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Journal Cover   Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
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   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 0027-5107
   Published by Elsevier Homepage  [2586 journals]
  • Methods for comparing mutation rates using fluctuation assay data
    • Abstract: Publication date: Available online 9 April 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Qi Zheng
      Comparing microbial mutation rates via the fluctuation assay protocol is an important routine task in the laboratory. However, methods for the comparison of mutation rates are still scarce and not well understood. This paper proposes new methods to address this situation. First, it provides a likelihood ratio test. Second, it explores the use of confidence intervals that can be readily computed. Third, it uses simulations to assess the new and existing methods. Both the likelihood ratio test and the use of confidence intervals were found to be superior to the general-purpose Mann-Whitney test, while the t-test was found to be unsuitable for fluctuation assay data. In addition, the method based on confidence intervals is suitable for comparison of experiments in which the terminal cell population sizes differ.


      PubDate: 2015-04-12T11:29:06Z
       
  • A novel method for monitoring functional lesion-specific recruitment of
           repair proteins in live cells
    • Abstract: Publication date: Available online 4 April 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Jordan Woodrick , Suhani Gupta , Pooja Khatkar , Kalpana Dave , Darya Levashova , Sujata Choudhury , Hadi Elias , Tapas Saha , Susette Mueller , Rabindra Roy
      DNA–protein relationships have been studied by numerous methods, but a particular gap in methodology lies in the study of DNA adduct-specific interactions with proteins in vivo, which particularly affects the field of DNA repair. Using the repair of a well-characterized and ubiquitous adduct, the abasic (AP) site, as a model, we have developed a comprehensive method of monitoring DNA lesion-specific recruitment of proteins in vivo over time. We utilized a surrogate system in which a Cy3-labeled plasmid containing a single AP-site was transfected into cells, and the interaction of the labeled DNA with BER enzymes, including APE1, Polβ, LIG1, and FEN1, was monitored by immunofluorescent staining of the enzymes by Alexafluor-488-conjugated secondary antibody. The recruitment of enzymes was characterized by quantification of Cy3-Alexafluor-488 co-localization. To validate the microscopy-based method, repair of the transfected AP-site DNA was also quantified at various time points post-transfection using a real time PCR-based method. Notably, the recruitment time kinetics for each enzyme were consistent with AP-site repair time kinetics. This microscopy-based methodology is reliable in detecting the recruitment of proteins to specific DNA substrates and can be extended to study other in vivo DNA–protein relationships in any DNA sequence and in the context of any DNA structure in transfectable proliferating or quiescent cells. The method may be applied to a variety of disciplines of nucleic acid transaction pathways, including repair, replication, transcription, and recombination.


      PubDate: 2015-04-08T17:29:05Z
       
  • Controlled exposure to diesel exhaust and traffic noise – Effects on
           oxidative stress and activation in mononuclear blood cells
    • Abstract: Publication date: Available online 28 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Jette Gjerke Hemmingsen , Peter Møller , Kim Jantzen , Bo A.G. Jönsson , Maria Albin , Aneta Wierzbicka , Anders Gudmundsson , Steffen Loft , Jenny Rissler
      Particulate air pollution increases risk of cancer and cardiopulmonary disease, partly through oxidative stress. Traffic-related noise increases risk of cardiovascular disease and may cause oxidative stress. In this controlled random sequence study, 18 healthy subjects were exposed for 3h to diesel exhaust (DE) at 276μg/m3 from a passenger car or filtered air, with co-exposure to traffic noise at 48 or 75dB(A). Gene expression markers of inflammation, (interleukin-8 and tumor necrosis factor), oxidative stress (heme oxygenase (decycling-1)) and DNA repair (8-oxoguanine DNA glycosylase (OGG1)) were unaltered in peripheral blood mononuclear cells (PBMCs). No significant differences in DNA damage levels, measured by the comet assay, were observed after DE exposure, whereas exposure to high noise levels was associated with significantly increased levels of hOGG1-sensitive sites in PBMCs. Urinary levels of 8-oxo-7,8-dihydro-2′-deoxyguanosine were unaltered. In auxiliary ex vivo experiments whole blood was incubated with particles from the exposure chamber for 3h without effects on DNA damage in PBMCs or intracellular reactive oxygen species production and expression of CD11b and CD62L adhesion molecules in leukocyte subtypes. Conclusion 3-h exposure to DE caused no genotoxicity, oxidative stress or inflammation in PBMCs, whereas exposure to noise might cause oxidatively damaged DNA.


      PubDate: 2015-04-04T03:03:13Z
       
  • Effect of chronic low dose natural radiation in human peripheral blood
           mononuclear cells: Evaluation of DNA damage and repair using the alkaline
           comet assay
    • Abstract: Publication date: Available online 28 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): P.R. Vivek Kumar , M. Seshadri , G. Jaikrishan , Birajalaxmi Das
      This study investigates whether peripheral blood mononuclear cells (PBMCs) from inhabitants of Kerala in southwest India, exposed to chronic low dose natural radiation in vivo (>1mSvyear−1), respond with a radioadaptive response to a challenging dose of gamma radiation. Toward this goal, PBMCs isolated from 77 subjects from high-level natural radiation areas (HLNRA) and 37 subjects from a nearby normal level natural radiation area (NLNRA) were challenged with 2Gy and 4Gy gamma radiation. Subjects from HLNRA were classified based on the mean annual effective dose received, into low dose group (LDG) and high dose group (HDG) with mean annual effective doses of 2.69mSv (N =43, range 1.07mSvyear−1 to 5.55mSvyear−1) and 9.62mSv (N =34, range 6.07mSvyear−1 to17.41mSvyear−1), respectively. DNA strand breaks and repair kinetics (at 7min, 15min and 30min after 4Gy) were evaluated using the alkaline single cell gel electrophoresis (comet) assay. Initial levels of DNA strand breaks observed after either a 2Gy or a 4Gy challenging dose were significantly lower in subjects of the HDG from HLNRA compared to subjects of NLNRA (2Gy, P =0.01; 4Gy, P =0.02) and LDG (2Gy P =0.01; 4Gy, P =0.05). Subjects of HDG from HLNRA showed enhanced rejoining of DNA strand breaks (HDG/NLNRA, P =0.06) during the early stage of repair (within 7min). However at later times a similar rate of rejoining of strand breaks was observed across the groups (HDG, LDG and NLNRA). Preliminary results from our study suggest in vivo chronic low-level natural radiation provides an initial exposure that allows an adaption to a subsequent higher radiation exposure, perhaps through improving DNA repair via an unknown mechanism. Therefore, further investigations would be necessary in this population to understand the human biological and health effects of chronic low-level natural radiation exposures.


      PubDate: 2015-04-04T03:03:13Z
       
  • Paternal irradiation perturbs the expression of circadian genes in
           offspring
    • Abstract: Publication date: Available online 28 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Andre M.G.F. Gomes , Ruth C. Barber , Yuri E. Dubrova
      The circadian system represents a complex network which influences the timing of many biological processes. Recent studies have established that circadian alterations play an important role in the susceptibility to many human diseases, including cancer. Here we report that paternal irradiation in mice significantly affects the expression of genes involved in rhythmic processes in their first-generation offspring. Using microarrays, the patterns of gene expression were established for brain, kidney, liver and spleen samples from the non-exposed offspring of irradiated CBA/Ca and BALB/c male mice. The most over-represented categories among the genes differentially expressed in the offspring of control and irradiated males were those involved in rhythmic process, circadian rhythm and DNA-dependent regulation of transcription. The results of our study therefore provide a plausible explanation for the transgenerational effects of paternal irradiation, including increased transgenerational carcinogenesis described in other studies.


      PubDate: 2015-04-04T03:03:13Z
       
  • Age dynamics of DNA damage and CpG methylation in the peripheral blood
           leukocytes of mice
    • Abstract: Publication date: Available online 28 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Ilya Velegzhaninov , Vera Mezenceva , Olga Shostal , Ancha Baranova , Alexey Moskalev
      Certain types of DNA damage are known to accumulate with age. Here we present the quantitative data describing the extent of the spontaneous DNA damage in 144 SHK mice of various ages. In each animal, we assessed double strand breaks, single strand breaks and alkali-labile sites, as well as amounts of oxidized purines, oxidized pyrimidines and misincorporated uracils. In addition, overall levels of genome DNA methylation were evaluated. The amounts of oxidized pyrimidines were correlated with age in males only, while the amounts of double strand breaks (DSB) in DNA samples were correlated with age in females only (R =0.26; p <0.035). No age-related accumulation of single-strand breaks (SSB) was observed. The hypomethylation of DNA was significant in aging females, but not in aging males. Various types of DNA damage were correlated to each other. In attempt to develop more stable indicator of age-dependent alterations in DNA, the DNA Damage Level Differential (DDLD) indices was developed for comet assaying of peripheral blood leukocytes. As expected, DDLD index was shown to be better correlated with age than any single quantitative measure reflecting certain type of DNA damage. A variability of effectiveness of various kinds of DNA repair in individual animals was larger than expected. This conclusion may have a substantial impact on subsequent studies of the mutagens and other kinds of environmental stressors in animal populations. Nor DDLD neither individual quantitative measures of DNA damage were capable of prediction post-sampling survival time.


      PubDate: 2015-04-04T03:03:13Z
       
  • l-Carnitine supplementation decreases DNA damage in treated MSUD patients
    • Abstract: Publication date: Available online 28 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Caroline Paula Mescka , Gilian Guerreiro , Tatiane Hammerschmidt , Jéssica Faverzani , Daniella de Moura Coelho , Vanusa Mandredini , Carlos Alberto Yasin Wayhs , Moacir Wajner , Carlos Severo Dutra-Filho , Carmen Regla Vargas
      Maple syrup urine disease (MSUD) is an inherited disorder caused by severe deficient activity of the branched-chain α-keto acid dehydrogenase complex involved in the degradation pathway of branched-chain amino acids (BCAAs) and their α-ketoacid derivatives. MSUD patients generally present ketoacidosis, poor feeding, ataxia, coma, psychomotor delay, mental retardation and brain abnormalites. Treatment consists of dietary restriction of the BCAA (low protein intake) supplemented by a BCAA-free amino acid mixture. Although the mechanisms of brain damage in MSUD are poorly known, previous studies have shown that oxidative stress may be involved in the neuropathology of this disorder. In this regard, it was recently reported that MSUD patients have deficiency of l-carnitine (l-car), a compound with antioxidant properties that is used as adjuvant therapy in various inborn errors of metabolism. In this work, we investigated DNA damage determined by the alkaline comet assay in peripheral whole blood leukocytes of MSUD patients submitted to a BCAA-restricted diet supplemented or not with l-car. We observed a significant increase of DNA damage index (DI) in leukocytes from MSUD patients under BCAA-restricted diet as compared to controls and that l-car supplementation significantly decreased DNA DI levels. It was also found a positive correlation between DI and MDA content, a marker of lipid peroxidation, and an inverse correlation between DI and l-car levels. Taken together, our present results suggest a role for reactive species and the involvement of oxidative stress in DNA damage in this disorder. Since l-car reduced DNA damage, it is presumed that dietary supplementation of this compound may serve as an adjuvant therapeutic strategy for MSUD patients in addition to other therapies.


      PubDate: 2015-04-04T03:03:13Z
       
  • Single-molecule PCR analysis of an unstable microsatellite for detecting
           mutations in sperm of mice exposed to chemical mutagens
    • Abstract: Publication date: Available online 30 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Marc A. Beal , Andrea Rowan-Carroll , Caleigh Campbell , Andrew Williams , Christopher M. Somers , Francesco Marchetti , Carole L. Yauk
      Single-molecule PCR (SM-PCR) analysis of long and repetitive DNA sequences, known as expanded simple tandem repeats (ESTRs), has been the most efficient method for studying germline mutation induction in endogenous sequences to date. However, the long length of these sequences makes mutation detection imprecise and laborious, and they have been characterized only in mice. Here, we explore the use of unstable microsatellite sequences that can be typed with high precision by capillary electrophoresis as alternative loci for detecting germline mutations. We screened 24 microsatellite loci across inbred mouse strains and identified Mm2.2.1 as the most polymorphic microsatellite locus. We then optimized SM-PCR of Mm2.2.1 to detect mutations in sperm. SM-PCR analysis of sperm from untreated B6C3F1 and Muta™Mouse samples revealed mutation frequencies that are consistent with rates derived from family pedigree analysis (∼5×10−3). To determine whether this locus can be used to detect chemically induced germline mutations, Muta™Mouse males were exposed by oral gavage to a single dose of 100mg/kg of N-ethyl-N-nitrosourea (ENU) or to 100mg/kg of benzo(a)pyrene (BaP) for 28 days alongside vehicle treated controls. Sperm were collected 10 weeks post-ENU exposure to sample sperm exposed as spermatogonial stem cells and 6 weeks post-BaP exposure to sample sperm that were dividing spermatogonia when the exposure was terminated. Both treatments resulted in a significant (approximately 2-fold) increase in mutation frequency in sperm compared to the control animals. The work establishes the utility of this microsatellite for studying mutation induction in the germ cells of mice. Because microsatellites are found in virtually every species, this approach holds promise for other organisms, including humans.


      PubDate: 2015-04-04T03:03:13Z
       
  • Electrophysiologic and Cellular Characteristics of Cardiomyocytes after
           X-ray Irradiation
    • Abstract: Publication date: Available online 4 April 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Johannes L. Frieß , Anja Heselich , Sylvia Ritter , Angelina Haber , Nicole Kaiser , Paul G. Layer , Christiane Thielemann
      The aim of this study was to investigate possible effects of ionizing irradiation on the electrophysiological functionality of cardiac myocytes in vitro. Primary chicken cardiomyocytes with spontaneous beating activity were irradiated with X-ray s (dose range of 0.5 to 7 Gy). Functional alterations of cardiac cell cultures were evaluated up to 7 days after irradiation using microelectrode arrays. As examined endpoints, cell proliferation, apoptosis, reactive oxygen species (ROS) and DNA damage were evaluated. The beat rate of the cardiac networks increased in a dose-dependent manner over one week. The duration of the single action potentials was slightly shortened. Additionally, we observed lower numbers of mitotic and S-phase cells at certain time points after irradiation. Also, the number of cells with γH2AX foci increased as a function of the dose. No significant changes in the level of ROS were detected. Induction of apoptosis was generally negligibly low. This is the first report to directly show alterations in cardiac electrophysiology caused by ionizing radiation, which were detectable up to one week after irradiation.


      PubDate: 2015-04-04T03:03:13Z
       
  • TITLE PAGE (EDI BOARD)
    • Abstract: Publication date: January 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 771




      PubDate: 2015-03-19T01:30:26Z
       
  • The impact of base excision DNA repair in age-related neurodegenerative
           diseases
    • Abstract: Publication date: Available online 4 January 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Giovana S. Leandro , Peter Sykora , Vilhelm A. Bohr
      The aging process and several age-related neurodegenerative disorders have been linked to elevated levels of DNA damage induced by ROS and deficiency in DNA repair mechanisms. DNA damage induced by ROS is a byproduct of cellular respiration and accumulation of damage over time, is a fundamental aspect of a main theory of aging. Mitochondria have a pivotal role in generating cellular oxidative stress, and mitochondrial dysfunction has been associated with several diseases. DNA base excision repair is considered the major pathway for repair of oxidized bases in DNA both in the nuclei and in mitochondria, and in neurons this mechanism is particularly important because non-diving cells have limited back-up DNA repair mechanisms. An association between elevated oxidative stress and a decrease in BER is strongly related to the aging process and has special relevance in age-related neurodegenerative diseases. Here, we review the role of DNA repair in aging, focusing on the implications of the DNA base excision repair pathways and how alterations in expression of these DNA repair proteins are related to the aging process and to age-related neurodegenerative diseases.


      PubDate: 2015-03-19T01:30:26Z
       
  • Genome instability biomarkers and blood micronutrient risk profiles
           associated with mild cognitive impairment and Alzheimer's disease
    • Abstract: Publication date: Available online 16 January 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Sau Lai Lee , Philip Thomas , Michael Fenech
      Successful maintenance of metabolic systems relating to accurate DNA replication and repair is critical for optimal lifelong human health. Should this homeostatic balance become impaired, genomic instability events can arise, compromising the integrity of the genome, which may result in gene expression and human disease. Both genome instability and micronutrient imbalance have been identified and implicated in diseases associated with accelerated ageing which potentially leads to an increased risk for the future development of clinically defined neurodegenerative disorders. Cognitive decline leading to the clinical diagnosis of mild cognitive impairment (MCI) has been shown to predict an increased risk in later life of developing Alzheimer's disease (AD). Knowledge on the impact of dietary factors in relation to MCI and AD risk is improving but incomplete; in particular the role of nutrient combinations (i.e. nutriomes) has not been thoroughly investigated. Currently, there is a need for preventative strategies as well as the identification of robust and reproducible diagnostic biomarkers that will allow identification of those individuals with increased risk for neurodegenerative diseases. Growing evidence suggests cells originating from different somatic tissues derived from individuals that have been clinically diagnosed with neurodegenerative disorders exhibit elevated frequencies of DNA damage compared to tissues of cognitively normal individuals which could be due to malnutrition. The objective of this review is to discuss current evidence and identify knowledge gaps relating to genome instability biomarkers and blood micronutrient profiles from human studies of MCI and AD that may be specific to and contribute to the increased risk of these diseases. This is a vital step in order to create research strategies for the future development of diagnostics that are indicative of dementia risk and to inform preventative therapies.


      PubDate: 2015-03-19T01:30:26Z
       
  • Effects of post mortem interval and gender in DNA base excision repair
           activities in rat brains
    • Abstract: Publication date: Available online 19 January 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Daniela Tathiana Soltys , Carolina Parga Martins Pereira , Gabriela Naomi Ishibe , Nadja Cristhina de Souza-Pinto
      Most human tissues used in research are of post mortem origin. This is the case for all brain samples, and due to the difficulty in obtaining a good number of samples, especially in the case of neurodegenerative diseases, male and female samples are often included in the same experimental group. However, the effects of post mortem interval (PMI) and gender differences in the endpoints being analyzed are not always fully understood, as is the case for DNA repair activities. To investigate these effects, in a controlled genetic background, base excision repair (BER) activities were measured in protein extracts obtained from Wistar rat brains from different genders and defined PMI up to 24hours, using a novel fluorescent-based in vitro incision assay. Uracil and AP-site incision activity in nuclear and mitochondrial extracts were similar in all groups included in this study. Our results show that gender and PMI up to 24hours have no influence in the activities of the BER proteins UDG and APE1 in rat brains. These findings demonstrate that these variables do not interfere on the BER activities included in these study, and provide a security window to work with UDG and APE1 proteins in samples of post mortem origin.


      PubDate: 2015-03-19T01:30:26Z
       
  • Damaged DNA-binding protein down-regulates epigenetic mark H3K56Ac through
           histone deacetylase 1 and 2
    • Abstract: Publication date: Available online 24 January 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Qianzheng Zhu , Aruna Battu , Alo Ray , Gulzar Wani , Jiang Qian , Jinshan He , Qi-en Wang , Altaf A. Wani
      Acetylated histone H3 lysine 56 (H3K56Ac) is one of the reversible histone post-translational modifications (PTMs) responsive to DNA damage. We previously described a biphasic decrease and increase of epigenetic mark H3K56Ac in response to ultraviolet radiation (UVR)-induced DNA damage. Here, we report a new function of UV damaged DNA-binding protein (DDB) in deacetylation of H3K56Ac through specific histone deacetylases (HDACs). We show that simultaneous depletion of HDAC1/2 compromises the deacetylation of H3K56Ac, while depletion of HDAC1 or HDAC2 alone has no effect on H3K56Ac. The H3K56Ac deacetylation does not require functional nucleotide excision repair (NER) factors XPA and XPC, but depends on the function of upstream factors DDB1 and DDB2. UVR enhances the association of DDB2 with HDAC1 and, enforced DDB2 expression leads to translocation of HDAC1 to UVR-damaged chromatin. HDAC1 and HDAC2 are recruited to UVR-induced DNA damage spots, which are visualized by anti-XPC immunofluorescence. Dual HDAC1/2 depletion decreases XPC ubiquitination, but does not affect the recruitment of DDB2 to DNA damage. By contrast, the local accumulation of γH2AX at UVR-induced DNA damage spots was compromised upon HDAC1 as well as dual HDAC1/2 depletions. Additionally, UVR-induced ATM activation decreased in H12899 cells expressing H3K56Ac-mimicing H3K56Q. These results revealed a novel role of DDB in H3K56Ac deacetylation during early step of NER and the existence of active functional cross-talk between DDB-mediated damage recognition and H3K56Ac deacetylation.


      PubDate: 2015-03-19T01:30:26Z
       
  • Gene polymorphisms and increased DNA damage in morbidly obese women
    • Abstract: Publication date: Available online 22 January 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): B.C.O. Luperini , D.C. Almeida , M.P. Porto , J.P.C. Marcondes , R.P. Prado , I. Rasera , M.R.M. Oliveira , D.M.F. Salvadori
      Obesity is characterized by increased adipose tissue mass resulting from a chronic imbalance between energy intake and expenditure. Furthermore, there is a clearly defined relationship among fat mass expansion, chronic low-grade systemic inflammation and reactive oxygen species (ROS) generation; leading to ROS-related pathological events. In the past years, genome-wide association studies have generated convincing evidence associating genetic variation at multiple regions of the genome with traits that reflect obesity. Therefore, the present study aimed to evaluate the relationships among the gene polymorphisms ghrelin (GHRL–rs26802), ghrelin receptor (GHSR–rs572169), leptin (LEP–rs7799039), leptin receptor (LEPR–rs1137101) and fat mass and obesity-associated (FTO–rs9939609) and obesity. The relationships among these gene variants and the amount of DNA damage were also investigated. Three hundred Caucasian morbidly obese and 300 eutrophic (controls) women were recruited. In summary, the results demonstrated that the frequencies of the GHRL, GHSR, LEP and LEPR polymorphisms were not different between Brazilian white morbidly obese and eutrophic women. Exceptions were the AA-FTO genotype and allele A, which were significantly more frequent in obese women than in the controls (0.23% vs. 0.10%; 0.46 vs. 0.36, respectively), and the TT-FTO genotype and the T allele, which were less frequent in morbidly obese women (p <0.01). Furthermore, significant differences in the amount of genetic lesions associated with FTO variants were observed only in obese women. In conclusion, this study demonstrated that the analyzed SNPs were not closely associated with morbid obesity, suggesting they are not the major contributors to obesity. Therefore, our data indicated that these gene variants are not good biomarkers for predicting risk susceptibility for obesity, whereas ROS generated by the inflammatory status might be one of the causes of DNA damage in obese women, favoring genetically related diseases as obesity comorbidities.


      PubDate: 2015-03-19T01:30:26Z
       
  • An epigenomic role of Fe65 in the cellular response to DNA damage
    • Abstract: Publication date: Available online 27 January 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Seungjin Ryu , Francesca Teles , Giuseppina Minopoli , Tommaso Russo , Michael G. Rosenfeld , Yousin Suh
      Previous findings describe Fe65 as a key protein in the cellular response to genotoxic stress. However, the precise molecular mechanism by which Fe65 contributes to DNA damage signaling remains unclear. In this study, we hypothesized that the transcriptional activity of Fe65 may contribute to DNA damage pathways by regulating gene expression patterns activated in response to genotoxic stress. To address this hypothesis, we mapped the global binding profile of Fe65 by chromatin immunoprecipitation (ChIP)-sequencing in the SK-N-SH cells exposed to genotoxic stress. Unexpectedly, the genome-wide location analysis showed a substantial enrichment of Fe65 in the promoter regions of coding genes linked to DNA damage signaling pathways. To further investigate the role of Fe65 in the transcriptional regulation of putative coding target genes identified by ChIP-seq, we performed microarray assays using wild-type (WT) or Fe65 deficient mouse embryonic fibroblasts (MEFs) exposed to oxidative stress with multiple recovery times. Gene ontology analysis of the Fe65-depedent transcriptome suggested that Fe65 modulates the expression of genes critical for DNA damage response. Motif enrichment analysis of regulatory regions occupied by Fe65 revealed a strong correlation with key transcription factors involved in DNA damage signaling pathways, including E2F1, p53, and Jun. Comparison of ChIP-sequencing results with microarray results ultimately identified 248 Fe65-depedent target genes, the majority of which were known regulators of cell cycle, cell death, and DNA replication and repair pathways. We validated the target genes identified by in silico analysis by qPCR experiments. Collectively, our results provide strong evidence that Fe65 plays a role in DNA damage response and cell viability by epigenomic regulation of specific transcriptional programs activated upon genotoxic stress.


      PubDate: 2015-03-19T01:30:26Z
       
  • Caenorhabditis elegans EXO-3 contributes to longevity and reproduction:
           Differential roles in somatic cells and germ cells
    • Abstract: Publication date: February 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 772
      Author(s): Yuichi Kato , Takahito Moriwaki , Masafumi Funakoshi , Qiu-Mei Zhang-Akiyama
      Apurinic/apyrimidinic (AP) sites are the major DNA damage generated continuously even under normal conditions, and inhibit DNA replication/transcription. AP endonucleases are ubiquitous enzymes required for the repair of AP sites and 3′ blocking ends, but their physiological roles in multicellular organisms are not fully understood. In this study, we investigated how an AP endonuclease functions in a multicellular organism (Caenorhabditis elegans (C. elegans)). EXO-3 is one of the AP endonucleases in C. elegans. Using an exo-3 mutant worm, we found that deletion of the exo-3 gene caused shortened lifespan in an ung-1-dependent manner. UNG-1 is a uracil DNA glycosylase in C. elegans, and the present finding suggested that UNG-1 is the major producer of AP sites that affects lifespan, and EXO-3 contributes to longevity by completing the repair of uracil. Next we found that the exo-3 gene was abundantly expressed in the gonads, and AP sites in the gonad were efficiently repaired, suggesting that EXO-3 functioned particularly in the gonad. Deletion of the exo-3 gene resulted in a significant decrease in self-brood size. This was rescued by deficiency of NTH-1, which is a bifunctional DNA glycosylase in C. elegans that recognizes oxidative base damage. This result suggested that the major substrate of EXO-3 in the gonad was 3′ blocking end generated by NTH-1, and that EXO-3 played an important role in reproduction. A contribution of EXO-3 to reproduction was also suggested by our finding here that the decrease of self-brood size of the exo-3 mutant became more marked when worms were treated with methyl methanesulfonate (MMS) and sodium bisulfite (NaHSO3). This study demonstrated differential roles of EXO-3 in somatic cells and germ cells.


      PubDate: 2015-03-19T01:30:26Z
       
  • The non-targeted effects of radiation are perpetuated by exosomes
    • Abstract: Publication date: February 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 772
      Author(s): Ammar Al-Mayah , Scott Bright , Kim Chapman , Sarah Irons , Ping Luo , David Carter , Edwin Goodwin , Munira Kadhim
      Exosomes contain cargo material from endosomes, cytosol, plasma membrane and microRNA molecules, they are released by a number of non-cancer and cancer cells into both the extracellular microenvironment and body fluids such as blood plasma. Recently we demonstrated radiation-induced non-targeted effects [NTE: genomic instability (GI) and bystander effects (BE)] are partially mediated by exosomes, particularly the RNA content. However the mechanistic role of exosomes in NTE is yet to be fully understood. The present study used MCF7 cells to characterise the longevity of exosome-induced activity in the progeny of irradiated and unirradiated bystander cells. Exosomes extracted from conditioned media of irradiated and bystander progeny were added to unirradiated cells. Analysis was carried out at 1 and 20/24 population doublings following medium/exosome transfer for DNA/chromosomal damage. Results confirmed exosomes play a significant role in mediating NTE of ionising radiation (IR). This effect was remarkably persistent, observed >20 doublings post-irradiation in the progeny of bystander cells. Additionally, cell progeny undergoing a BE were themselves capable of inducing BE in other cells via exosomes they released. Furthermore we investigated the role of exosome cargo. Culture media from cells exposed to 2Gy X-rays was subjected to ultracentrifugation and four inoculants prepared, (a) supernatants with exosomes removed, and pellets with (b) exosome proteins denatured, (c) RNA degraded, and (d) a combination of protein–RNA inactivation. These were added to separate populations of unirradiated cells. The BE was partially inhibited when either exosome protein or exosome RNA were inactivated separately, whilst combined RNA–protein inhibition significantly reduced or eliminated the BE. These results demonstrate that exosomes are associated with long-lived signalling of the NTE of IR. Both RNA and protein molecules of exosomes work in a synergistic manner to initiate NTE, spread these effects to naïve cells, and perpetuate GI in the affected cells.


      PubDate: 2015-03-19T01:30:26Z
       
  • Anxious phenotypes plus environmental stressors are related to brain DNA
           damage and changes in NMDA receptor subunits and glutamate uptake
    • Abstract: Publication date: February 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 772
      Author(s): Gislaine Z. Réus , Helena M. Abaleira , Monique Michels , Débora B. Tomaz , Maria Augusta B. dos Santos , Anelise S. Carlessi , Beatriz I. Matias , Daniela D. Leffa , Adriani P. Damiani , Vitor de C. Gomes , Vanessa M. Andrade , Felipe Dal-Pizzol , Jesus Landeira-Fernadez , João Quevedo
      This study aimed at investigating the effects of chronic mild stress on DNA damage, NMDA receptor subunits and glutamate transport levels in the brains of rats with an anxious phenotype, which were selected to represent both the high-freezing (CHF) and low-freezing (CLF) lines. The anxious phenotype induced DNA damage in the hippocampus, amygdala and nucleus accumbens (NAc). CHF rats subjected to chronic stress presented a more pronounced DNA damage in the hippocampus and NAc. NMDAR1 were increased in the prefrontal cortex (PC), hippocampus and amygdala of CHF, and decreased in the hippocampus, amygdala and NAc of CHF stressed. NMDAR2A were decreased in the amygdala of the CHF and stressed; and increased in CHF stressed. NMDRA2A in the NAc was increased after stress, and decreased in the CLF. NMDAR2B were increased in the hippocampus of CLF and CHF. In the amygdala, there was a decrease in the NMDAR2B for stress in the CLF and CHF. NMDAR2B in the NAc were decreased for stress and increased in the CHF; in the PC NMDAR2B increased in the CHF. EAAT1 increased in the PC of CLF+stress. In the hippocampus, EAAT1 decreased in all groups. In the amygdala, EAAT1 decreased in the CLF+stress and CHF. EAAT2 were decreased in the PC for stress, and increased in CHF+control. In the hippocampus, the EAAT2 were increased for the CLF and decreased in the CLF+stress. In the amygdala, there was a decrease in the EATT2 in the CLF+stress and CHF. These findings suggest that an anxious phenotype plus stress may induce a more pronounced DNA damage, and promote more alterations in the glutamatergic system. These findings may help to explain, at least in part, the common point of the mechanisms involved with the pathophysiology of depression and anxiety.


      PubDate: 2015-03-19T01:30:26Z
       
  • SirT1 knockdown potentiates radiation-induced bystander effect through
           promoting c-Myc activity and thus facilitating ROS accumulation
    • Abstract: Publication date: February 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 772
      Author(s): Yuexia Xie , Wenzhi Tu , Jianghong Zhang , Mingyuan He , Shuang Ye , Chen Dong , Chunlin Shao
      Radiation-induced bystander effect (RIBE) has important implications for secondary cancer risk assessment during cancer radiotherapy, but the bystander signaling processes, especially under hypoxic condition, are still largely unclear. The present study found that micronuclei (MN) formation could be induced in the non-irradiated HL-7702 hepatocyte cells after being treated with the conditioned medium from irradiated hepatoma HepG2 and SK-Hep-1 cells under either normoxia or hypoxia. This bystander response was dramatically diminished or enhanced when the SirT1 gene of irradiated hepatoma cells was overexpressed or knocked down, respectively, especially under hypoxia. Meanwhile, SirT1 knockdown promoted transcriptional activity for c-Myc and facilitated ROS accumulation. But both of the increased bystander responses and ROS generation due to SirT1-knockdown were almost completely suppressed by c-Myc interference. Moreover, ROS scavenger effectively abolished the RIBE triggered by irradiated hepatoma cells even with SirT1 depletion. These findings provide new insights that SirT1 has a profound role in regulating RIBE where a c-Myc-dependent release of ROS may be involved.


      PubDate: 2015-03-19T01:30:26Z
       
  • Association of polymorphisms in long non-coding RNA H19 with coronary
           artery disease risk in a Chinese population
    • Abstract: Publication date: February 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 772
      Author(s): Wei Gao , Meng Zhu , Hao Wang , Shan Zhao , Di Zhao , Yang Yang , Ze-Mu Wang , Fang Wang , Zhi-Jian Yang , Xiang Lu , Lian-Sheng Wang
      H19 is an imprinted gene transcribing a long non-coding RNA and is downregulated postnatally. Re-expression of H19 has been observed in patients with atherosclerosis. However, to date, no data has been published on the association of H19 polymorphisms with the risk of coronary artery disease (CAD). In this study, four polymorphisms, rs217727, rs2067051, rs2251375, rs4929984, were analyzed in 701 CAD patients and 873 age- and sex-matched control subjects. Polymorphisms were genotyped by TaqMan technology. Our data showed that the T variant of rs217727 was associated with an increased risk of CAD [additive model: odds ratio (OR)=2.05, 95%CI=1.35–3.12; dominant model: OR=1.46, 95% confidence interval (CI)=1.12–1.90; recessive model: OR=1.75, 95%CI=1.18–2.58], while A variant of rs2067051 was associated with a decreased risk of CAD (additive model: OR=0.66, 95%CI=0.45–0.96; recessive model: OR=0.71, 95%CI=0.50–0.99). Combined analysis showed that subjects carrying 3 or 4 risk alleles had a significantly increased risk of CAD, relative to those with 0–2 risk alleles (OR=1.61, 95%CI=1.20–2.15). Moreover, CAD patients with 3 or 4 risk alleles also had significantly higher Gensini scores than those with 0–2 risk alleles (P =0.001). Further haplotype-based analysis revealed that individuals with C-G-C-C, T-G-A-A, and T-A-A-A haplotypes indicated a higher prevalence of CAD (OR=1.88, 95%CI=1.03–3.43; OR=2.26, 95%CI=1.19–4.31; OR=2.66, 95%CI=1.34–5.25, respectively), compared to individuals with the most common C-G-A-C haplotype. In conclusion, our study demonstrates for the first time that common polymorphisms of H19 are associated with the risk and severity of CAD in a Chinese population. Future studies are needed to explore the underlying mechanisms of our findings.


      PubDate: 2015-03-19T01:30:26Z
       
  • Further acatalasemia mutations in human patients from Hungary with
           diabetes and microcytic anemia
    • Abstract: Publication date: February 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 772
      Author(s): Terez Nagy , Erika Paszti , Miklos Kaplar , Harjit Pal Bhattoa , Laszlo Goth
      In blood, the hydrogen peroxide concentration is regulated by catalase. Decreased activity of catalase may lead to increased hydrogen peroxide concentration, which may contribute to the manifestation of age-related disease. The aim of this study is to examine association of decreased blood catalase activity and catalase exon mutations in patients (n =617) with diabetes (n =380), microcytic anemia (n =58), beta-thalassemia (n =43) and presbycusis (n =136) and in controls (n =295). Overall, 51 patients (8.3%) had less than half of normal blood catalase activity. Their genomic DNA was used for mutation screening of all exons and exon/intron boundaries with polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and PCR-heteroduplex analyses, and mutations were verified with nucleotide sequencing. Seven patients (type 2 diabetes (n =3), gestational diabetes (n =1), microcytic anemia (n =2)) had four novel catalase exon mutations namely, c.106_107insC, p.G36Afs*5(n =3, Hungarian type G1), c.379C>T, p.R127Y (n =2, Hungarian type H1), c.390T>C, p.R129L, (n =1, Hungarian type H2) and c.431A>T, p.N143V (n =1, Hungarian type H3). In patients with decreased blood catalase, the incidence of acatalasemia mutations was significantly high (P <0.0002) in microcytic anemia, type 2 and gestational diabetes. The four novel mutations were probably responsible for low blood catalase activity in 7/51 patients. In the remainder of the cases, other polymorphisms and epigenetic/regulatory factors may be involved.


      PubDate: 2015-03-19T01:30:26Z
       
  • Publisher's Note
    • Abstract: Publication date: February 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 772




      PubDate: 2015-03-19T01:30:26Z
       
  • Editorial
    • Abstract: Publication date: February 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 772
      Author(s): Jan Vijg



      PubDate: 2015-03-19T01:30:26Z
       
  • Genomic and post-genomic effects of anti-glaucoma drugs preservatives in
           trabecular meshwork
    • Abstract: Publication date: February 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 772
      Author(s): Alberto Izzotti , Sebastiano La Maestra , Rosanna Tindara Micale , Maria Grazia Longobardi , Sergio Claudio Saccà
      Oxidative stress plays an important role in glaucoma. Some preservatives of anti-glaucoma drugs, commonly used in glaucoma therapy, can prevent or induce oxidative stress in the trabecular meshwork. The aim of this study is to evaluate cellular and molecular damage induced in trabecular meshwork by preservatives contained in anti-glaucoma drugs. Cell viability (MTT test), DNA fragmentation (Comet test), oxidative DNA damage (8-oxo-dG), and gene expression (cDNA microarray) have been evaluated in trabecular meshwork specimens and in human trabecular meshwork cells treated with benzalkonium chloride, polyQuad, purite, and sofzia-like mixture. Moreover, antimicrobial effectiveness and safety of preservative contents in drugs was tested. In ex vivo experiments, benzalkonium chloride and polyQuad induced high level of DNA damage in trabecular meshwork specimens, while the effect of purite and sofzia were more attenuated. The level of DNA fragmentation induced by benzalkonium chloride was 2.4-fold higher in subjects older than 50 years than in younger subjects. Benzalkonium chloride, and polyQuad significantly increased oxidative DNA damage as compared to sham-treated specimens. Gene expression was altered by benzalkonium chloride, polyQuad, and purite but not by sofzia. In in vitro experiments, benzalkonium chloride and polyQuad dramatically decreased trabecular meshwork cell viability, increased DNA fragmentation, and altered gene expression. A lesser effect was also exerted by purite and sofzia. Genes targeted by these alterations included Fas and effector caspase-3. The efficacy of the preservatives in inhibiting bacterial growth increased the adverse effects in trabecular meshwork in terms of DNA damage and alteration of gene expression. Presented data indicates the delicate balance between efficacy and safety of drug preservatives as not yet optimized.


      PubDate: 2015-03-19T01:30:26Z
       
  • Assessment of DNA damage and mRNA/miRNA transcriptional expression
           profiles in hyperglycemic versus non-hyperglycemic patients with type 2
           diabetes mellitus
    • Abstract: Publication date: Available online 9 February 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Danilo J. Xavier , Paula Takahashi , Adriane F. Evangelista , Maria C. Foss-Freitas , Milton C. Foss , Eduardo A. Donadi , Geraldo A. Passos , Elza T. Sakamoto-Hojo
      The development of type 2 diabetes mellitus (T2D) is associated with a number of genetic and environmental factors. Hyperglycemia, a T2D hallmark, is related to several metabolic complications, comorbidities and increased DNA damage. However, the molecular alterations of a proper glucose control are still unclarified. In this study, we aimed to evaluate DNA damage (comet assay), as well as to compare the transcriptional expression (mRNA and miRNA analyzed by the microarray technique) displayed by peripheral blood mononuclear cells (PBMCs) from three distinct groups: hyperglycemic T2D patients (T2D-H, n =14), non-hyperglycemic T2D patients (T2D-N, n =15), and healthy non-diabetic individuals (n =16). The comet assay revealed significantly (p <0.05) higher levels of DNA damage in T2D-H group compared to both T2D-N and control groups, while a significant difference was not observed between the control and T2D-N groups. After bioinformatics analysis, the differentially expressed mRNAs were subjected to functional enrichment analysis (DAVID) and inflammatory response was among the enriched terms found when comparing T2D-N with controls and T2D-H with T2D-N. Concerning the gene set enrichment and gene set analyses, among the differentially expressed gene sets, three were of interest: regulation of DNA repair (T2D-H versus T2D-N), superoxide response (T2D-H versus control group), and response to endoplasmic reticulum stress (T2D-H versus control group). We also identified miRNAs related with T2D and hyperglycemia not yet associated with these conditions in the literature. Some of the differentially expressed mRNAs were among the predicted targets of the differentially expressed miRNAs. Our results showed the association of hyperglycemia with increased DNA damage and aberrant expression of miRNAs and genes related to several biological processes, such as inflammation, DNA repair, ROS production and antioxidant defense, highlighting the importance of proper glycemic control. Moreover, the transcriptional expression of miRNAs provided novel information for understanding the regulatory mechanisms involved in the T2D progression.


      PubDate: 2015-03-19T01:30:26Z
       
  • TITLE PAGE (EDI BOARD)
    • Abstract: Publication date: February 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 772




      PubDate: 2015-03-19T01:30:26Z
       
  • The impact of chronic Aflatoxin B1 exposure and p53 genotype on base
           excision repair in mouse lung and liver
    • Abstract: Publication date: March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 773
      Author(s): Jeanne E. Mulder , Genevieve S. Bondy , Rekha Mehta , Thomas E. Massey
      Aflatoxin B1 (AFB1) is produced by species of Aspergillus, and is a known human carcinogen. AFB1-induced oxidative DNA damage, specifically 8-hydroxy-2-deoxyguanosine (8-OHdG) lesions, has been demonstrated in both animal models and in humans, and is repaired by base excision repair (BER). The tumour suppressor gene p53 is implicated in the regulation of DNA repair, and heterozygous p53 knockouts have an attenuated nucleotide excision repair response to AFB1. Male heterozygous p53 knockout mice and their wild-type controls were exposed to 0, 0.2 or 1.0ppm AFB1 for 26 weeks in their diet. BER activity of lung and liver was assessed with an in vitro assay, using 8-OHdG-damaged plasmid DNA as a substrate. BER activity did not differ between livers or lungs from untreated wild-type versus heterozygous p53 knockout mice. In wild-type mice, repair was 65% lower in liver extracts from mice exposed to 1.0ppm AFB1 than in liver extracts from mice exposed to 0.2ppm AFB1 (p <0.05), but not significantly lower than that in liver extracts from control mice. AFB1 did not affect BER in lung extracts from wild-type mice, or in lung and liver extracts from heterozygous p53 knockout mice. In liver and lung, AFB1 exposure did not alter levels of 8-oxoguanine glycosylase protein, a key enzyme in the repair of 8-OHdG, and did not cause hepatotoxicity, as indicated by plasma alanine aminotransferase levels. In conclusion, chronic exposure to AFB1 did not affect BER in lungs or livers of heterozygous p53 knockout mice. BER activity was lower in livers from p53 wild type mice exposed to 1.0ppm AFB1 versus those exposed to 0.2ppm AFB1, an effect that was not attributable to liver cell death or altered levels of 8-oxoguanine glycosylase.


      PubDate: 2015-03-19T01:30:26Z
       
  • Target irradiation induced bystander effects between stem-like and non
           stem-like cancer cells
    • Abstract: Publication date: March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 773
      Author(s): Yu Liu , Alisa Kobayashi , Takeshi Maeda , Qibin Fu , Masakazu Oikawa , Gen Yang , Teruaki Konishi , Yukio Uchihori , Tom K. Hei , Yugang Wang
      Tumors are heterogeneous in nature and consist of multiple cell types. Among them, cancer stem-like cells (CSCs) are suggested to be the principal cause of tumor metastasis, resistance and recurrence. Therefore, understanding the behavior of CSCs in direct and indirect irradiations is crucial for clinical radiotherapy. Here, the CSCs and their counterpart non stem-like cancer cells (NSCCs) in human HT1080 fibrosarcoma cell line were sorted and labeled, then the two cell subtypes were mixed together and chosen separately to be irradiated via a proton microbeam. The radiation-induced bystander effect (RIBE) between the CSCs and NSCCs was measured by imaging 53BP1 foci, a widely used indicator for DNA double strand break (DSB). CSCs were found to be less active than NSCCs in both the generation and the response of bystander signals. Moreover, the nitric oxide (NO) scavenger c-PTIO can effectively alleviate the bystander effect in bystander NSCCs but not in bystander CSCs, indicating a difference of the two cell subtypes in NO signal response. To our knowledge, this is the first report shedding light on the RIBE between CSCs and NSCCs, which might contribute to a further understanding of the out-of-field effect in cancer radiotherapy.


      PubDate: 2015-03-19T01:30:26Z
       
  • Dynamic alteration in H3 serine 10 phosphorylation is G1-phase specific
           during ionization radiation induced DNA damage response in human cells
    • Abstract: Publication date: March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 773
      Author(s): Ajit K. Sharma , Saikat Bhattacharya , Shafqat A. Khan , Bharat Khade , Sanjay Gupta
      Chromatin acts as a natural barrier in DNA-damage recognition and repair. Histones undergo differential post-translational modification(s) to facilitate DNA damage response (DDR). Importance of modifications like phosphorylation of histone variant H2A.X in DNA repair is very well understood, however, ambiguous results exist in literature regarding the levels of certain histone modifications and their possible role in repair. In the present study, we have investigated in depth the alteration in the level of the highly dynamic histone mark H3S10P as it plays a dual role in different phases of the cell cycle. We show here that H3S10P decreases specifically from irradiated G1-enriched cells irrespective of the damaging agent or the cell line used in the study. Interestingly, the loss occurs predominantly from H3.3 variant which is a transcription activation mark like H3S10P itself, suggesting that the alteration might be implicated in transcription repression. The decrease in other transcription marks like H3K9Ac, H3K14Ac, H3K56Ac and H3S28P along with the occurrence of chromatin condensation in response to DNA damage in G1 phase strengthens the hypothesis. In addition, the alteration in the level of H3S10P shows an inverse correlation with that of γH2AX in a dose-dependent manner and probably occurs from the same mononucleosome. We propose that the drop in the levels of histone H3S10 phosphorylation is a universal phenomenon in response to DNA damage and is a trigger to induce transcription repressive state to facilitate repair.


      PubDate: 2015-03-19T01:30:26Z
       
  • Kinetoplast adaptations in American strains from Trypanosoma vivax
    • Abstract: Publication date: March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 773
      Author(s): Gonzalo Greif , Matías Rodriguez , Armando Reyna-Bello , Carlos Robello , Fernando Alvarez-Valin
      The mitochondrion role changes during the digenetic life cycle of African trypanosomes. Owing to the low abundance of glucose in the insect vector (tsetse flies) the parasites are dependent upon a fully functional mitochondrion, capable of performing oxidative phosphorylation. Nevertheless, inside the mammalian host (bloodstream forms), which is rich in nutrients, parasite proliferation relies on glycolysis, and the mitochondrion is partially redundant. In this work we perform a comparative study of the mitochondrial genome (kinetoplast) in different strains of Trypanosoma vivax. The comparison was conducted between a West African strain that goes through a complete life cycle and two American strains that are mechanically transmitted (by different vectors) and remain as bloodstream forms only. It was found that while the African strain has a complete and apparently fully functional kinetoplast, the American T. vivax strains have undergone a drastic process of mitochondrial genome degradation, in spite of the recent introduction of these parasites in America. Many of their genes exhibit different types of mutations that are disruptive of function such as major deletions, frameshift causing indels and missense mutations. Moreover, all but three genes (A6-ATPase, RPS12 and MURF2) are not edited in the American strains, whereas editing takes place normally in all (editable) genes from the African strain. Two of these genes, A6-ATPase and RPS12, are known to play an essential function during bloodstream stage. Analysis of the minicircle population shows that its diversity has been greatly reduced, remaining mostly those minicircles that carry guide RNAs necessary for the editing of A6-ATPase and RPS12. The fact that these two genes remain functioning normally, as opposed to that reported in Trypanosoma brucei-like trypanosomes that restrict their life cycle to the bloodstream forms, along with other differences, is indicative that the American T. vivax strains are following a novel evolutionary pathway.


      PubDate: 2015-03-19T01:30:26Z
       
  • Cyclobutane pyrimidine dimers photolyase from extremophilic microalga:
           Remarkable UVB resistance and efficient DNA damage repair
    • Abstract: Publication date: March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 773
      Author(s): Chongjie Li , Li Ma , Shanli Mou , Yibin Wang , Zhou Zheng , Fangming Liu , Xiaoqing Qi , Meiling An , Hao Chen , Jinlai Miao
      Bacteria living in the Antarctic region have developed several adaptive features for growth and survival under extreme conditions. Chlamydomonas sp. ICE-Lis well adapted to high levels of solar UV radiation. A putative photolyase was identified in the Chlamydomonas sp. ICE-L transcriptome. The complete cDNA sequence was obtained by RACE-PCR. This PHR encoding includes a polypeptide of 579 amino acids with clear photolyase signatures belonging to class II CPD-photolyases, sharing a high degree of homology with Chlamydomonas reinhardtii (68%). Real-time PCR was performed to investigate the potential DNA damage and responses following UVB exposure. CPD photolyase mRNA expression level increased over 50-fold in response to UVB radiation for 6h. Using photolyase complementation assay, we demonstrated that DNA photolyase increased photo-repair more than 116-fold in Escherichia coli strain SY2 under 100μw/cm2 UVB radiation. To determine whether photolyase is active in vitro, CPD photolyase was over-expressed. It was shown that pyrimidine dimers were split by the action of PHR2. This study reports the unique structure and high activity of the enzyme. These findings are relevant for further understanding of molecular mechanisms of photo-reactivation, and will accelerate the utilization of photolyase in the medical field.


      PubDate: 2015-03-19T01:30:26Z
       
  • Modulation of modeled microgravity on radiation-induced bystander effects
           in Arabidopsis thaliana
    • Abstract: Publication date: March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 773
      Author(s): Ting Wang , Qiao Sun , Wei Xu , Fanghua Li , Huasheng Li , Jinying Lu , Lijun Wu , Yuejin Wu , Min Liu , Po Bian
      Both space radiation and microgravity have been demonstrated to have inevitable impact on living organisms during space flights and should be considered as important factors for estimating the potential health risk for astronauts. Therefore, the question whether radiation effects could be modulated by microgravity is an important aspect in such risk evaluation. Space particles at low dose and fluence rate, directly affect only a fraction of cells in the whole organism, which implement radiation-induced bystander effects (RIBE) in cellular response to space radiation exposure. The fact that all of the RIBE experiments are carried out in a normal gravity condition bring forward the need for evidence regarding the effect of microgravity on RIBE. In the present study, a two-dimensional rotation clinostat was adopted to demonstrate RIBE in microgravity conditions, in which the RIBE was assayed using an experimental system of root-localized irradiation of Arabidopsis thaliana (A. thaliana) plants. The results showed that the modeled microgravity inhibited significantly the RIBE-mediated up-regulation of expression of the AtRAD54 and AtRAD51 genes, generation of reactive oxygen species (ROS) and transcriptional activation of multicopy P35S:GUS, but made no difference to the induction of homologous recombination by RIBE, showing divergent responses of RIBE to the microgravity conditions. The time course of interaction between the modeled microgravity and RIBE was further investigated, and the results showed that the microgravity mainly modulated the processes of the generation or translocation of the bystander signal(s) in roots.


      PubDate: 2015-03-19T01:30:26Z
       
  • The effects of extremely low frequency magnetic fields on mutation
           induction in mice
    • Abstract: Publication date: March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 773
      Author(s): James W. Wilson , Jackie Haines , Zenon Sienkiewicz , Yuri E. Dubrova
      The growing human exposure to extremely low frequency (ELF) magnetic fields has raised a considerable concern regarding their genotoxic effects. The aim of this study was to evaluate the in vivo effects of ELF magnetic fields irradiation on mutation induction in the germline and somatic tissues of male mice. Seven week old BALB/c×CBA/Ca F1 hybrid males were exposed to 10, 100 or 300μT of 50Hz magnetic fields for 2 or 15h. Using single-molecule PCR, the frequency of mutation at the mouse Expanded Simple Tandem Repeat (ESTR) locus Ms6-hm was established in sperm and blood samples of exposed and matched sham-treated males. ESTR mutation frequency was also established in sperm and blood samples taken from male mice exposed to 1Gy of acute X-rays. The frequency of ESTR mutation in DNA samples extracted from blood of mice exposed to magnetic fields did not significantly differ from that in sham-treated controls. However, there was a marginally significant increase in mutation frequency in sperm but this was not dose-dependent. In contrast, acute exposure X-rays led to significant increases in mutation frequency in sperm and blood of exposed males. The results of our study suggest that, within the range of doses analyzed here, the in vivo mutagenic effects of ELF magnetic fields are likely to be minor if not negligible.


      PubDate: 2015-03-19T01:30:26Z
       
  • piRNA-mediated transposon regulation and the germ-line mutation rate in
           Drosophila melanogaster males
    • Abstract: Publication date: March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 773
      Author(s): Michael J. Simmons , Mark P. Peterson , Michael W. Thorp , Jared T. Buschette , Stephanie N. DiPrima , Christine L. Harter , Matthew J. Skolnick
      Transposons, especially retrotransposons, are abundant in the genome of Drosophila melanogaster. These mobile elements are regulated by small RNAs that interact with the Piwi family of proteins—the piwi-interacting or piRNAs. The Piwi proteins are encoded by the genes argonaute3 (ago3), aubergine (aub), and piwi. Heterochromatin Protein 1 (HP1), a chromatin-organizing protein encoded by the Suppressor of variegation 205 [Su(var)205] gene, also plays a role in this regulation. To assess the mutational impact of weakening the system for transposon regulation, we measured the frequency of recessive X-linked lethal mutations occurring in the germ lines of males from stocks that were heterozygous for mutant alleles of the ago3, aub, piwi, or Su(var)205 genes. These mutant alleles are expected to deplete the wild-type proteins encoded by these genes by as much as 50%. The mutant alleles of piwi and Su(var)205 significantly increased the X-linked lethal mutation frequency, whereas the mutant alleles of ago3 did not. An increased mutation frequency was also observed in males from one of two mutant aub stocks, but this increase may not have been due to the aub mutant. The increased mutation frequency caused by depleting Piwi or HP1suggests that chromatin-organizing proteins play important roles in minimizing the germ-line mutation rate, possibly by stabilizing the structure of the heterochromatin in which many transposons are situated.


      PubDate: 2015-03-19T01:30:26Z
       
  • Anthracyclines induce double-strand DNA breaks at active gene promoters
    • Abstract: Publication date: March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 773
      Author(s): Fan Yang , Christopher J. Kemp , Steven Henikoff
      Doxorubicin is a widely used chemotherapeutic drug that intercalates between DNA base-pairs and poisons Topoisomerase II, although the mechanistic basis for cell killing remains speculative. Doxorubicin and related anthracycline compounds have been shown to increase nucleosome turnover and/or eviction around promoters, which suggests that the resulting enhanced exposure of DNA might underlie cell killing. Previously, we showed that low doses of anthracyclines increase nucleosome turnover around active gene promoters, which suggests that loss of nucleosomes might contribute to cancer cell killing. Here we apply a genome-wide method to precisely map DNA double-strand breaks (DSBs) in cancer cells. We find that spontaneous DSBs occur preferentially around promoters of active genes, and that both anthracyclines and etoposide, a Topoisomerase II poison, increase DSBs around promoters, although CpG islands are conspicuously protected from DSBs. We propose that torsion-based enhancement of nucleosome turnover by anthracyclines exposes promoter DNA, ultimately causing DSBs around promoters.


      PubDate: 2015-03-19T01:30:26Z
       
  • TITLE PAGE (EDI BOARD)
    • Abstract: Publication date: March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 773




      PubDate: 2015-03-19T01:30:26Z
       
  • Benzo[a]pyrene-induced cell cycle progression occurs via ERK-induced Chk1
           pathway activation in human lung cancer cells
    • Abstract: Publication date: March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 773
      Author(s): Bing-Yen Wang , Sung-Yu Wu , Sheau-Chung Tang , Chien-Hung Lai , Chu-Chyn Ou , Ming-Fang Wu , Yi-Min Hsiao , Jiunn-Liang Ko
      Benzo[a]pyrene (B[a]P) is a potent lung carcinogen derived from tobacco smoking and environmental contamination. This study aimed to investigate the signal transduction pathway responsible for B[a]P-induced non-small cell lung cancer (NSCLC) development. We exposed the human NSCLC cell lines Calu-1, CL3, H1299, CH27, H23, and H1355 to B[a]P and assessed cell cycle progression using flow cytometry. Expression of cell cycle mediators was measured using Western blot analyses and electrophoretic mobility shift assays (EMSAs). B[a]P exposure dramatically induced S-phase accumulation in H1355 cells. Phospho-p53 (Ser15 and Ser20), phospho-ERK, phospho-p38, and Bax were significantly increased in H1355 cells whereas phospho-Rb was decreased in these cells. In addition, B[a]P induced phosphorylation of checkpoint kinase-1 (Chk1) but not Chk2. EMSA experiments revealed a slower migrating band after c-Myc bound the E-box in response to B[a]P treatment, which was abolished upon the addition of the ERK inhibitor PD98059 in H1355 cells. Phospho-ERK inhibition and dominant negative mutant Chk1 expression reversed B[a]P-induced S phase accumulation and downregulated phospho-Chk1 and phospho-ERK expression. Taken together, these results suggest that activation of ERK and its downstream mediator Chk1 may contribute to B[a]P-induced S phase accumulation in H1355 cells. The results could help in the development of lung cancer treatments that target the Chk1 pathway through ERK.
      Graphical abstract image

      PubDate: 2015-03-19T01:30:26Z
       
  • Bisphenol A and congenital developmental defects in humans
    • Abstract: Publication date: Available online 6 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Maurizio Guida , Jacopo Troisi , Carla Ciccone , Giovanni Granozio , Cosimo Cosimato , Attilio di Spiezio Sardo , Cinzia Ferrara , Marco Guida , Carmine Nappi , Fulvio Zullo , Costantino Di Carlo
      Over 50% of the causes of fetal malformations in humans are still unknown. Recent evidence suggests the relationship between environmental exposure to endocrine disruptors and fetal malformations. Our study aims to establish the role of Bisphenol A (BPA), if any, in altering human reproduction. We enrolled 151 pregnant women who were divided into two groups: case group (CS, n =101), women with established diagnosis of developmental defect, and control group (CL, n =50), pregnant women with normally developed fetus. Total, free and conjugated BPA were measured in their blood using GC–MS with isotopic dilution. The results show a correlation between environmental exposure to BPA and the genesis of fetal malformations. Conjugated BPA, which was higher in the CL, casts light on the hypothesis that a reduced ability to metabolize the chemical in the mother can concur to the occurrence of malformation. In a more detailed manner, in case of chromosomal malformations, the average value of free BPA appears to be nearly three times greater than that of the controls. Similarly, in case of central and peripheral nervous system non-chromosomal malformations, the value of free BPA is nearly two times greater than that of the controls.


      PubDate: 2015-03-19T01:30:26Z
       
  • WRN translocation from nucleolus to nucleoplasm is regulated by SIRT1 and
           required for DNA repair and the development of chemoresistance
    • Abstract: Publication date: Available online 11 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Sun-Young Lee , Hyunwoo Lee , Eun-Sun Kim , Sojin Park , Jiyoen Lee , Byungchan Ahn
      When defective or absent, Werner syndrome protein (WRN) causes a genetic premature aging disorder called Werner syndrome. Several studies have reported that defects in WRN function are responsible for not only progeria syndrome but also genomic instability via the deregulation of DNA repair, replication, recombination, and telomere stability. Given the importance of WRN in the repair process, we herein investigated the potential role of WRN in drug response by evaluating the DNA repair following exposure to cisplatin in human cancer cell lines. We found that the down-regulation of SIRT1 and inhibition of SIRT1 deacetylase activity blocked the translocation of WRN from the nucleolus to the nucleoplasm in response to genotoxic stresses. In addition, cells expressing low levels of WRN responded favorably to cisplatin, whereas cells expressing high levels responded poorly to cisplatin. The forced expression of WRN protein in chemosensitive cells resulted in an approximately two-fold increase in cell viability in response to cisplatin compared with vector controls and promoted DNA repair, while WRN-deficient cells accumulate unrepaired double-strand breaks following cisplatin exposure. These results suggest that WRN is regulated by SIRT1 and increased expression of WRN might be one of the determinants for the development of chemotherapeutic drug resistance.


      PubDate: 2015-03-19T01:30:26Z
       
  • The effect of low dose ionizing radiation on homeostasis and functional
           integrity in an organotypic human skin model
    • Abstract: Publication date: Available online 16 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Claere von Neubeck , Matthew J. Geniza , Paula M. Kauer , R. Joe Robinson , William B. Chrisler , Marianne B. Sowa
      Outside the protection of earth's atmosphere, astronauts are exposed to low doses of high linear energy transfer (LET) radiation. Future NASA plans for deep space missions or a permanent settlement on the moon are limited by the health risks associated with space radiation exposures. There is a paucity of direct epidemiological data for low dose exposures to space radiation-relevant high LET ions. Health risk models are used to estimate the risk for such exposures, though these models are based on high dose experiments. There is increasing evidence, however, that low and high dose exposures result in different signaling events at the molecular level, and may involve different response mechanisms. Further, despite their low abundance, high LET particles have been identified as the major contributor to health risk during manned space flight. The human skin is exposed in every external radiation scenario, making it an ideal epithelial tissue model in which to study radiation induced effects. Here, we exposed an in vitro three dimensional (3-D) human organotypic skin tissue model to low doses of high LET oxygen (O), silicon (Si) and iron (Fe) ions. We measured proliferation and differentiation profiles in the skin tissue and examined the integrity of the skin's barrier function. We discuss the role of secondary particles in changing the proportion of cells receiving a radiation dose, emphasizing the possible impact on radiation-induced health issues in astronauts.


      PubDate: 2015-03-19T01:30:26Z
       
  • MYC impairs resolution of site-specific DNA double-strand breaks repair
    • Abstract: Publication date: April 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 774
      Author(s): Susanna Ambrosio , Stefano Amente , Giuliana Napolitano , Giacomo Di Palo , Luigi Lania , Barbara Majello
      Although it is established that when overexpressed, the MYC family proteins can cause DNA double-stand breaks (DSBs) and genome instability, the mechanisms involved remain unclear. MYC induced genetic instability may result from increased DNA damage and/or reduced DNA repair. Here we show that when overexpressed, MYC proteins induce a sustained DNA damage response (DDR) and reduce the wave of DSBs repair. We used a cell-based DSBs system whereby, upon induction of an inducible restriction enzyme AsiSI, hundreds of site-specific DSBs are generated across the genome to investigate the role of MYC proteins on DSB. We found that high levels of MYC do not block accumulation of γH2AX at AsiSI sites, but delay its clearance, indicating an inefficient repair, while the initial recognition of DNA damage is largely unaffected. Repair of both homologous and nonhomologous repair-prone segments, characterized by high or low levels of recruited RAD51, respectively, was delayed. Collectively, these data indicate that high levels of MYC proteins delay the resolution of DNA lesions engineered to occur in cell cultures.


      PubDate: 2015-03-19T01:30:26Z
       
  • MWCNT uptake in Allium cepa root cells induces cytotoxic and genotoxic
           responses and results in DNA hyper-methylation
    • Abstract: Publication date: Available online 16 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Manosij Ghosh , Sreetama Bhadra , Aremu Adegoke , Maumita Bandyopadhyay , Anita Mukherjee
      Advances in nanotechnology have led to the large-scale production of nanoparticles, which, in turn, increases the chances of environmental exposure. While humans (consumers/workers) are primarily at risk of being exposed to the adverse effect of nanoparticles, the effect on plants and other components of the environment cannot be ignored. The present work investigates the cytotoxic, genotoxic, and epigenetic (DNA methylation) effect of MWCNT on the plant system- Allium cepa. MWCNT uptake in root cells significantly altered cellular morphology. Membrane integrity and mitochondrial function were also compromised. The nanotubes induced significant DNA damage, micronucleus formation and chromosome aberration. DNA laddering assay revealed the formation of internucleosomal fragments, which is indicative of apoptotic cell death. This finding was confirmed by an accumulation of cells in the sub-G0 phase of the cell cycle. An increase in CpG methylation was observed using the isoschizomers MspI/HpaII. HPLC analysis of DNA samples revealed a significant increase in the levels of 5-methyl-deoxy-cytidine (5mdC). These results confirm the cyto-genotoxic effect of MWCNT in the plant system and simultaneously highlight the importance of this epigenetic study in nanoparticle toxicity.


      PubDate: 2015-03-19T01:30:26Z
       
  • Conservation of CFTR codon frequency through Primates suggests synonymous
           mutations could have a functional effect
    • Abstract: Publication date: Available online 17 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Lucilla Pizzo , Andrés Iriarte , Fernando Alvarez-Valin , Mónica Marín
      Cystic Fibrosis is an inherited chronic disease that affects the lungs and digestive system, with a prevalence of about 1:3000 people. Cystic Fibrosis is caused by mutations in CFTR gene, which lead to a defective function of the chloride channel, the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). Up-to-date, more than 1900 mutations have been reported in CFTR. However for an important proportion of them, their functional effects and the relation to disease are still not understood. Many of these mutations are silent (or synonymous), namely they do not alter the encoded amino acid. These synonymous mutations have been considered as neutral to protein function. However, more recent evidence in bacterial and human proteins has put this concept under revision. With the aim of understanding possible functional effects of synonymous mutations in CFTR, we analyzed human and Primates CFTR codon usage and divergence patterns. We report the presence of regions enriched in rare and frequent codons. This spatial pattern of codon preferences is conserved in Primates, but this cannot be explained by sequence conservation alone. In sum, the results presented herein suggest a functional implication of these regions of the gene that may be maintained by purifying selection acting to preserve a particular codon usage pattern along the sequence. Overall these results support the idea that several synonymous mutations in CFTR may have functional importance, and could be involved in the disease.
      Graphical abstract image

      PubDate: 2015-03-19T01:30:26Z
       
  • T-cells enhance stem cell mutagenesis in the mouse colon
    • Abstract: Publication date: April 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 774
      Author(s): Ryan D. Whetstone , Barry Gold
      A role of inflammation in the etiology of cancer is attributed to the production of reactive oxygen/nitrogen species that can damage DNA. To test this hypothesis, we determined the mutation frequency (MF) in colonic stem cells in C57Bl/6 mice exposed to azoxymethane (AOM), dextran sulfate sodium (DSS) and a combination of AOM and DSS (AOM+DSS). AOM+DSS efficiently and rapidly produces colon tumors in B6 mice. AOM produces promutagenic O6-methylguanine lesions in DNA but does not induce colon tumors in C57Bl/6 mice as a single agent. DSS produces inflammation in the colon but does not produce tumors except upon multiple cycles of treatment in some DNA repair deficient mouse models. In addition, using TCRβ null mice we tested whether α/β T cells have any effect on the colonic stem cell MF in mice treated with AOM, DSS and AOM+DSS. The TCRβ−/− mice are devoid of the critical receptor required for normal cytolytic and regulatory α/β T-cell functions. The MF in the untreated and DSS treated WT and TCRβ−/− mice was the same (<10−5) indicating that DSS and subsequent inflammation does not generate stem cell mutations in mice that are WT for DNA repair. AOM yielded mutant crypts in WT and TCRβ−/− mice with MF's of ∼4×10−4 and 2×10−4, respectively, which represents a statistically significant decrease in the MF in the immune compromised mice. The combined treatment of AOM+DSS afforded fully mutated crypts in both strains with a statistically significant lower MF in the TCRβ−/− mice. In addition, the MF in both strains of mice after the combination of AOM+DSS is lower than observed with AOM alone indicating that DSS inflammation destroyed pre-existing AOM mutated crypts. Using the MF in WT mice, the efficiency for the conversion of promutagenic O6-methylguanine lesions into a stem cell mutations was calculated to be ∼0.4%.


      PubDate: 2015-03-19T01:30:26Z
       
  • Effect of phytochemical intervention on dibenzo[a,l]pyrene-induced DNA
           adduct formation
    • Abstract: Publication date: April 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 774
      Author(s): Gilandra K. Russell , Ramesh C. Gupta , Manicka V. Vadhanam
      Dibenzo[a,l]pyrene (DBP) has been found to be the most potent carcinogen of the polycyclic aromatic hydrocarbons (PAHs). Primary sources for DBP in the environment are combustion of wood and coal burning, gasoline and diesel exhaust, and tires. Given the likelihood of environmental exposure to DBP and strong experimental evidence of its potency, it is likely to contribute to lung cancer development. Intervention with compounds of natural origin (“phytochemicals”) is considered an effective means to prevent cancer development and favorably modulate the underlying mechanisms, including DNA adduct formation. In this study, several agents have been identified that inhibit environmental carcinogen-induced DNA adduct formation using a cell-free microsomal system. Of the ten agents tested, resveratrol (648±26 adducts/109 nucleotides), oltipraz (1007±348 adducts/109 nucleotides), delphinidin (1252±142 adducts/109 nucleotides), tanshinone I (1981±213 adducts/109 nucleotides), tanshinone IIA (2606±478 adducts/109 nucleotides) and diindoylmethane (3643±469 adducts/109 nucleotides) were the most effective compared to vehicle treatment (14,062±1097 adducts/109 nucleotides). DBP is metabolized by phase I metabolizing enzymes CYP1A1, CYP1A2, and CYP1B1. DBP-induced DNA adducts can be inhibited by several mechanisms. We found that all the test agents inhibited DNA adducts by inhibiting one or more of these enzymes. Oltipraz inhibited DNA adducts entirely by inhibiting the CYP450s, while resveratrol and delphinidin inhibited DNA adducts by also interacting directly with the carcinogenic metabolite, anti-dibenzo(a,l)pyrene-11,12-dihydrodiol-13,14-epoxide.


      PubDate: 2015-03-19T01:30:26Z
       
  • Expression of human poly (ADP-ribose) polymerase 1 in Saccharomyces
           cerevisiae: Effect on survival, homologous recombination and
           identification of genes involved in intracellular localization
    • Abstract: Publication date: April 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Volume 774
      Author(s): Marco La Ferla , Alberto Mercatanti , Giulia Rocchi , Samuele Lodovichi , Tiziana Cervelli , Luca Pignata , Maria Adelaide Caligo , Alvaro Galli
      The poly (ADP-ribose) polymerase 1 (PARP-1) actively participates in a series of functions within the cell that include: mitosis, intracellular signaling, cell cycle regulation, transcription and DNA damage repair. Therefore, inhibition of PARP1 has a great potential for use in cancer therapy. As resistance to PARP inhibitors is starting to be observed in patients, thus the function of PARP-1 needs to be studied in depth in order to find new therapeutic targets. To gain more information on the PARP-1 activity, we expressed PARP-1 in yeast and investigated its effect on cell growth and UV induced homologous recombination. To identify candidate genes affecting PARP-1 activity and cellular localization, we also developed a yeast genome wide genetic screen. We found that PARP-1 strongly inhibited yeast growth, but when yeast was exposed to the PARP-1 inhibitor 6(5-H) phenantridinone (PHE), it recovered from the growth suppression. Moreover, we showed that PARP-1 produced PAR products in yeast and we demonstrated that PARP-1 reduced UV-induced homologous recombination. By genome wide screening, we identified 99 mutants that suppressed PARP-1 growth inhibition. Orthologues of human genes were found for 41 of these yeast genes. We determined whether the PARP-1 protein level was altered in strains which are deleted for the transcription regulator GAL3, the histone H1 gene HHO1, the HUL4 gene, the deubiquitination enzyme gene OTU1, the nuclear pore protein POM152 and the SNT1 that encodes for the Set3C subunit of the histone deacetylase complex. In these strains the PARP-1 level was roughly the same as in the wild type. PARP-1 localized in the nucleus more in the snt1Δ than in the wild type strain; after UV radiation, PARP-1 localized in the nucleus more in hho1 and pom152 deletion strains than in the wild type indicating that these functions may have a role on regulating PARP-1 level and activity in the nucleus.


      PubDate: 2015-03-19T01:30:26Z
       
  • Breast cancer risk and possible mechanisms of radiation-induced genomic
           instability in the Swedish hemangioma cohort after reanalyzed dosimetry
    • Abstract: Publication date: Available online 11 March 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Markus Eidemüller , Erik Holmberg , Peter Jacob , Marie Lundell , Per Karlsson
      The cohort of 17,200 female Swedish hemangioma patients, who had been exposed to ionizing radiation because of skin hemangioma, was analyzed for breast cancer incidence with descriptive excess relative risk models and mechanistic models of carcinogenesis. The dosimetry system has recently been updated, leading to substantially reduced doses for the most highly exposed part of the Stockholm cohort. The follow-up includes persons until December 2009 with 877 breast cancer cases. All models agree on the risk estimates. The excess relative and excess absolute risk at the age of 50 years are 0.48 Gy−1 (95% CI 0.28; 0.69) and 10.4 ( 10 4 PYR Gy ) − 1 (95% CI 6.1; 14.4), respectively. These risk estimates are about a factor of two higher than previous analyses of this cohort as a consequence of the re-evaluation of the dosimetry system. Explicit models incorporating effects of genomic instability were developed and applied to the hemangioma cohort. It was found that a radiation-induced transition towards genomic instability was highly significant. The models indicate that the main effect of radiation-induced genomic instability is to increase the rate of transition of non-initiated cells to initiated cells with a proliferative advantage. The magnitude of such an acceleration cannot be inferred from epidemiological data alone, but must be complemented by radiobiological measurements.


      PubDate: 2015-03-15T04:20:08Z
       
  • Single-cell transcriptogenomics reveals transcriptional exclusion of
           ENU-mutated alleles
    • Abstract: Publication date: Available online 16 January 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Wenge Li , R. Brent Calder , Jessica C. Mar , Jan Vijg
      Great progress has been made in single cell genomics and transcriptomics. Here, we present an integrative method, termed single-cell transcriptogenomics (SCTG), in which whole exome sequencing and RNA-seq is performed concurrently on single cells. This methodology enables one to track germline and somatic variants directly from the genome to the transcriptome in individual cells. Mouse embryonic fibroblasts were treated with the powerful mutagen ethylnitrosourea (ENU) and subjected to SCGT. Interestingly, while germline variants were found to be transcribed in an allelically balanced fashion, a significantly different pattern of allelic exclusion was observed for ENU-mutant variants. These results suggest that the adverse effects of induced mutations, in contrast to germline variants, may be mitigated by allelically biased transcription. They also illustrate how SCGT can be instrumental in the direct assessment of phenotypic consequences of genomic variants.


      PubDate: 2015-02-08T16:16:11Z
       
  • TP53 mutations induced by BPDE in Xpa-WT and Xpa-Null human TP53 knock-in
           (Hupki) mouse embryo fibroblasts
    • Abstract: Publication date: Available online 30 January 2015
      Source:Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
      Author(s): Jill E. Kucab , Harry van Steeg , Mirjam Luijten , Heinz H. Schmeiser , Paul A. White , David H. Phillips , Volker M. Arlt
      Somatic mutations in the tumour suppressor gene TP53 occur in more than 50% of human tumours; in some instances exposure to environmental carcinogens can be linked to characteristic mutational signatures. The Hupki (human TP53 knock-in) mouse embryo fibroblast (HUF) immortalisation assay (HIMA) is a useful model for studying the impact of environmental carcinogens on TP53 mutagenesis. In an effort to increase the frequency of TP53-mutated clones achievable in the HIMA, we generated nucleotide excision repair (NER)-deficient HUFs by crossing the Hupki mouse with an Xpa-knockout (Xpa-Null) mouse. We hypothesized that carcinogen-induced DNA adducts would persist in the TP53 sequence of Xpa-Null HUFs leading to an increased propensity for mismatched base pairing and mutation during replication of adducted DNA. We found that Xpa-Null Hupki mice, and HUFs derived from them, were more sensitive to the environmental carcinogen benzo[a]pyrene (BaP) than their wild-type (Xpa-WT) counterparts. Following treatment with the reactive metabolite of BaP, benzo[a]pyrene-7,8-diol-9,10-epoxide (BPDE), Xpa-WT and Xpa-Null HUF cultures were subjected to the HIMA. A significant increase in TP53 mutations on the transcribed strand was detected in Xpa-Null HUFs compared to Xpa-WT HUFs, but the TP53-mutant frequency overall was not significantly different between the two genotypes. BPDE induced mutations primarily at G:C base pairs, with approximately half occurring at CpG sites, and the predominant mutation type was G:C>T:A in both Xpa-WT and Xpa-Null cells. Further, several of the TP53 mutation hotspots identified in smokers’ lung cancer were mutated by BPDE in HUFs (codons 157, 158, 245, 248, 249, 273). Therefore, the pattern and spectrum of BPDE-induced TP53 mutations in the HIMA are consistent with TP53 mutations detected in lung tumours of smokers. While Xpa-Null HUFs exhibited increased sensitivity to BPDE-induced damage on the transcribed strand, NER-deficiency did not enhance TP53 mutagenesis resulting from damage on the non-transcribed strand in this model.


      PubDate: 2015-02-03T08:37:16Z
       
 
 
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