exposure. The target sites responded similarly between the two laboratories and revealed a higher average MF in intergenic regions. These results, demonstrating remarkable reproducibility across time and laboratory for both MF and spectrum, support the high value of DS for characterizing chemical mutagenicity in both research and regulatory evaluation.
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Affiliation(s)
- Eunnara Cho
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada
| | | | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | | | - Leslie Recio
- Inotiv-RTP, Research Triangle Park, NC, USA; Scitovation, Research Triangle Park, NC, USA
| | - Kristine L Witt
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | | | | | | | - Phu Van
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | - Fang Yin Lo
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | | | | | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Stephanie L Smith-Roe
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada; Department of Biology, University of Ottawa, Ottawa, ON, Canada.
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2
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Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias and the predictability of evolution. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220055. [PMID: 37004719 PMCID: PMC10067271 DOI: 10.1098/rstb.2022.0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Predicting evolutionary outcomes is an important research goal in a diversity of contexts. The focus of evolutionary forecasting is usually on adaptive processes, and efforts to improve prediction typically focus on selection. However, adaptive processes often rely on new mutations, which can be strongly influenced by predictable biases in mutation. Here, we provide an overview of existing theory and evidence for such mutation-biased adaptation and consider the implications of these results for the problem of prediction, in regard to topics such as the evolution of infectious diseases, resistance to biochemical agents, as well as cancer and other kinds of somatic evolution. We argue that empirical knowledge of mutational biases is likely to improve in the near future, and that this knowledge is readily applicable to the challenges of short-term prediction. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Alejandro V Cano
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bryan L Gitschlag
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Hana Rozhoňová
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Arlin Stoltzfus
- Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Rockville, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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3
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Ulhusna A, Murata A, Nakatani K. Inhibitory Effects of Mismatch Binding Molecules on the Repair Reaction of Uracil-Containing DNA. Biochemistry 2022; 61:2522-2530. [PMID: 36250600 DOI: 10.1021/acs.biochem.2c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stable R-loop formed during transcription induces enzyme-mediated deamination of cytosine, and the uracil in the DNA produced activates the base excision repair (BER) pathway. DNA cleavage involved in the BER pathway is thought to be one of the possible causes of trinucleotide repeat instability. Here, we performed an in vitro assay to investigate the effect of a DNA-binding small molecule, naphthyridine carbamate dimer (NCD), on BER enzyme reactions. The gel electrophoretic mobility shift assay (EMSA) and thermal melting analysis revealed the binding of NCD to a 5'-XGG-3'/5'-XGG-3' triad (X = C or U or apurinic/apyrimidinic site), which is a mimic of a BER enzyme substrate. Polyacrylamide gel electrophoresis (PAGE) of the reaction products of these substrates with hSMUG1 and APE1 enzymes in the presence of NCD showed that NCD interfered with the repair reaction in the 5'-XGG-3'/5'-XGG-3' triad. These findings would broaden the potential of small molecules in modulating trinucleotide repeat instability.
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Affiliation(s)
- Anisa Ulhusna
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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4
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Deymier S, Louvat C, Fiorini F, Cimarelli A. ISG20: an enigmatic antiviral RNase targeting multiple viruses. FEBS Open Bio 2022; 12:1096-1111. [PMID: 35174977 PMCID: PMC9157404 DOI: 10.1002/2211-5463.13382] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/31/2022] [Accepted: 02/15/2022] [Indexed: 11/25/2022] Open
Abstract
Interferon‐stimulated gene 20 kDa protein (ISG20) is a relatively understudied antiviral protein capable of inhibiting a broad spectrum of viruses. ISG20 exhibits strong RNase properties, and it belongs to the large family of DEDD exonucleases, present in both prokaryotes and eukaryotes. ISG20 was initially characterized as having strong RNase activity in vitro, suggesting that its inhibitory effects are mediated via direct degradation of viral RNAs. This mechanism of action has since been further elucidated and additional antiviral activities of ISG20 highlighted, including direct degradation of deaminated viral DNA and translational inhibition of viral RNA and nonself RNAs. This review focuses on the current understanding of the main molecular mechanisms of viral inhibition by ISG20 and discusses the latest developments on the features that govern specificity or resistance to its action.
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Affiliation(s)
- Séverine Deymier
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon Inserm, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieur de Lyon, U1111, Lyon, France
| | | | | | - Andrea Cimarelli
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon Inserm, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieur de Lyon, U1111, Lyon, France
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5
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Gkountakos A, Delfino P, Lawlor RT, Scarpa A, Corbo V, Bria E. Harnessing the epigenome to boost immunotherapy response in non-small cell lung cancer patients. Ther Adv Med Oncol 2021; 13:17588359211006947. [PMID: 34104224 PMCID: PMC8161860 DOI: 10.1177/17588359211006947] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
The introduction of immune checkpoint inhibitor (ICI)-based therapy for non-oncogene addicted non-small cell lung cancer (NSCLC) has significantly transformed the treatment landscape of the disease. Inhibitors of the programmed cell death protein 1/programmed death-ligand 1 (PD-1/PD-L1) immune checkpoint axis, which were initially considered as a late-line treatment option, gradually became the standard of care as first-line treatment for subgroups of NSCLC patients. However, a significant fraction of patients either fails to respond or progresses after a partial response to ICI treatment. Thus, the identification of mechanisms responsible for innate and acquired resistance to immunotherapy within a rapidly evolving tumor microenvironment (TME) is urgently required, as is the identification of reliable predictive biomarkers beyond PD-L1 expression. The deregulation of the epigenome is a key driver of cancer initiation and progression, and it has also been shown to drive therapeutic resistance. Tumor education of infiltrating myeloid cells towards an immuno-suppressive phenotype as well as induction of T-cell dysfunction in the TME is also driven by epigenome reprogramming. As it stands and, given their dynamic nature, epigenetic changes in cancer and non-cancer cells represent an attractive target to increase immunotherapy activity in NSCLC. Accordingly, clinical trials of combinatorial immuno-epigenetic drug regimens have been associated with tumor response in previously immunotherapy-resistant NSCLC patients irrespective of their PD-L1 status. Moreover, epigenetic signatures might represent valuable theragnostic biomarkers as they can be assayed easily in liquid biopsy and provide multiple layers of information. In this review, we discuss the current knowledge regarding the dysregulated epigenetic mechanisms contributing to immunotherapy resistance in NSCLC. Although the clinical data are still maturing, we highlight the attractive perspective that the synergistic model of immuno-epigenetic strategies might overcome the current limitations of immunotherapy alone and will be translated into durable clinical benefit for a broader NSCLC population.
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Affiliation(s)
- Anastasios Gkountakos
- ARC-NET Applied Research on Cancer Center, University of Verona, P.le L.A. Scuro 10, Verona, 37134, Italy
| | - Pietro Delfino
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Rita T. Lawlor
- ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Vincenzo Corbo
- ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Emilio Bria
- Comprehensive Cancer Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Department of Medical Oncology, Università Cattolica Del Sacro Cuore, Rome, Italy
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6
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Fasching L, Jang Y, Tomasi S, Schreiner J, Tomasini L, Brady MV, Bae T, Sarangi V, Vasmatzis N, Wang Y, Szekely A, Fernandez TV, Leckman JF, Abyzov A, Vaccarino FM. Early developmental asymmetries in cell lineage trees in living individuals. Science 2021; 371:1245-1248. [PMID: 33737484 DOI: 10.1126/science.abe0981] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/09/2021] [Indexed: 12/13/2022]
Abstract
Mosaic mutations can be used to track cell lineages in humans. We used cell cloning to analyze embryonic cell lineages in two living individuals and a postmortem human specimen. Of 10 reconstructed postzygotic divisions, none resulted in balanced contributions of daughter lineages to tissues. In both living individuals, one of two lineages from the first cleavage was dominant across tissues, with 90% frequency in blood. We propose that the efficiency of DNA repair contributes to lineage imbalance. Allocation of lineages in postmortem brain correlated with anterior-posterior axis, associating lineage history with cell fate choices in embryos. We establish a minimally invasive framework for defining cell lineages in any living individual, which paves the way for studying their relevance in health and disease.
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Affiliation(s)
- Liana Fasching
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Simone Tomasi
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | | | - Livia Tomasini
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | - Melanie V Brady
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | - Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Vivekananda Sarangi
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nikolaos Vasmatzis
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Anna Szekely
- Department of Neurology, Yale University, New Haven, CT 06520, USA
| | - Thomas V Fernandez
- Child Study Center, Yale University, New Haven, CT 06520, USA.,Department of Psychiatry, Yale University, New Haven, CT 06520, USA
| | - James F Leckman
- Child Study Center, Yale University, New Haven, CT 06520, USA.,Department of Psychiatry, Yale University, New Haven, CT 06520, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA.
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT 06520, USA. .,Department of Neuroscience, Yale University, New Haven, CT 06520, USA.,Yale Kavli Institute for Neuroscience, New Haven, CT 06520, USA
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7
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Heilbrun EE, Merav M, Adar S. Exons and introns exhibit transcriptional strand asymmetry of dinucleotide distribution, damage formation and DNA repair. NAR Genom Bioinform 2021; 3:lqab020. [PMID: 33817640 PMCID: PMC8002178 DOI: 10.1093/nargab/lqab020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/24/2021] [Accepted: 03/22/2021] [Indexed: 12/29/2022] Open
Abstract
Recent cancer sequencing efforts have uncovered asymmetry in DNA damage induced mutagenesis between the transcribed and non-transcribed strands of genes. Here, we investigate the major type of damage induced by ultraviolet (UV) radiation, the cyclobutane pyrimidine dimers (CPDs), which are formed primarily in TT dinucleotides. We reveal that a transcriptional asymmetry already exists at the level of TT dinucleotide frequency and therefore also in CPD damage formation. This asymmetry is conserved in vertebrates and invertebrates and is completely reversed between introns and exons. We show the asymmetry in introns is linked to the transcription process itself, and is also found in enhancer elements. In contrast, the asymmetry in exons is not correlated to transcription, and is associated with codon usage preferences. Reanalysis of nucleotide excision repair, normalizing repair to the underlying TT frequencies, we show repair of CPDs is more efficient in exons compared to introns, contributing to the maintenance and integrity of coding regions. Our results highlight the importance of considering the primary sequence of the DNA in determining DNA damage sensitivity and mutagenic potential.
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Affiliation(s)
- Elisheva E Heilbrun
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 91120, Israel
| | - May Merav
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 91120, Israel
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 91120, Israel
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8
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Vandenbussche I, Sass A, Van Nieuwerburgh F, Pinto-Carbó M, Mannweiler O, Eberl L, Coenye T. Detection of cytosine methylation in Burkholderia cenocepacia by single-molecule real-time sequencing and whole-genome bisulfite sequencing. MICROBIOLOGY-SGM 2021; 167. [PMID: 33565960 DOI: 10.1099/mic.0.001027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Research on prokaryotic epigenetics, the study of heritable changes in gene expression independent of sequence changes, led to the identification of DNA methylation as a versatile regulator of diverse cellular processes. Methylation of adenine bases is often linked to regulation of gene expression in bacteria, but cytosine methylation is also frequently observed. In this study, we present a complete overview of the cytosine methylome in Burkholderia cenocepacia, an opportunistic respiratory pathogen in cystic fibrosis patients. Single-molecule real-time (SMRT) sequencing was used to map all 4mC-modified cytosines, as analysis of the predicted MTases in the B. cenocepacia genome revealed the presence of a 4mC-specific phage MTase, M.BceJII, targeting GGCC sequences. Methylation motif GCGGCCGC was identified, and out of 6850 motifs detected across the genome, 2051 (29.9 %) were methylated at the fifth position. Whole-genome bisulfite sequencing (WGBS) was performed to map 5mC methylation and 1635 5mC-modified cytosines were identified in CpG motifs. A comparison of the genomic positions of the modified bases called by each method revealed no overlap, which confirmed the authenticity of the detected 4mC and 5mC methylation by SMRT sequencing and WGBS, respectively. Large inter-strain variation of the 4mC-methylated cytosines was observed when B. cenocepacia strains J2315 and K56-2 were compared, which suggests that GGCC methylation patterns in B. cenocepacia are strain-specific. It seems likely that 4mC methylation of GGCC is not involved in regulation of gene expression but rather is a remnant of bacteriophage invasion, in which methylation of the phage genome was crucial for protection against restriction-modification systems of B. cenocepacia.
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Affiliation(s)
- Ian Vandenbussche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | | | - Marta Pinto-Carbó
- Department of Plant and Microbial Microbiology, University of Zurich, Zurich, Switzerland
| | - Olga Mannweiler
- Department of Plant and Microbial Microbiology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Microbiology, University of Zurich, Zurich, Switzerland
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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Ajjugal Y, Tomar K, Rao DK, Rathinavelan T. Spontaneous and frequent conformational dynamics induced by A…A mismatch in d(CAA)·d(TAG) duplex. Sci Rep 2021; 11:3689. [PMID: 33574412 PMCID: PMC7878774 DOI: 10.1038/s41598-021-82669-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 01/20/2021] [Indexed: 01/20/2023] Open
Abstract
Base pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc. Here, the influence of A…A mismatch in the context of 5′CAA·5′TAG sequence is explored using molecular dynamics (MD) simulation, umbrella sampling MD, circular dichroism (CD), microscale thermophoresis (MST) and NMR techniques. MD simulations reveal that the A…A mismatch experiences several transient events such as base flipping, base extrusion, etc. facilitating B–Z junction formation. A…A mismatch may assume such conformational transitions to circumvent the effect of nonisostericity with the flanking canonical base pairs so as to get accommodated in the DNA. CD and 1D proton NMR experiments further reveal that the extent of B–Z junction increases when the number of A…A mismatch in d(CAA)·d(T(A/T)G) increases (1–5). CD titration studies of d(CAA)·d(TAG)n=5 with the hZαADAR1 show the passive binding between the two, wherein, the binding of protein commences with B–Z junction recognition. Umbrella sampling simulation indicates that the mismatch samples anti…+ syn/+ syn…anti, anti…anti & + syn…+ syn glycosyl conformations. The concomitant spontaneous transitions are: a variety of hydrogen bonding patterns, stacking and minor or major groove extrahelical movements (with and without the engagement of hydrogen bonds) involving the mismatch adenines. These transitions frequently happen in anti…anti conformational region compared with the other three regions as revealed from the lifetime of these states. Further, 2D-NOESY experiments indicate that the number of cross-peaks diminishes with the increasing number of A…A mismatches implicating its dynamic nature. The spontaneous extrahelical movement seen in A…A mismatch may be a key pre-trapping event in the mismatch repair due to the accessibility of the base(s) to the sophisticated mismatch repair machinery.
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Affiliation(s)
- Yogeeshwar Ajjugal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy District, Telangana State, 502285, India
| | - Kripi Tomar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy District, Telangana State, 502285, India
| | - D Krishna Rao
- Tata Institute of Fundamental Research, 36/P, Gopanpally Mandal, Ranga Reddy District, Hyderabad, Telangana State, 500107, India
| | - Thenmalarchelvi Rathinavelan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy District, Telangana State, 502285, India.
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10
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Ajjugal Y, Rathinavelan T. Sequence dependent influence of an A…A mismatch in a DNA duplex: An insight into the recognition by hZα ADAR1 protein. J Struct Biol 2020; 213:107678. [PMID: 33307177 DOI: 10.1016/j.jsb.2020.107678] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/29/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
Base pair mismatches can erroneously be incorporated in the DNA. An adenine pairing with another adenine is one of the eight possible mismatches. The atomistic insights about the structure and dynamics of an A…A mismatch in a DNA (unbound form) is not yet accessible to any experimental technique. Earlier molecular dynamics (MD) simulations have shown that A…A mismatch in the midst of 5'CAG/3'GAC, 5'GAC/3'CAG and 5'CAA/3'GAT (underline represents the mismatch) are highly dynamic in nature. By employing MD simulation, the influence of an A…A mismatch in the midst of 5'GAA/3'CAT, 5'GAG/3'CAC, 5'AAC/3'TAG, 5'AAG/3'TAC, 5'TAA/3'AAT, 5'TAT/3'AAA and 5'AAT/3'TAA sequences have been investigated here. The results indicate that irrespective of the flanking sequences, the mismatch samples a variety of transient conformations, including a B-Z junction. Further, circular dichroism studies have been carried out to explore the ability of these sequences to bind with hZαADAR1 which specifically recognizes B-Z junction/Z-DNA. The results indicate that hZαADAR1 could not lead to a complete B to Z transition in the above sequences. Notably, a complete transition to Z-form has been reported earlier for 5'GAC/3'CAG upon titrating with hZαADAR1. Intriguingly, 5'AAC/3'TAG, 5'AAG/3'TAC and 5'GAA/3'CAT exhibit a B-Z junction formation rather than a complete transition to Z-form, similar to the situation of 5'CAA/3'GAT. These indicate that although A…A mismatch could induce a local B-Z junction transiently, hZαADAR1 requires the presence of a G…C/C…G base pair adjacent to the A…A mismatch for the binding. Additionally, the extent of B-Z junction has enhanced upon binding with hZαADAR1 in the presence of the A…A mismatch (specifically when CG, CA, AC, GA and AG steps occur), but not in the presence of the canonical base pairs. These confirm the inclination of A…A mismatch towards the B-Z junction.
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Affiliation(s)
- Yogeeshwar Ajjugal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi Campus, Telangana State 502285, India
| | - Thenmalarchelvi Rathinavelan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi Campus, Telangana State 502285, India.
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11
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Savva R. The Essential Co-Option of Uracil-DNA Glycosylases by Herpesviruses Invites Novel Antiviral Design. Microorganisms 2020; 8:microorganisms8030461. [PMID: 32214054 PMCID: PMC7143999 DOI: 10.3390/microorganisms8030461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 01/10/2023] Open
Abstract
Vast evolutionary distances separate the known herpesviruses, adapted to colonise specialised cells in predominantly vertebrate hosts. Nevertheless, the distinct herpesvirus families share recognisably related genomic attributes. The taxonomic Family Herpesviridae includes many important human and animal pathogens. Successful antiviral drugs targeting Herpesviridae are available, but the need for reduced toxicity and improved efficacy in critical healthcare interventions invites novel solutions: immunocompromised patients presenting particular challenges. A conserved enzyme required for viral fitness is Ung, a uracil-DNA glycosylase, which is encoded ubiquitously in Herpesviridae genomes and also host cells. Research investigating Ung in Herpesviridae dynamics has uncovered an unexpected combination of viral co-option of host Ung, along with remarkable Subfamily-specific exaptation of the virus-encoded Ung. These enzymes apparently play essential roles, both in the maintenance of viral latency and during initiation of lytic replication. The ubiquitously conserved Ung active site has previously been explored as a therapeutic target. However, exquisite selectivity and better drug-like characteristics might instead be obtained via targeting structural variations within another motif of catalytic importance in Ung. The motif structure is unique within each Subfamily and essential for viral survival. This unique signature in highly conserved Ung constitutes an attractive exploratory target for the development of novel beneficial therapeutics.
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Affiliation(s)
- Renos Savva
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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12
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Umesaki K, Odai K. A Kinetic Approach to Double Proton Transfer in Watson–Crick DNA Base Pairs. J Phys Chem B 2020; 124:1715-1722. [DOI: 10.1021/acs.jpcb.9b11874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Keisho Umesaki
- School of Science and Engineering, Kokushikan University, Setagaya-ku, Tokyo 154-8515, Japan
| | - Kei Odai
- School of Science and Engineering, Kokushikan University, Setagaya-ku, Tokyo 154-8515, Japan
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Koliadenko V, Wilanowski T. Additional functions of selected proteins involved in DNA repair. Free Radic Biol Med 2020; 146:1-15. [PMID: 31639437 DOI: 10.1016/j.freeradbiomed.2019.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Protein moonlighting is a phenomenon in which a single polypeptide chain can perform a number of different unrelated functions. Here we present our analysis of moonlighting in the case of selected DNA repair proteins which include G:T mismatch-specific thymine DNA glycosylase (TDG), methyl-CpG-binding domain protein 4 (MBD4), apurinic/apyrimidinic endonuclease 1 (APE1), AlkB homologs, poly (ADP-ribose) polymerase 1 (PARP-1) and single-strand selective monofunctional uracil DNA glycosylase 1 (SMUG1). Most of their additional functions are not accidental and clear patterns are emerging. Participation in RNA metabolism is not surprising as bases occurring in RNA are the same or very similar to those in DNA. Other common additional function involves regulation of transcription. This is not unexpected as these proteins bind to specific DNA regions for DNA repair, hence they can also be recruited to regulate transcription. Participation in demethylation and replication of DNA appears logical as well. Some of the multifunctional DNA repair proteins play major roles in many diseases, including cancer. However, their moonlighting might prove a major difficulty in the development of new therapies because it will not be trivial to target a single protein function without affecting its other functions that are not related to the disease.
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Affiliation(s)
- Vlada Koliadenko
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland.
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Jin L, Qin G, Zhao C, Yu X, Lu J, Meng H. The deamination mechanism of the 5,6-dihydro-6-hydro-6-hydroxylcytosine and 5,6-dihydro-5-methyl-6-hydroxylcytosine under typical bisulfite conditions. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1541105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Gongwei Qin
- Bioresources Key Laboratory of Shaanxi Province, College of Biological Science and Technology, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Caibin Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Xiaohu Yu
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Jiufu Lu
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Hao Meng
- College of Physics and Telecom Engineering, Shaanxi University of Technology, Hanzhong, People’s Republic of China
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Todhunter ME, Sayaman RW, Miyano M, LaBarge MA. Tissue aging: the integration of collective and variant responses of cells to entropic forces over time. Curr Opin Cell Biol 2018; 54:121-129. [PMID: 29908481 PMCID: PMC6258070 DOI: 10.1016/j.ceb.2018.05.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/13/2018] [Accepted: 05/30/2018] [Indexed: 01/08/2023]
Abstract
Aging is driven by unavoidable entropic forces, physicochemical in nature, that damage the raw materials that constitute biological systems. Single cells experience and respond to stochastic physicochemical insults that occur either to the cells themselves or to their microenvironment, in a dynamic and reciprocal manner, leading to increased age-related cell-to-cell variation. We will discuss the biological mechanisms that integrate cell-to-cell variation across tissues resulting in stereotypical phenotypes of age.
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Affiliation(s)
- Michael E Todhunter
- Department of Populations Sciences, and Center for Cancer and Aging, Beckman Research Institute at City of Hope, 1500 E Duarte Rd, Duarte, CA 91011 USA
| | - Rosalyn W Sayaman
- Department of Populations Sciences, and Center for Cancer and Aging, Beckman Research Institute at City of Hope, 1500 E Duarte Rd, Duarte, CA 91011 USA
| | - Masaru Miyano
- Department of Populations Sciences, and Center for Cancer and Aging, Beckman Research Institute at City of Hope, 1500 E Duarte Rd, Duarte, CA 91011 USA
| | - Mark A LaBarge
- Department of Populations Sciences, and Center for Cancer and Aging, Beckman Research Institute at City of Hope, 1500 E Duarte Rd, Duarte, CA 91011 USA.
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Molaro A, Young JM, Malik HS. Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals. Genome Res 2018; 28:460-473. [PMID: 29549088 PMCID: PMC5880237 DOI: 10.1101/gr.229799.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/13/2018] [Indexed: 12/11/2022]
Abstract
Eukaryotic genomes must accomplish both compact packaging for genome stability and inheritance, as well as accessibility for gene expression. They do so using post-translational modifications of four ancient canonical histone proteins (H2A, H2B, H3, and H4) and by deploying histone variants with specialized chromatin functions. Some histone variants are conserved across all eukaryotes, whereas others are lineage-specific. Here, we performed detailed phylogenomic analyses of “short H2A histone” variants found in mammalian genomes. We discovered a previously undescribed typically-sized H2A variant in monotremes and marsupials, H2A.R, which may represent the common ancestor of the short H2As. We also discovered a novel class of short H2A histone variants in eutherian mammals, H2A.Q. We show that short H2A variants arose on the X Chromosome in the common ancestor of all eutherian mammals and diverged into four evolutionarily distinct clades: H2A.B, H2A.L, H2A.P, and H2A.Q. However, the repertoires of short histone H2A variants vary extensively among eutherian mammals due to lineage-specific gains and losses. Finally, we show that all four short H2As are subject to accelerated rates of protein evolution relative to both canonical and other variant H2A proteins including H2A.R. Our analyses reveal that short H2As are a unique class of testis-restricted histone variants displaying an unprecedented evolutionary dynamism. Based on their X-Chromosomal localization, genetic turnover, and testis-specific expression, we hypothesize that short H2A variants may participate in genetic conflicts involving sex chromosomes during reproduction.
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Affiliation(s)
- Antoine Molaro
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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Luk ADW, Lee PP, Mao H, Chan KW, Chen XY, Chen TX, He JX, Kechout N, Suri D, Tao YB, Xu YB, Jiang LP, Liew WK, Jirapongsananuruk O, Daengsuwan T, Gupta A, Singh S, Rawat A, Abdul Latiff AH, Lee ACW, Shek LP, Nguyen TVA, Chin TJ, Chien YH, Latiff ZA, Le TMH, Le NNQ, Lee BW, Li Q, Raj D, Barbouche MR, Thong MK, Ang MCD, Wang XC, Xu CG, Yu HG, Yu HH, Lee TL, Yau FYS, Wong WHS, Tu W, Yang W, Chong PCY, Ho MHK, Lau YL. Family History of Early Infant Death Correlates with Earlier Age at Diagnosis But Not Shorter Time to Diagnosis for Severe Combined Immunodeficiency. Front Immunol 2017; 8:808. [PMID: 28747913 PMCID: PMC5506088 DOI: 10.3389/fimmu.2017.00808] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/26/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Severe combined immunodeficiency (SCID) is fatal unless treated with hematopoietic stem cell transplant. Delay in diagnosis is common without newborn screening. Family history of infant death due to infection or known SCID (FH) has been associated with earlier diagnosis. OBJECTIVE The aim of this study was to identify the clinical features that affect age at diagnosis (AD) and time to the diagnosis of SCID. METHODS From 2005 to 2016, 147 SCID patients were referred to the Asian Primary Immunodeficiency Network. Patients with genetic diagnosis, age at presentation (AP), and AD were selected for study. RESULTS A total of 88 different SCID gene mutations were identified in 94 patients, including 49 IL2RG mutations, 12 RAG1 mutations, 8 RAG2 mutations, 7 JAK3 mutations, 4 DCLRE1C mutations, 4 IL7R mutations, 2 RFXANK mutations, and 2 ADA mutations. A total of 29 mutations were previously unreported. Eighty-three of the 94 patients fulfilled the selection criteria. Their median AD was 4 months, and the time to diagnosis was 2 months. The commonest SCID was X-linked (n = 57). A total of 29 patients had a positive FH. Candidiasis (n = 27) and bacillus Calmette-Guérin (BCG) vaccine infection (n = 19) were the commonest infections. The median age for candidiasis and BCG infection documented were 3 months and 4 months, respectively. The median absolute lymphocyte count (ALC) was 1.05 × 109/L with over 88% patients below 3 × 109/L. Positive FH was associated with earlier AP by 1 month (p = 0.002) and diagnosis by 2 months (p = 0.008), but not shorter time to diagnosis (p = 0.494). Candidiasis was associated with later AD by 2 months (p = 0.008) and longer time to diagnosis by 0.55 months (p = 0.003). BCG infections were not associated with age or time to diagnosis. CONCLUSION FH was useful to aid earlier diagnosis but was overlooked by clinicians and not by parents. Similarly, typical clinical features of SCID were not recognized by clinicians to shorten the time to diagnosis. We suggest that lymphocyte subset should be performed for any infant with one or more of the following four clinical features: FH, candidiasis, BCG infections, and ALC below 3 × 109/L.
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Affiliation(s)
- Anderson Dik Wai Luk
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Pamela P. Lee
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Huawei Mao
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Shenzhen Primary Immunodeficiency Diagnostic and Therapeutic Laboratory, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Koon-Wing Chan
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Tong-Xin Chen
- Department of Allergy and Immunology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Xin He
- Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | | | - Deepti Suri
- Allergy Immunology Unit, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Yin Bo Tao
- Guangzhou Children’s Hospital, Guangzhou, China
| | - Yong Bin Xu
- Guang Zhou Women and Children’s Medical Center, Guangzhou, China
| | - Li Ping Jiang
- Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Woei Kang Liew
- KK Women’s and Children’s Hospital, Singapore, Singapore
| | | | | | - Anju Gupta
- Allergy Immunology Unit, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Surjit Singh
- Allergy Immunology Unit, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Rawat
- Allergy Immunology Unit, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | | | | | | | - Tek Jee Chin
- Sarawak General Hospital Malaysia, Kuching, Malaysia
| | - Yin Hsiu Chien
- National Taiwan University Children’s Hospital, Taipei, Taiwan
| | | | | | | | - Bee Wah Lee
- National University of Singapore, Singapore, Singapore
| | - Qiang Li
- Sichuan Second West China Hospital, Sichuan, China
| | - Dinesh Raj
- Department of Paediatrics, Holy Family Hospital, New Delhi, India
| | - Mohamed-Ridha Barbouche
- Department of Immunology, Institut Pasteur de Tunis and University Tunis-El Manar, Tunis, Tunisia
| | - Meow-Keong Thong
- Faculty of Medicine, Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | - Chen Guang Xu
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hai Guo Yu
- Nanjing Children’s Hospital, Nanjing, China
| | - Hsin-Hui Yu
- National Taiwan University Children’s Hospital, Taipei, Taiwan
| | - Tsz Leung Lee
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Wilfred Hing-Sang Wong
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wenwei Tu
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Shenzhen Primary Immunodeficiency Diagnostic and Therapeutic Laboratory, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Wangling Yang
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Shenzhen Primary Immunodeficiency Diagnostic and Therapeutic Laboratory, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Patrick Chun Yin Chong
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Marco Hok Kung Ho
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yu Lung Lau
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Shenzhen Primary Immunodeficiency Diagnostic and Therapeutic Laboratory, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- *Correspondence: Yu Lung Lau,
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Xu X, Watt DS, Liu C. Multifaceted roles for thymine DNA glycosylase in embryonic development and human carcinogenesis. Acta Biochim Biophys Sin (Shanghai) 2016; 48:82-9. [PMID: 26370152 DOI: 10.1093/abbs/gmv083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/12/2015] [Indexed: 01/03/2023] Open
Abstract
Thymine DNA glycosylase (TDG) is a multifunctional protein that plays important roles in DNA repair, DNA demethylation, and transcriptional regulation. These diverse functions make TDG a unique enzyme in embryonic development and carcinogenesis. This review discusses the molecular function of TDG in human cancers and the previously unrecognized value of TDG as a potential target for drug therapy.
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Affiliation(s)
- Xuehe Xu
- Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0509, USA
| | - David S Watt
- Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0509, USA
| | - Chunming Liu
- Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0509, USA
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19
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Torti A, Lever MA, Jørgensen BB. Origin, dynamics, and implications of extracellular DNA pools in marine sediments. Mar Genomics 2015; 24 Pt 3:185-96. [DOI: 10.1016/j.margen.2015.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 08/29/2015] [Indexed: 12/17/2022]
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20
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Castro JC, Maddox JD, Cobos M, Requena D, Zimic M, Bombarely A, Imán SA, Cerdeira LA, Medina AE. De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis. BMC Genomics 2015; 16:997. [PMID: 26602763 PMCID: PMC4658800 DOI: 10.1186/s12864-015-2225-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 11/17/2015] [Indexed: 01/13/2023] Open
Abstract
Background Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to AsA biosynthesis. Results In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs. Conclusions This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with the empirically observed capability of M. dubia to synthesize and accumulate AsA and other important molecules, and adds to our current knowledge of the molecular biology and biochemistry of their production in plants. By providing insights into the mechanisms underpinning these metabolic processes, these results can be used to direct efforts to genetically manipulate this organism in order to enhance the production of these bioactive phytochemicals. The accumulation of AsA precursor and discovery of genes associated with their biosynthesis and metabolism in M. dubia is intriguing and worthy of further investigation. The sequences and pathways produced here present the genetic framework required for further studies. Quantitative transcriptomics in concert with studies of the genome, proteome, and metabolome under conditions that stimulate production and accumulation of AsA and their precursors are needed to provide a more comprehensive view of how these pathways for AsA metabolism are regulated and linked in this species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2225-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan C Castro
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú. .,Círculo de Investigación en Plantas con Efecto en Salud (FONDECYT N° 010-2014), Lima, Perú.
| | - J Dylan Maddox
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum of Natural History, Chicago, IL, USA.
| | - Marianela Cobos
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP), Av. Abelardo Quiñones km 2.5, San Juan Bautista, Iquitos, Perú.
| | - David Requena
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | | | - Sixto A Imán
- Área de Conservación de Recursos Fitogenéticos, Instituto Nacional de Innovación Agraria (INIA), Calle San Roque 209, Iquitos, Perú.
| | - Luis A Cerdeira
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
| | - Andersson E Medina
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
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Fortes FP, Kuasne H, Marchi FA, Miranda PM, Rogatto SR, Achatz MI. DNA methylation patterns of candidate genes regulated by thymine DNA glycosylase in patients with TP53 germline mutations. ACTA ACUST UNITED AC 2015; 48:610-5. [PMID: 25945745 PMCID: PMC4512099 DOI: 10.1590/1414-431x20154026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 02/05/2015] [Indexed: 01/07/2023]
Abstract
Li-Fraumeni syndrome (LFS) is a rare, autosomal dominant, hereditary cancer predisposition disorder. In Brazil, the p.R337H TP53 founder mutation causes the variant form of LFS, Li-Fraumeni-like syndrome. The occurrence of cancer and age of disease onset are known to vary, even in patients carrying the same mutation, and several mechanisms such as genetic and epigenetic alterations may be involved in this variability. However, the extent of involvement of such events has not been clarified. It is well established that p53 regulates several pathways, including the thymine DNA glycosylase (TDG) pathway, which regulates the DNA methylation of several genes. This study aimed to identify the DNA methylation pattern of genes potentially related to the TDG pathway (CDKN2A, FOXA1, HOXD8, OCT4, SOX2, and SOX17) in 30 patients with germline TP53 mutations, 10 patients with wild-type TP53, and 10 healthy individuals. We also evaluated TDG expression in patients with adrenocortical tumors (ADR) with and without the p.R337H TP53 mutation. Gene methylation patterns of peripheral blood DNA samples assessed by pyrosequencing revealed no significant differences between the three groups. However, increased TDG expression was observed by quantitative reverse transcription PCR in p.R337H carriers with ADR. Considering the rarity of this phenotype and the relevance of these findings, further studies using a larger sample set are necessary to confirm our results.
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Affiliation(s)
- F P Fortes
- CIPE, Laboratrio de Oncogentica Molecular, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - H Kuasne
- CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - F A Marchi
- CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - P M Miranda
- CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - S R Rogatto
- CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - M I Achatz
- CIPE, Laboratrio de Oncogentica Molecular, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
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22
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Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Sci Rep 2014; 4:5559. [PMID: 24993353 PMCID: PMC4081896 DOI: 10.1038/srep05559] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/16/2014] [Indexed: 11/08/2022] Open
Abstract
Genomic methylation is variable under biotic and abiotic stresses in plants. In particular, viral infection is thought to significantly increase genomic methylation with particularly high activity around transposable elements. Here we present the genomic methylation profiles of grains of archaeological barley (Hordeum vulgare) from several strata from a site in southern Egypt, from the Napatan to the Islamic periods (800 BCE - 1812 CE). One sample tested positive for viral infection and exhibits an unusually high degree of genomic methylation compared to the rest. A decreasing trend in global methylation levels according to deposition date shows in-situ de-methylation of 5-methylcytosine, which can be described as a diagenetic process. This is most likely a deamination mediated de-methylation process and is expected to lead to 5 mC > T base modifications in addition to the C > U modifications due to cytosine deamination, so represents a time-dependent process of DNA diagenesis in ancient DNA.
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23
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Chen RAJ, Stempor P, Down TA, Zeiser E, Feuer SK, Ahringer J. Extreme HOT regions are CpG-dense promoters in C. elegans and humans. Genome Res 2014; 24:1138-46. [PMID: 24653213 PMCID: PMC4079969 DOI: 10.1101/gr.161992.113] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 12/26/2013] [Indexed: 12/20/2022]
Abstract
Most vertebrate promoters lie in unmethylated CpG-dense islands, whereas methylation of the more sparsely distributed CpGs in the remainder of the genome is thought to contribute to transcriptional repression. Nonmethylated CG dinucleotides are recognized by CXXC finger protein 1 (CXXC1, also known as CFP1), which recruits SETD1A (also known as Set1) methyltransferase for trimethylation of histone H3 lysine 4, an active promoter mark. Genomic regions enriched for CpGs are thought to be either absent or irrelevant in invertebrates that lack DNA methylation, such as C. elegans; however, a CXXC1 ortholog (CFP-1) is present. Here we demonstrate that C. elegans CFP-1 targets promoters with high CpG density, and these promoters are marked by high levels of H3K4me3. Furthermore, as for mammalian promoters, high CpG content is associated with nucleosome depletion irrespective of transcriptional activity. We further show that highly occupied target (HOT) regions identified by the binding of a large number of transcription factors are CpG-rich promoters in C. elegans and human genomes, suggesting that the unusually high factor association at HOT regions may be a consequence of CpG-linked chromatin accessibility. Our results indicate that nonmethylated CpG-dense sequence is a conserved genomic signal that promotes an open chromatin state, targeting by a CXXC1 ortholog, and H3K4me3 modification in both C. elegans and human genomes.
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Affiliation(s)
- Ron A.-J. Chen
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Przemyslaw Stempor
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Thomas A. Down
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Eva Zeiser
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Sky K. Feuer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
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Abstract
DNA methylation is a significant regulator of gene expression, and its role in carcinogenesis recently has been a subject of remarkable interest. The aim of this review is to analyze the mechanism and cell regulatory effects of both hypo- and hyper-DNA methylation on cancer. In this review, we report new developments and their implications regarding the effects of DNA methylation on cancer development. Indeed, alteration of the pattern of DNA methylation has been a constant finding in cancer cells of the same type and differences in the pattern of DNA methylation not only occur in a variety of tumor types, but also in developmental processes Furthermore, the pattern of histone modification appears to be a predicator of the risk of recurrence of human cancers. It is well known that hypermethylation represses transcription of the promoter sections of tumor-suppressor genes leading to gene silencing. However, hypomethylation also has been identified as a cause of oncogenesis. Furthermore, experiments concerning the mechanism of methylation and its control have led to the discovery of many regulatory enzymes and proteins. This review reports on methods developed for the detection of 5-hydroxymethylcytosine methylation at the 5-methylcytosine of protein domains in the CpG context compared to non-methylated DNA, histone modification, and microRNA change.
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Wyatt MD. Advances in understanding the coupling of DNA base modifying enzymes to processes involving base excision repair. Adv Cancer Res 2014; 119:63-106. [PMID: 23870509 DOI: 10.1016/b978-0-12-407190-2.00002-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This chapter describes some of the recent, exciting developments that have characterized and connected processes that modify DNA bases with DNA repair pathways. It begins with AID/APOBEC or TET family members that covalently modify bases within DNA. The modified bases, such as uracil or 5-formylcytosine, are then excised by DNA glycosylases including UNG or TDG to initiate base excision repair (BER). BER is known to preserve genome integrity by removing damaged bases. The newer studies underscore the necessity of BER following enzymes that deliberately damage DNA. This includes the role of BER in antibody diversification and more recently, its requirement for demethylation of 5-methylcytosine in mammalian cells. The recent advances have shed light on mechanisms of DNA demethylation, and have raised many more questions. The potential hazards of these processes have also been revealed. Dysregulation of the activity of base modifying enzymes, and resolution by unfaithful or corrupt means can be a driver of genome instability and tumorigenesis. The understanding of both DNA and histone methylation and demethylation is now revealing the true extent to which epigenetics influence normal development and cancer, an abnormal development.
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Affiliation(s)
- Michael D Wyatt
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina, USA.
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26
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The effects of p53 Arg72Pro polymorphism on glioma susceptibility: a meta-analysis. Tumour Biol 2014; 35:3725-30. [DOI: 10.1007/s13277-013-1494-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 11/28/2013] [Indexed: 10/25/2022] Open
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27
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Léger H, Smet-Nocca C, Attmane-Elakeb A, Morley-Fletcher S, Benecke AG, Eilebrecht S. A TDG/CBP/RARα ternary complex mediates the retinoic acid-dependent expression of DNA methylation-sensitive genes. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:8-18. [PMID: 24394593 PMCID: PMC4411359 DOI: 10.1016/j.gpb.2013.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 11/27/2013] [Accepted: 11/28/2013] [Indexed: 11/28/2022]
Abstract
The thymine DNA glycosylase (TDG) is a multifunctional enzyme, which is essential for embryonic development. It mediates the base excision repair (BER) of G:T and G:U DNA mismatches arising from the deamination of 5-methyl cytosine (5-MeC) and cytosine, respectively. Recent studies have pointed at a role of TDG during the active demethylation of 5-MeC within CpG islands. TDG interacts with the histone acetylase CREB-binding protein (CBP) to activate CBP-dependent transcription. In addition, TDG also interacts with the retinoic acid receptor α (RARα), resulting in the activation of RARα target genes. Here we provide evidence for the existence of a functional ternary complex containing TDG, CBP and activated RARα. Using global transcriptome profiling, we uncover a coupling of de novo methylation-sensitive and RA-dependent transcription, which coincides with a significant subset of CBP target genes. The introduction of a point mutation in TDG, which neither affects overall protein structure nor BER activity, leads to a significant loss in ternary complex stability, resulting in the deregulation of RA targets involved in cellular networks associated with DNA replication, recombination and repair. We thus demonstrate for the first time a direct coupling of TDG’s epigenomic and transcription regulatory function through ternary complexes with CBP and RARα.
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Affiliation(s)
- Hélène Léger
- Vaccine Research Institute, INSERM U955, Institut Mondor de Recherche Biomédicale, 94011 Créteil, France; Institut des Hautes Études Scientifiques, 91440 Bures sur Yvette, France
| | - Caroline Smet-Nocca
- Unité de Glycobiologie Structurale et Fonctionnelle - CNRS UMR 8576, Group of NMR and Structural Biology, Université Lille 1, 59655 Villeneuve d'Ascq, France
| | | | - Sara Morley-Fletcher
- Unité de Glycobiologie Structurale et Fonctionnelle - CNRS UMR 8576, Neuroplasticity Team, Université Lille 1, 59655 Villeneuve d'Ascq, France
| | - Arndt G Benecke
- Institut des Hautes Études Scientifiques, 91440 Bures sur Yvette, France; CNRS UMR 7224, Université Pierre et Marie Curie, 75005 Paris, France.
| | - Sebastian Eilebrecht
- Vaccine Research Institute, INSERM U955, Institut Mondor de Recherche Biomédicale, 94011 Créteil, France; Institut des Hautes Études Scientifiques, 91440 Bures sur Yvette, France
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Jin L, Wang W, Hu D, Min S. Effects of Protonation and C5 Methylation on the Electrophilic Addition Reaction of Cytosine: A Computational Study. J Phys Chem B 2012; 117:3-12. [DOI: 10.1021/jp304282z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Lingxia Jin
- Key Laboratory for
Macromolecular Science of Shaanxi Province, School of
Chemistry and Chemical Engineering, Shaanxi Normal University, Xi′an 710062, China
- School of Chemical
and Environmental Sciences, Shaanxi University of Technology, Hanzhong 723001, China
| | - Wenliang Wang
- Key Laboratory for
Macromolecular Science of Shaanxi Province, School of
Chemistry and Chemical Engineering, Shaanxi Normal University, Xi′an 710062, China
| | - Daodao Hu
- Key Laboratory for
Macromolecular Science of Shaanxi Province, School of
Chemistry and Chemical Engineering, Shaanxi Normal University, Xi′an 710062, China
| | - Suotian Min
- School of Chemical
and Environmental Sciences, Shaanxi University of Technology, Hanzhong 723001, China
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Marinelli M, Peragine N, Di Maio V, Chiaretti S, De Propris MS, Raponi S, Tavolaro S, Mauro FR, Del Giudice I, Guarini A, Foà R. Identification of molecular and functional patterns of p53 alterations in chronic lymphocytic leukemia patients in different phases of the disease. Haematologica 2012; 98:371-5. [PMID: 22983585 DOI: 10.3324/haematol.2012.069906] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We analyzed TP53 mutations in 483 chronic lymphocytic leukemia patients at different phases of the disease and found a higher incidence of mutations at the later phases and a distinctive mutation profile in each phase. p53 function evaluated by immunoblotting and flow cytometry after cell irradiation was impaired in 28 of 109 cases. Three phenotypically different dysfunctions were observed: type I, associated with heterozygous missense TP53 mutations (typically present at diagnosis) and partially resistant to radiation-induced killing; types II and III, with a higher incidence of microdeletions, nonsense mutations and bi-allelic TP53 defects (common in progressive and chemoresistant cases) and a complete radioresistance. Furthermore, in 4 of 28 patients, all chemoresistant, we found p53 dysfunctions without TP53 mutations. In chronic lymphocytic leukemia patients, a disease phase-specific variability in the p53 mutation profile and function takes place, and both analyses could be useful to guide treatment choices.
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Affiliation(s)
- Marilisa Marinelli
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
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30
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Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 2011; 146:1029-41. [PMID: 21925323 DOI: 10.1016/j.cell.2011.08.016] [Citation(s) in RCA: 283] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 05/09/2011] [Accepted: 08/10/2011] [Indexed: 12/12/2022]
Abstract
During germ cell and preimplantation development, mammalian cells undergo nearly complete reprogramming of DNA methylation patterns. We profiled the methylomes of human and chimp sperm as a basis for comparison to methylation patterns of ESCs. Although the majority of promoters escape methylation in both ESCs and sperm, the corresponding hypomethylated regions show substantial structural differences. Repeat elements are heavily methylated in both germ and somatic cells; however, retrotransposons from several subfamilies evade methylation more effectively during male germ cell development, whereas other subfamilies show the opposite trend. Comparing methylomes of human and chimp sperm revealed a subset of differentially methylated promoters and strikingly divergent methylation in retrotransposon subfamilies, with an evolutionary impact that is apparent in the underlying genomic sequence. Thus, the features that determine DNA methylation patterns differ between male germ cells and somatic cells, and elements of these features have diverged between humans and chimpanzees.
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31
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Jha P, Jha P, Pathak P, Chosdol K, Suri V, Sharma MC, Kumar G, Singh M, Mahapatra AK, Sarkar C. TP53 polymorphisms in gliomas from Indian patients: Study of codon 72 genotype, rs1642785, rs1800370 and 16 base pair insertion in intron-3. Exp Mol Pathol 2010; 90:167-72. [PMID: 21115003 DOI: 10.1016/j.yexmp.2010.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 11/08/2010] [Indexed: 01/08/2023]
Abstract
Several single nucleotide polymorphisms of the TP53 gene have been reported, amongst which polymorphism in codon 72 (rs1042522) has received significant attention and shown to be associated with disease susceptibility in different cancer types. However, there are variable reports on this polymorphism in gliomas from worldwide with inconsistent results. In addition, the implications of other polymorphic loci are not much explored in gliomas. Hence, in the present study the TP53 sequence was analyzed for all polymorphism and mutations in a total of 84 gliomas of different types and grades from patients of Indian origin. The complete sequence of all coding exons (2 to 11) and introns 2, 3, 5 and 8 of TP53 gene were studied while for introns 1, 4, 6, 7, 9 and 10, only exon flanking regions could be studied. The polymorphic loci were compared with control population. In addition to the well known codon 72 polymorphism (rs1042522), three other polymorphisms rs1642785, rs1800370 and a 16 base pair insertion in intron-3 were found. At codon 72, our study showed higher Arg/Arg genotype in gliomas compared to normal population (38% versus 13%). The Arg allele frequency in glioma patients was comparatively higher than controls (0.55 versus 0.45; P=0.037). The Arg allele frequency was also high in adult glioblastomas compared to paediatric counterparts (0.55 versus 0.36). However, there was no significant association of TP53 mutations with any genotype of codon 72. At rs1642785, the G allele frequency was significantly higher in gliomas than in control population (0.55 versus 0.36, P=0.005). The genotype at a 16 base pair insertion in intron-3 was almost similar in case and control. However, the polymorphism at rs1800370 was exclusive to gliomas. This is the first report of TP53 gene polymorphism in glioma patients from India. Our study also delineates the frequency of four polymorphisms in gliomas for the first time. The codon 72 variant (rs1042522) and rs1642785 polymorphisms possibly poses risk to glioma development in Indian population. However, the functional significance of these polymorphism needs further elucidation.
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Affiliation(s)
- Prerana Jha
- Department of Pathology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
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Jacobus J, Wang B, Maddox C, Esch H, Lehmann L, Robertson L, Wang K, Kirby P, Ludewig G. 3-Methylcholanthrene (3-MC) and 4-chlorobiphenyl (PCB3) genotoxicity is gender-related in Fischer 344 transgenic rats. ENVIRONMENT INTERNATIONAL 2010; 36:970-979. [PMID: 20739065 PMCID: PMC2949545 DOI: 10.1016/j.envint.2010.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 06/16/2010] [Accepted: 07/27/2010] [Indexed: 05/29/2023]
Abstract
Polychlorinated biphenyls (PCBs) are a class of persistent organic pollutants with myriad biological effects, including carcinogenicity. We present data showing gender-specific genotoxicity in Fischer 344 transgenic BigBlue rodents exposed to 4-chlorobiphenyl (PCB3), a hydroxylated metabolite, and the positive control 3-methylcholanthrene (3-MC) where female rats are more resistant to the genotoxic effects of the test compounds compared to their male counterparts. This difference is further highlighted through our examination of gene expression, organ-specific weight changes, and tissue morphology. The purpose of the present study was to explore the complex and multifaceted issues of lower molecular weight PCBs as initiators of carcinogenesis, by examining the mutagenicity of PCB3, a hydroxylated metabolite (4'-OH-PCB3), and 3-methylcholanthrene (3-MC, positive control) in a transgenic rodent model. Previous findings indicated that PCB3 is mutagenic in the liver of male BigBlue transgenic rats under identical exposure conditions. We expected that female rats would be equally, if not more sensitive than male rats, since a 2-year carcinogenesis bioassay with Sprague-Dawley rats and commercial PCB mixtures reported much higher liver cancer rates in female than in male rats. The current study, however, revealed a similar trend in the mutation frequencies across all four treatment groups in females as reported previously in males, but increased variability among animals within each group and a lower overall effect, led to non significant differences in mutation frequencies. A closer analysis of the possible reasons for this negative result using microarray, organ weight and histology data comparisons shows that female Fischer 344 rats 1) had a higher baseline mutation frequency in the corn oil control group and greater variability than male rats; 2) responded with robust gene expression changes, which may also play a role in our observation of 3) highly increased liver, spleen, and lung weight in 3-MC and PCB3-treated female rats and thus changed distribution and kinetics of the test compounds. Our analysis indicates that female transgenic BigBlue Fischer 344 rats are more resistant to PCB3 and 3-MC genotoxicity compared to their male counterparts.
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Affiliation(s)
- J.A. Jacobus
- Department of Occupational and Environmental Health, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
| | - B. Wang
- Department of Occupational and Environmental Health, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
| | - C. Maddox
- Department of Occupational and Environmental Health, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
| | - H. Esch
- Department of Occupational and Environmental Health, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
| | - L. Lehmann
- Department of Occupational and Environmental Health, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
| | - L.W. Robertson
- Department of Occupational and Environmental Health, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
| | - K. Wang
- Department of Biostatistics, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
| | - P. Kirby
- Department of Pathology; University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
| | - G. Ludewig
- Department of Occupational and Environmental Health, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, 100 Oakdale Campus # 124 IREH, Iowa City, IA 52242-5000
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Smet-Nocca C, Wieruszeski JM, Chaar V, Leroy A, Benecke A. The thymine-DNA glycosylase regulatory domain: residual structure and DNA binding. Biochemistry 2010; 47:6519-30. [PMID: 18512959 DOI: 10.1021/bi7022283] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymine-DNA glycosylases (TDGs) initiate base excision repair by debasification of the erroneous thymine or uracil nucleotide in G.T and G.U mispairs which arise at high frequency through spontaneous or enzymatic deamination of methylcytosine and cytosine, respectively. Human TDG has furthermore been shown to have a functional role in transcription and epigenetic regulation through the interaction with transcription factors from the nuclear receptor superfamily, transcriptional coregulators, and a DNA methyltransferase. The TDG N-terminus encodes regulatory functions, as it assures both G.T versus G.U specificity and contains the sites for interaction and posttranslational modification by transcription-related activities. While the molecular function of the evolutionarily conserved central catalytic domain of TDG in base excision repair has been elucidated by determination of its three-dimensional structure, the mechanisms by which the N-terminus exerts its regulatory roles, as well as the function of TDG in transcription regulation, remain to be understood. We describe here the residual structure of the TDG N-terminus in both contexts of the isolated domain and the entire protein. These studies lead to the characterization of a small structural domain in the TDG N-terminal region preceding the catalytic core and coinciding with the region of functional regulation of TDG's activities. This regulatory domain exhibits a small degree of organization and is implicated in dynamic molecular interactions with the catalytic domain and nonselective interactions with double-stranded DNA, providing a molecular explanation for the evolutionarily acquired G.T mismatch processing activity of TDG.
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Affiliation(s)
- Caroline Smet-Nocca
- Institut de Recherche Interdisciplinaire, USR CNRS 3078, Université de Lille 1, 1 rue du Professeur Calmette, 59021 Lille Cedex, France
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Przybylski JL, Wetmore SD. Modeling the dissociative hydrolysis of the natural DNA nucleosides. J Phys Chem B 2010; 114:1104-13. [PMID: 20039632 DOI: 10.1021/jp9098717] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two-dimensional PCM-B3LYP/6-31+G(d) potential energy surfaces for the hydrolysis of the four natural 2'-deoxyribonucleosides (2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and thymidine) are characterized using a model that includes both implicit (bulk) solvent effects and (three or four) explicit water molecules in the optimization routine. For the first time, the experimentally predicted dissociative (S(N)1) mechanism is found to be favored over the synchronous (S(N)2) pathway for all nucleosides studied. Due to the success of our model in stabilizing the charge-separated intermediates along the S(N)1 pathway, it is proposed that the new model presented here is the smallest system capable of generating the experimentally predicted oxacarbenium cation intermediate. We therefore stress that dissociative mechanisms should be studied with methodologies that account for the (bulk) environment in the optimization routine, where these effects are often only included as a correction to the energy in the current literature. In addition to accounting for charge stabilization through implicit solvation, nucleophile activation and leaving group stabilization should also be explicitly introduced into the model to further stabilize the system. Our work also emphasizes the importance of studying the Gibbs surface, which in some cases provides a better description of chemically important regions of the reaction surface or changes the calculated trend in the magnitude of dissociative barriers. In addition, it is proposed that the methodology presented in this study can be used to calculate uncatalyzed deglycosylation barriers for a range of DNA nucleosides, which when compared to the corresponding enzyme-catalyzed reactions, will allow the prediction of the rate enhancement (barrier reduction) due to the enzyme.
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Affiliation(s)
- Jennifer L Przybylski
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta T1K 3M4, Canada
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Hosseini-khalili A, Haines DD, Modirian E, Soroush M, Khateri S, Joshi R, Zendehdel K, Ghanei M, Giardina C. Mustard gas exposure and carcinogenesis of lung. Mutat Res 2009; 678:1-6. [PMID: 19559099 PMCID: PMC2811761 DOI: 10.1016/j.mrgentox.2009.05.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 05/14/2009] [Accepted: 05/18/2009] [Indexed: 12/22/2022]
Abstract
UNLABELLED Sulfur mustard (SM), also known as mustard gas, is an alkylating compound used as a chemical weapon in World War I and by Iraqi forces against Iranians and indigenous Iraqi Kurds during the Iran-Iraq War of the 1980s. Although SM is a proven carcinogen there are conflicting views regarding the carcinogenicity of a single exposure. The present study characterizes lung cancers formed in mustard gas victims from the Iran-Iraq War. METHODS AND MATERIALS Demographic information and tumor specimens were collected from 20 Iranian male lung cancer patients with single high-dose SM exposures during the Iran-Iraq War. Formalin-fixed, paraffin-embedded lung cancers were analyzed by immunohistochemistry for p53 protein. In addition, DNA was extracted from the tissues, PCR amplified and sequenced to identify mutations in the p53 and KRAS genes associated with SM exposure. RESULTS A relatively early age of lung cancer onset (ranging from 28 to 73 with a mean of 48) in mustard gas victims, particularly those in the non-smoking population (mean age of 40.7), may be an indication of a unique etiology for these cancers. Seven of the 20 patients developed lung cancer before the age of 40. Five of 16 cancers from which DNA sequence data was obtainable provided information on eight p53 mutations (within exons 5-8). These mutations were predominately G to A transitions; a mutation consistent with the DNA lesion caused by SM. Two of the lung cancers had multiple p53 point mutations, similar to results obtained from factory workers chronically exposed to mustard agent. No mutations were detected in the KRAS gene. DISCUSSION The distinguishing characteristics of lung carcinogenesis in these mustard gas victims suggest that a single exposure may increase the risk of lung cancer development in some individuals.
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Abstract
The purpose of this review is to summarize the evidence that can be used to reconstruct the etiology of human cancers from mutations found in tumors. Mutational spectra of the tumor suppressor gene p53 (TP53) are tumor specific. In several cases, these mutational spectra can be linked to exogenous carcinogens, most notably for sunlight-associated skin cancers, tobacco-associated lung cancers, and aristolochic acid-related urothelial tumors. In the TP53 gene, methylated CpG dinucleotides are sequences selectively targeted by endogenous and exogenous mutagenic processes. Recent high-throughput sequencing efforts analyzing a large number of genes in cancer genomes have so far, for the most part, produced mutational spectra similar to those in TP53 but have unveiled a previously unrecognized common G to C transversion mutation signature at GpA dinucleotides in breast cancers and several other cancers. Unraveling the origin of these G to C mutations will be of importance for understanding cancer etiology.
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Labet V, Morell C, Cadet J, Eriksson LA, Grand A. Hydrolytic Deamination of 5-Methylcytosine in Protic Medium—A Theoretical Study. J Phys Chem A 2009; 113:2524-33. [DOI: 10.1021/jp808902j] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vanessa Labet
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Christophe Morell
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Jean Cadet
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Leif A. Eriksson
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - André Grand
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
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Lamers R, Hayter S, Matheson CD. Postmortem miscoding lesions in sequence analysis of human ancient mitochondrial DNA. J Mol Evol 2008; 68:40-55. [PMID: 19067027 DOI: 10.1007/s00239-008-9184-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 11/11/2008] [Accepted: 11/11/2008] [Indexed: 11/26/2022]
Abstract
Genetic miscoding lesions can cause inaccuracies during the interpretation of ancient DNA sequence data. In this study, genetic miscoding lesions were identified and assessed by cloning and direct sequencing of degraded, amplified mitochondrial DNA (mtDNA) extracted from human remains. Forty-two individuals, comprising nine collections from five geographic locations, were analyzed for the presence of DNA damage that can affect the generation of a correct mtDNA profile. In agreement with previous studies, high levels (56.5% of all damage sites) of proposed hydrolytic damage products were observed. Among these, type 2 transitions (cytosine --> thymine or guanine --> adenine), which are highly indicative of hydrolytic deamination, were observed in 50% of all misincorporations that occurred. In addition to hydrolytic damage products, oxidative damage products were also observed in this study and were responsible for approximately 43.5% of all misincorporations. This level of misincorporation is in contrast to previous studies characterizing miscoding lesions from the analysis of bone and teeth, where few to no oxidative damage products were observed. Of all the oxidative damage products found in this study, type 2 transversions (cytosine --> adenine/guanine --> thymine or cytosine --> guanine/guanine --> cytosine), which are commonly formed through the generation of 8-hydroxyguanine, accounted for 30.3% of all genetic miscoding lesions observed. This study identifies the previously unreported presence of oxidative DNA damage and proposes that damage to degraded DNA templates is highly specific in type, correlating with the geographic location and the taphonomic conditions of the depositional environment from which the remains are recovered.
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Affiliation(s)
- Ryan Lamers
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
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Shimmyo T, Okada A, Hashimoto T, Kobayashi Y, Miyagi Y, Ishikawa Y, Nakagawa K, Osada H, Tsuchiya E. Etiologic value of p53 mutation spectra and differences with histology in lung cancers. Cancer Sci 2008; 99:287-95. [PMID: 18271927 PMCID: PMC11159117 DOI: 10.1111/j.1349-7006.2007.00686.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A total of 297 resected Japanese non-small cell lung cancers (74 squamous cell carcinomas and 223 adenocarcinomas) were analyzed to evaluate the validity of the p53 mutation spectrum as a fingerprint for mutagenic substances as etiological factors. Frequencies of G-->T transversions in smokers were significantly higher than in non-smokers (P = 0.003) and the average incidence of G-->T at hot spot codons of adduct formation was higher than that in other codons in smokers and in the hot spots in non-smokers. Further, the mutation showed a marked strand bias. G-->A transitions at CpG sites (CpG-->CpA) were equally distributed in smokers and non-smokers, and on both strands. A-->G transitions did not show any variation with smoking status in terms of frequency, but exhibited a marked strand bias. Taken together, the G-->T may be a fingerprint of direct mutagenic action of tobacco-related compounds, the A-->G being a new marker for other environmental chemicals, while the CpG-->CpA may be attributable to endogenous spontaneous mutation, for active in lung carcinogenesis.
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Affiliation(s)
- Takuo Shimmyo
- Laboratory of Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, 1-1-2 Nakao, Asahi, Yokohama, Kanagawa 241-0815, Japan
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40
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Lehmann L, Esch HL, Kirby PA, Robertson LW, Ludewig G. 4-monochlorobiphenyl (PCB3) induces mutations in the livers of transgenic Fisher 344 rats. Carcinogenesis 2006; 28:471-8. [PMID: 16950798 DOI: 10.1093/carcin/bgl157] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
4-monochlorobiphenyl (PCB3) is found in small amounts in commercial PCB mixtures, indoor and outdoor air, and in food. In contrast to highly chlorinated congeners that are more resistant to metabolic attack, PCB3 is more readily converted by xenobiotic-metabolizing enzymes to monohydroxy-PCBs and further to dihydroxy-metabolites, which can be oxidized to quinones. Our recent studies demonstrated the initiating action of PCB3 in the livers of male rats. Therefore we hypothesized that PCB3 and/or its metabolite(s) are mutagenic in rat livers in vivo. To investigate the mutagenicity and the types of mutations generated by PCB3, male Fischer 344 BigBlue rats, transgenic for the lacI gene, were injected intraperitoneally with PCB3 (600 micromol/kg), 4-hydroxy-PCB3 (4-HO-PCB3, 400 micromol/kg), 3-methylcholanthrene (3-MC, 300 micromol/kg, positive control) and corn oil (negative control) once per week, for 4 weeks. Animals were killed 17 days after the last injection and the mutant frequency of the liver lacI gene determined. 3-MC induced a 4-fold increase of the mutant frequency of the lacI gene in the liver. The mutant frequency in PCB3-treated animals was also significantly elevated. In contrast, 4-HO-PCB3 induced a non-significant doubling of the mutant frequency. The mutation spectrum of solvent control mutants was characterized by transitions, whereas in 3-MC-animals, transversion and frameshift mutations predominated. The PCB3-induced mutation spectrum was similar to that of the 3-MC-induced mutants. In contrast, the mutation spectrum of the 4-HO-PCB3 group hardly differed from that of the control animals. This study demonstrates for the first time the mutagenicity of a PCB in vivo.
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Affiliation(s)
- Leane Lehmann
- Institute of Applied Biosciences, Section of Food Chemistry and Toxicology, University of Karlsruhe (TH) Kaiserstrasse 12, D-76131 Karlsruhe, Germany
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Abstract
5-Methylcytosine in DNA is genetically unstable. Methylated CpG (mCpG) sequences frequently undergo mutation resulting in a general depletion of this dinucleotide sequence in mammalian genomes. In human genetic disease- and cancer-relevant genes, mCpG sequences are mutational hotspots. It is an almost universally accepted dogma that these mutations are caused by random deamination of 5-methylcytosines. However, it is plausible that mCpG transitions are not caused simply by spontaneous deamination of 5-methylcytosine in double-stranded DNA but by other processes including, for example, mCpG-specific base modification by endogenous or exogenous mutagens or, alternatively, by secondary factors operating at mCpG sequences and promoting deamination. We also discuss that mCpG sequences are favored targets for specific exogenous mutagens and carcinogens. When adjacent to another pyrimidine, 5-methylcytosine preferentially undergoes sunlight-induced pyrimidine dimer formation. Certain polycyclic aromatic hydrocarbons form guanine adducts and induce G to T transversion mutations with high selectivity at mCpG sequences.
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Affiliation(s)
- G P Pfeifer
- Division of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005; 437:69-87. [PMID: 16136131 DOI: 10.1038/nature04072] [Citation(s) in RCA: 1543] [Impact Index Per Article: 81.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Accepted: 07/20/2005] [Indexed: 12/18/2022]
Abstract
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.
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Wang P, Ren J. Separation of purine and pyrimidine bases by capillary electrophoresis using β-cyclodextrin as an additive. J Pharm Biomed Anal 2004; 34:277-83. [PMID: 15013141 DOI: 10.1016/s0731-7085(03)00502-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2003] [Revised: 09/08/2003] [Accepted: 09/08/2003] [Indexed: 10/26/2022]
Abstract
Capillary electrophoresis was applied to separate purine and pyrimidine bases in the basis of their partial ionization in the alkaline buffer. The effects of buffer pH, buffer and beta-cylclodextrin concentration were systematically investigated using a commercial capillary electrophoresis instrument with UV detector at 254nm. We found that the resolutions of bases (especially for adenine and thymine) were significantly improved in the presence of beta-cylclodextrin. The satisfactory separation of five bases such as cytosine, thymine, adenine, guanine and uracil were achieved by capillary electrophoresis using beta-cylclodextrin as an additive. Under the optimal conditions, the linear range was from 2 to 200microg/ml for bases (R= 0,991-0,9977 ) and the detection limits were from 0.8 to 1.8microg/ml (S/N = 2). The detection limit of 0.05microg/ml ( S/N=2 ) for uracil was obtained by stacking injection mode. The assay was used to determine the deamination of cytosine to uracil by heating in the presence of sodium hydroxide. Our primarily results show that capillary electrophoresis is a very useful tool for determination of purine and pyrimidine bases and study on nucleic acids.
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Affiliation(s)
- Ping Wang
- College of Chemistry and Chemical Engineering, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, PR China
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Lee DH, Pfeifer GP. Deamination of 5-methylcytosines within cyclobutane pyrimidine dimers is an important component of UVB mutagenesis. J Biol Chem 2003; 278:10314-21. [PMID: 12525487 DOI: 10.1074/jbc.m212696200] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
UVB mutagenesis is characterized by an abundance of C --> T and 5-methylcytosine --> T transitions at dipyrimidine sequences. It is not known how these mutations might arise. One hypothesis is that UV-induced mutations occur only after deamination of the cytosine or 5-methylcytosine within the pyrimidine dimer. It is not clear how methylation of cytosines at the 5-position influences deamination and how this affects mutagenesis. We have now conducted experiments with a CpG-methylated supF shuttle vector that was irradiated with UVB and then incubated at 37 degrees C to allow time for deamination before passage through a human cell line to establish mutations. This led to a significantly increased frequency of CC --> TT mutations and of transition mutations at 5'-PymCG-3' sequences. A spectrum of deaminated cis-syn cyclobutane pyrimidine dimers in the supF gene was determined using the mismatch glycosylase activities of MBD4 protein in combination with ligation-mediated PCR. Methylation at the C-5 position promoted the deamination of cytosines within cis-syn cyclobutane pyrimidine dimers, and these two events combined led to a significantly increased frequency of UVB-induced transition mutations at 5'-PymCG-3' sequences. Under these conditions, the majority of all supF mutations were transition mutations at 5'-PymCG-3', and they clustered at several mutational hot spots. Exactly these types of mutations are frequently observed in the p53 gene of nonmelanoma skin tumors. This particular mutagenic pathway may become prevalent under conditions of inefficient DNA repair and slow proliferation of cells in the human epidermis.
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Affiliation(s)
- Dong-Hyun Lee
- Division of Biology, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
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Abstract
DNA methylation is not just for basic scientists any more. There is a growing awareness in the medical field that having the correct pattern of genomic methylation is essential for healthy cells and organs. If methylation patterns are not properly established or maintained, disorders as diverse as mental retardation, immune deficiency, and sporadic or inherited cancers may follow. Through inappropriate silencing of growth regulating genes and simultaneous destabilisation of whole chromosomes, methylation defects help create a chaotic state from which cancer cells evolve. Methylation defects are present in cells before the onset of obvious malignancy and therefore cannot be explained simply as a consequence of a deregulated cancer cell. Researchers are now able to detect with exquisite sensitivity the cells harbouring methylation defects, sometimes months or years before the time when cancer is clinically detectable. Furthermore, aberrant methylation of specific genes has been directly linked with the tumour response to chemotherapy and patient survival. Advances in our ability to observe the methylation status of the entire cancer cell genome have led us to the unmistakable conclusion that methylation abnormalities are far more prevalent than expected. This methylomics approach permits the integration of an ever growing repertoire of methylation defects with the genetic alterations catalogued from tumours over the past two decades. Here we discuss the current knowledge of DNA methylation in normal cells and disease states, and how this relates directly to our current understanding of the mechanisms by which tumours arise.
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Affiliation(s)
- J F Costello
- The Brain Tumor Research Center and the Department of Neurological Surgery, University of California, 2340 Sutter, Room N261, San Francisco, San Francisco, CA 94143-0875, USA.
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Fallows S, Price J, Atkinson RJ, Johnston PG, Hickey I, Russell SE. P53 mutation does not affect prognosis in ovarian epithelial malignancies. J Pathol 2001; 194:68-75. [PMID: 11329143 DOI: 10.1002/path.857] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mutations of the p53 tumour suppressor gene have been found in most human cancers, including ovarian epithelial malignancies. This study investigated whether the presence or absence of p53 mutation was associated with outcome following platinum-based chemotherapy in patients with ovarian cancer. DNA samples from tumour tissue and blood were obtained from 73 patients with primary tumours, 50 of whom received platinum-based adjuvant chemotherapy. Single-strand conformation polymorphism analysis and direct DNA sequencing of exons 5-8 detected mutations in 44% (32 of 73) of tumours. These were more common in late-stage (III or IV) than in early-stage disease (I or II) (p=0.03). There was no association with histological type, volume of residual disease following surgery, or initial CA125 levels. No significant association was found between p53 status and overall survival or disease-free survival following chemotherapy. Likewise, there was no correlation between p53 mutation and response to chemotherapy as defined by normalization of CA125 levels. Tumours with p53 missense mutations recurred within a significantly shorter time than those with normal p53 (p=0.04). In addition, there was a tendency for tumours with missense mutations to have a shorter disease-free survival than those with non-missense mutations, although this did not reach statistical significance (p=0.07).
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Affiliation(s)
- S Fallows
- Department of Obstetrics and Gynaecology, Belfast City Hospital, Belfast BT9 7AB, UK
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You YH, Pfeifer GP. Similarities in sunlight-induced mutational spectra of CpG-methylated transgenes and the p53 gene in skin cancer point to an important role of 5-methylcytosine residues in solar UV mutagenesis. J Mol Biol 2001; 305:389-99. [PMID: 11152598 DOI: 10.1006/jmbi.2000.4322] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the p53 gene of human sunlight-associated skin cancers, 35 % of the mutations involve trinucleotide sequences with the rare base 5-methylcytosine (5'PymCG). In order to determine the involvement of 5-methylcytosine in sunlight-induced mutations, we have analyzed the cII transgene in mouse cells, a mutational target gene that we found is methylated at most CpG sequences. We report that the mutational spectra produced by irradiation with 254 nm UVC radiation and simulated sunlight, respectively, differ most dramatically by the much higher involvement of dipyrimidine structures containing 5-methylcytosine in the solar UV mutation spectrum (32 % versus 9 % of all mutations). A distinct mutational hotspot induced by simulated sunlight occurs at a sequence 5'TmCG and is associated with high levels of cis-syn cyclobutane pyrimidine dimer formation. A comparison of sunlight-induced mutational spectra of the cII and lacI transgenes, as well as the p53 gene in skin tumors, shows that 5-methylcytosine is involved in 25 to 40 % of all mutations in all three systems. The combined data make a strong case that cyclobutane pyrimidine dimers forming preferentially at dipyrimidine sequences with 5-methylcytosine are responsible for a considerable fraction of the mutations induced by sunlight in mammalian cells.
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Affiliation(s)
- Y H You
- Department of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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48
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Hashimoto T, Tokuchi Y, Hayashi M, Kobayashi Y, Nishida K, Hayashi S, Ishikawa Y, Nakagawa K, Hayashi J, Tsuchiya E. Different subtypes of human lung adenocarcinoma caused by different etiological factors. Evidence from p53 mutational spectra. THE AMERICAN JOURNAL OF PATHOLOGY 2000; 157:2133-41. [PMID: 11106585 PMCID: PMC1885779 DOI: 10.1016/s0002-9440(10)64851-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Human lung adenocarcinomas are only relatively weakly associated with tobacco smoke, and other etiological factors need to be clarified. These may also vary with the histopathology. Because the p53 mutation status (frequency and spectrum) of a carcinoma can provide clues to causative agents, we subclassified 113 adenocarcinomas into five cell types: hobnail, columnar/cuboidal, mixed, polygonal, and goblet (54, 23, 18, 13, and 5, respectively) and investigated relationships with p53 mutations and smoking history. In the hobnail cell type, a low mutational frequency (37%) and a high proportion of transitions (65%), especially G:C to A:T transitions at CpG dinucleotides (45%) associated with spontaneous mutations, were found with a weak relation to tobacco smoke. In contrast, a high mutation frequency (70%) with a higher proportion of transversions (50%), especially G:C to T:A (44%) on the nontranscribed DNA strand, caused by exogenous carcinogenic agents like tobacco smoke, were observed for the columnar cell type, as with squamous cell carcinomas. These results indicate that two major subtypes of lung adenocarcinoma exist, one probably caused by tobacco smoke, and the other possibly due to spontaneous mutations. For the prevention of lung adenocarcinomas, in addition to stopping tobacco smoking, the elucidation of endogenous mechanisms is important.
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Affiliation(s)
- T Hashimoto
- Laboratory of Cancer Diagnosis and Therapy, Saitama Cancer Center Research Institute, Saitama, Japan
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Hardeland U, Bentele M, Jiricny J, Schär P. Separating substrate recognition from base hydrolysis in human thymine DNA glycosylase by mutational analysis. J Biol Chem 2000; 275:33449-56. [PMID: 10938281 DOI: 10.1074/jbc.m005095200] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human thymine DNA glycosylase (TDG) was discovered as an enzyme that can initiate base excision repair at sites of 5-methylcytosine- or cytosine deamination in DNA by its ability to release thymine or uracil from G.T and G.U mismatches. Crystal structure analysis of an Escherichia coli homologue identified conserved amino acid residues that are critical for its substrate recognition/interaction and base hydrolysis functions. Guided by this revelation, we performed a mutational study of structure function relationships with the human TDG. Substitution of the postulated catalytic site asparagine with alanine (N140A) resulted in an enzyme that bound mismatched substrates but was unable to catalyze base removal. Mutation of Met-269 in a motif with a postulated role in protein-substrate interaction selectively inactivated stable binding of the enzyme to mismatched substrates but not so its glycosylase activity. These results establish that the structure function model postulated for the E. coli enzyme is largely applicable to the human TDG. We further provide evidence for G.U being the preferred substrate of TDG, not only at the mismatch recognition step of the reaction but also in base hydrolysis, and for the importance of stable complementary strand interactions by TDG to compensate for its comparably poor hydrolytic potential.
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Affiliation(s)
- U Hardeland
- Institute of Medical Radiobiology, University of Zürich and the Paul Scherrer Institute, August Forel Strasse 7, Zürich 8008, Switzerland
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50
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Affiliation(s)
- G P Pfeifer
- Department of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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