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de Lima E Souza Mesquita GC, Da Cruz ER, Corrêa DS, de Barros Falcão Ferraz A, Miri JM, Farias IV, Reginatto FH, Boaretto FBM, Dos Santos DM, da Silva J, Grivicich I, Picada JN. Genotoxic and antiproliferative properties of Endopleura uchi bark aqueous extract. J Toxicol Environ Health A 2024; 87:516-531. [PMID: 38619152 DOI: 10.1080/15287394.2024.2340069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The bark extract from Endopleura uchi has been widely used in traditional medicine to treat gynecological-related disorders, diabetes, and dyslipidemias albeit without scientific proof. In addition, E. uchi bark extract safety, especially regarding mutagenic activities, is not known. The aim of this study was to determine the chemical composition, antitumor, and toxicological parameters attributed to an E. uchi bark aqueous extract. The phytochemical constitution was assessed by colorimetric and chromatographic analyzes. The antiproliferative effect was determined using sulforhodamine B (SRB) assay using 4 cancer cell lines. Cytotoxic and genotoxic activities were assessed utilizing MTT and comet assays, respectively, while mutagenicity was determined through micronucleus and Salmonella/microsome assays. The chromatographic analysis detected predominantly the presence of gallic acid and isoquercitrin. The antiproliferative effect was more pronounced in human colon adenocarcinoma (HT-29) and human breast cancer (MCF-7) cell lines. In the MTT assay, the extract presented an IC50 = 39.1 µg/ml and exhibited genotoxic (comet assay) and mutagenic (micronucleus test) activities at 20 and 40 µg/ml in mouse fibroblast cell line (L929) and mutagenicity in the TA102 and TA97a strains in the absence of S9 mix. Data demonstrated that E. uchi bark possesses bioactive compounds which exert cytotoxic and genotoxic effects that might be associated with its antitumor potential. Therefore, E. uchi bark aqueous extract consumption needs to be approached with caution in therapeutic applications.
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Affiliation(s)
| | - Elkejer Ribeiro Da Cruz
- Laboratory of Genetic Toxicology, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
- Center for Research in Product and Development (CEPPED), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Dione Silva Corrêa
- Center for Research in Product and Development (CEPPED), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Alexandre de Barros Falcão Ferraz
- Pharmacognosy Laboratory, Department of Industrial Pharmaceutical, Health Sciences Center, Federal University of Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Jéssica Machado Miri
- Laboratory of Cancer Biology, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Ingrid Vicente Farias
- Pharmacognosy Laboratory, Department of Pharmaceutical Sciences, Health Sciences Center, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Flávio Henrique Reginatto
- Pharmacognosy Laboratory, Department of Pharmaceutical Sciences, Health Sciences Center, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | | | - Duani Maria Dos Santos
- Laboratory of Genetic Toxicology, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Juliana da Silva
- Laboratory of Genetic Toxicology, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
- Laboratory of Genetics Toxicology, La Salle University, Canoas, RS, Brazil
| | - Ivana Grivicich
- Laboratory of Cancer Biology, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
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Faulstich L, Wollenweber S, Reinhardt-Imjela C, Arendt R, Schulte A, Hollert H, Schiwy S. Ecotoxicological evaluation of surface waters in Northern Namibia. Environ Monit Assess 2024; 196:456. [PMID: 38630192 PMCID: PMC11024038 DOI: 10.1007/s10661-024-12613-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
The increasing pressure on freshwater systems due to intensive anthropogenic use is a big challenge in central-northern Namibia and its catchment areas, the Kunene and the Kavango Rivers, and the Cuvelai-Etosha Basin, that provide water for more than 1 million people. So far, there is no comprehensive knowledge about the ecological status and only few knowledge about the water quality. Therefore, it is crucial to learn about the state of the ecosystem and the ecological effects of pollutants to ensure the safe use of these resources. The surface waters of the three systems were sampled, and three bioassays were applied on three trophic levels: algae, daphnia, and zebrafish embryos. Additionally, in vitro assays were performed to analyze mutagenicity (Ames fluctuation), dioxin-like potential (micro-EROD), and estrogenicity (YES) by mechanism-specific effects. The results show that acute toxicity to fish embryos and daphnia has mainly been detected at all sites in the three catchment areas. The systems differ significantly from each other, with the sites in the Iishana system showing the highest acute toxicity. At the cellular level, only weak effects were identified, although these were stronger in the Iishana system than in the two perennial systems. Algae growth was not inhibited, and no cytotoxic effects could be detected in any of the samples. Mutagenic effects and an estrogenic potential were detected at three sites in the Iishana system. These findings are critical in water resource management as the effects can adversely impact the health of aquatic ecosystems and the organisms within them.
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Affiliation(s)
- L Faulstich
- Freie Universität Berlin, Berlin, Germany.
- Goethe-Universität Frankfurt, Frankfurt, Germany.
| | | | | | - R Arendt
- Freie Universität Berlin, Berlin, Germany
| | - A Schulte
- Freie Universität Berlin, Berlin, Germany
| | - H Hollert
- Goethe-Universität Frankfurt, Frankfurt, Germany
| | - S Schiwy
- Goethe-Universität Frankfurt, Frankfurt, Germany
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3
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Chancharoen M, Yang Z, Dalvie ED, Gubina N, Ruchirawat M, Croy RG, Fedeles BI, Essigmann JM. 5-Chloro-2'-deoxycytidine Induces a Distinctive High-Resolution Mutational Spectrum of Transition Mutations In Vivo. Chem Res Toxicol 2024; 37:486-496. [PMID: 38394377 PMCID: PMC10952010 DOI: 10.1021/acs.chemrestox.3c00358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/15/2023] [Accepted: 01/18/2024] [Indexed: 02/25/2024]
Abstract
The biomarker 5-chlorocytosine (5ClC) appears in the DNA of inflamed tissues. Replication of a site-specific 5ClC in a viral DNA genome results in C → T mutations, which is consistent with 5ClC acting as a thymine mimic in vivo. Direct damage of nucleic acids by immune-cell-derived hypochlorous acid is one mechanism by which 5ClC could appear in the genome. A second, nonmutually exclusive mechanism involves damage of cytosine nucleosides or nucleotides in the DNA precursor pool, with subsequent utilization of the 5ClC deoxynucleotide triphosphate as a precursor for DNA synthesis. The present work characterized the mutagenic properties of 5ClC in the nucleotide pool by exposing cells to the nucleoside 5-chloro-2'-deoxycytidine (5CldC). In both Escherichia coli and mouse embryonic fibroblasts (MEFs), 5CldC in the growth media was potently mutagenic, indicating that 5CldC enters cells and likely is erroneously incorporated into the genome from the nucleotide pool. High-resolution sequencing of DNA from MEFs derived from the gptΔ C57BL/6J mouse allowed qualitative and quantitative characterization of 5CldC-induced mutations; CG → TA transitions in 5'-GC(Y)-3' contexts (Y = a pyrimidine) were dominant, while TA → CG transitions appeared at a much lower frequency. The high-resolution mutational spectrum of 5CldC revealed a notable similarity to the Catalogue of Somatic Mutations in Cancer mutational signatures SBS84 and SBS42, which appear in human lymphoid tumors and in occupationally induced cholangiocarcinomas, respectively. SBS84 is associated with the expression of activation-induced cytidine deaminase (AID), a cytosine deaminase associated with inflammation, as well as immunoglobulin gene diversification during antibody maturation. The similarity between the spectra of AID activation and 5CldC could be coincidental; however, the administration of 5CldC did induce some AID expression in MEFs, which have no inherent expression of its gene. In summary, this work shows that 5CldC induces a distinct pattern of mutations in cells. Moreover, that pattern resembles human mutational signatures induced by inflammatory processes, such as those triggered in certain malignancies.
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Affiliation(s)
- Marisa Chancharoen
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
- Chulabhorn
Research Institute and Chulabhorn Graduate Institute, Bangkok 10210, Thailand
| | - Zhiyu Yang
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Esha D. Dalvie
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Nina Gubina
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Mathuros Ruchirawat
- Chulabhorn
Research Institute and Chulabhorn Graduate Institute, Bangkok 10210, Thailand
| | - Robert G. Croy
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Bogdan I. Fedeles
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - John M. Essigmann
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
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Tintori SC, Çağlar D, Ortiz P, Chyzhevskyi I, Mousseau TA, Rockman MV. Environmental radiation exposure at Chornobyl has not systematically affected the genomes or chemical mutagen tolerance phenotypes of local worms. Proc Natl Acad Sci U S A 2024; 121:e2314793121. [PMID: 38442158 PMCID: PMC10945782 DOI: 10.1073/pnas.2314793121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/18/2024] [Indexed: 03/07/2024] Open
Abstract
The 1986 disaster at the Chornobyl Nuclear Power Plant transformed the surrounding region into the most radioactive landscape known on the planet. Whether or not this sudden environmental shift selected for species, or even individuals within a species, that are naturally more resistant to mutagen exposure remains an open question. In this study, we collected, cultured, and cryopreserved 298 wild nematode isolates from areas varying in radioactivity within the Chornobyl Exclusion Zone. We sequenced and assembled genomes de novo for 20 Oscheius tipulae strains, analyzed their genomes for evidence of recent mutation acquisition in the field, and observed no evidence of an association between mutation and radioactivity at the sites of collection. Multigenerational exposure of each of these strains to several chemical mutagens in the lab revealed that strains vary heritably in tolerance to each mutagen, but mutagen tolerance cannot be predicted based on the radiation levels at collection sites, and Chornobyl isolates were not systematically more resistant than strains from undisturbed habitats. In sum, the absence of mutational signatures does not reflect unique capacity for tolerating DNA damage.
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Affiliation(s)
- Sophia C. Tintori
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY10003
| | - Derin Çağlar
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY10003
| | - Patrick Ortiz
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY10003
| | - Ihor Chyzhevskyi
- Department of Coordination of International Projects of the State Specialized Enterprise “Ecocentre”, Kyiv01133, Ukraine
| | - Timothy A. Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC29208
| | - Matthew V. Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY10003
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Zhang J, Fei C, Qi S, Fu J, Zhou S, Wang Z, Li J, Zhao Y, Wu D. The toxicity response of the electrochemical signal of the cell to the drug metabolized by the S9 system. Analyst 2024; 149:1921-1928. [PMID: 38375539 DOI: 10.1039/d4an00010b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
The electrochemical detection method of cytotoxicity using intracellular purines as biomarkers has shown great potential for in vitro drug toxicity evaluation. However, no electrochemical detection system based on an in vitro drug metabolism mechanism has been devised. In this paper, electrochemical voltammetry was used to investigate the effect of the S9 system on the electrochemical behavior of HepG2 cells, and benzo[a]pyrene, fluoranthene, and pyrene were employed to investigate the sensitivity of electrochemical signals of cells to the cytotoxicity of drugs metabolized by the S9 system. The results showed that, within 8 h of exposure to the S9 system, the electrochemical signal of HepG2 cells at 0.7 V did not alter noticeably. The levels of xanthine, guanine, hypoxanthine, and adenine in the cells were not significantly altered. Compared with the absence of S9 system metabolism, benzo[a]pyrene and fluoranthene processed by the S9 system decreased the electrochemical signal of the cells in a dose-dependent manner, while pyrene did not change it appreciably. HPLC also revealed that benzo[a]pyrene and fluoranthene metabolized by the S9 system decreased the intracellular purine levels, whereas pyrene had no effect on them before and after S9 system metabolism. The cytotoxicity results of the three drugs examined by electrochemical voltammetry and MTT assay showed a strong correlation and good agreement. The S9 system had no effect on the intracellular purine levels or the electrochemical signal of cells. When the drug was metabolized by the S9 system, variations in cytotoxicity could be precisely detected by electrochemical voltammetry.
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Affiliation(s)
- Jiahuan Zhang
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
| | - Chaoqun Fei
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
| | - Shulan Qi
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
| | - Jiaqi Fu
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
| | - Shi Zhou
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
| | - Zhong Wang
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
- College of Biology and Agriculture, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China
| | - Jinlian Li
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
| | - Yanli Zhao
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
| | - Dongmei Wu
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
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Au CW, Manfield I, Webb ME, Paci E, Turnbull WB, Ross JF. The Mutagenic Plasticity of the Cholera Toxin B-Subunit Surface Residues: Stability and Affinity. Toxins (Basel) 2024; 16:133. [PMID: 38535799 PMCID: PMC10974167 DOI: 10.3390/toxins16030133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 04/01/2024] Open
Abstract
Mastering selective molecule trafficking across human cell membranes poses a formidable challenge in healthcare biotechnology while offering the prospect of breakthroughs in drug delivery, gene therapy, and diagnostic imaging. The cholera toxin B-subunit (CTB) has the potential to be a useful cargo transporter for these applications. CTB is a robust protein that is amenable to reengineering for diverse applications; however, protein redesign has mostly focused on modifications of the N- and C-termini of the protein. Exploiting the full power of rational redesign requires a detailed understanding of the contributions of the surface residues to protein stability and binding activity. Here, we employed Rosetta-based computational saturation scans on 58 surface residues of CTB, including the GM1 binding site, to analyze both ligand-bound and ligand-free structures to decipher mutational effects on protein stability and GM1 affinity. Complimentary experimental results from differential scanning fluorimetry and isothermal titration calorimetry provided melting temperatures and GM1 binding affinities for 40 alanine mutants among these positions. The results showed that CTB can accommodate diverse mutations while maintaining its stability and ligand binding affinity. These mutations could potentially allow modification of the oligosaccharide binding specificity to change its cellular targeting, alter the B-subunit intracellular routing, or impact its shelf-life and in vivo half-life through changes to protein stability. We anticipate that the mutational space maps presented here will serve as a cornerstone for future CTB redesigns, paving the way for the development of innovative biotechnological tools.
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Affiliation(s)
- Cheuk W. Au
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Iain Manfield
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Michael E. Webb
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Emanuele Paci
- Dipartimento di Fisica e Astronomia “Augusto Righi”, Viale Berti Pichat 6/2, 40127 Bologna, Italy
| | - W. Bruce Turnbull
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - James F. Ross
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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Kaur S, Vashistt J, Sharma A, Parkash J, Kumar A, Duseja A, Changotra H. Mutagenic primer-based novel multiplex PCR-RFLP technique to genotype BECN1 SNPs rs10512488 and rs11552192. Mol Biol Rep 2024; 51:384. [PMID: 38438793 DOI: 10.1007/s11033-024-09277-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/22/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Single Nucleotide Polymorphisms (SNPs) in candidate autophagy gene BECN1 could influence its functions thereby autophagy process. BECN1 noncoding SNPs were found to be significantly associated with neurodegenerative disease and type 2 diabetes mellitus. This study aimed to develop a simultaneous genotyping technique for two BECN1 SNPs (rs10512488 and rs11552192). METHODS A mutagenic primer-based approach was used to introduce a NdeI restriction site to genotype rs10512488 by Artificial-Restriction Fragment Length Polymorphism (A-RFLP) along with rs11552192 by Polymerase Chain Reaction (PCR)-RFLP. Multiplexing PCR and restriction digestion reactions were set up for simultaneous genotyping of both SNPs in 100 healthy individuals. Genotypic and allele frequencies were manually calculated, and the Hardy-Weinberg Equilibrium was assessed using the chi-square test. RESULTS We successfully developed PCR and RFLP conditions for the amplification and restriction digestion of both SNPs within the same tube for genotyping. The results of genotyping by newly developed multiplexing PCR-RFLP technique were concordant with the genotypes obtained by Sanger sequencing of samples. Allelic frequencies of rs10512488 obtained were 0.15 (A) and 0.85 (G), whereas allelic frequencies of rs11552192 were 0.16 (T) and 0.84 (A). CONCLUSION The newly developed technique is rapid, cost-effective and time-saving for large-scale applications compared to sequencing methods and would play an important role in low-income settings. For the first time, allelic frequencies of rs10512488 and rs11552192 were reported among the North Indian population.
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Affiliation(s)
- Sargeet Kaur
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Himachal Pradesh, Waknaghat, Solan, 173 234, India
| | - Jitendraa Vashistt
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Himachal Pradesh, Waknaghat, Solan, 173 234, India
| | - Arti Sharma
- Department of Computational Biology, School of Biological Sciences, Central University of Punjab, Bathinda 151 401, Punjab, India
| | - Jyoti Parkash
- Department of Zoology, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151 001, India
| | - Ajay Kumar
- Translational Health Science and Technology Institute (THSTI), Faridabad, 121001, Haryana, India
| | - Ajay Duseja
- Department of Hepatology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160 012, India
| | - Harish Changotra
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, 143 005, Punjab, India.
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Köksal Karayıldırım Ç, Üstündağ Okur N, Okur ME, Caglar EŞ, Nalbantsoy A, Alsakını KAMH, Karabay Yavasoglu NÜ. Preparation, characterization, and toxicity evaluation of microemulsion formulation containing prunetin for potential oral applications. Drug Chem Toxicol 2024; 47:235-242. [PMID: 37990576 DOI: 10.1080/01480545.2023.2282373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/02/2023] [Indexed: 11/23/2023]
Abstract
Phytochemicals as therapeutic alternatives can have a fundamental impact on the various stages of inflammation and its resolution. Prunetin is a naturally occurring isoflavone and has been claimed to have numerous therapeutic potentials. The objective of this study is preparation, characterization, and toxicity evaluation of microemulsion formulation containing prunetin (PMF) for potential oral applications. With this research, it was targeted to emphasize the way of improving the therapeutic efficacy of natural biomolecules with a nontoxic and effective formulation. In the study, the pseudo-ternary phase diagram was developed and PMF was characterized by conductivity, droplet size, viscosity and pH. Effects against to cytokines (IL-1β and IL-6) and TNF-α levels of the PMF were determined by ELISA technique. Genotoxicity and acute oral toxicity tests were carried out according to OECD guidelines. The results showed that PMF is a colloid system that reduced proinflammatory cytokine levels in LPS-induced macrophage cells compared to the control group. PMF demonstrated no mutagenic activity against TA98, TA100, TA1535, and TA1537 Salmonella strains. The in vivo oral acute toxicity test results indicated that PMF did not show mortality or significant side effects even at 2000 mg/kg bw. This study represents PMF showed a good safety profile in animal study. It is thought that this formulation may have anti-inflammatory potential with further in vivo testing.
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Affiliation(s)
| | - Neslihan Üstündağ Okur
- Faculty of Pharmacy, Department of Pharmaceutical Technology, University of Health Sciences, Istanbul, Turkey
| | - Mehmet Evren Okur
- Faculty of Pharmacy, Department of Pharmacology, University of Health Sciences, Istanbul, Turkey
| | - Emre Şefik Caglar
- Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, University of Health Sciences, Istanbul, Turkey
| | - Ayşe Nalbantsoy
- Faculty of Engineering, Department of Bioengineering, Ege University, Izmir, Turkey
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Pescke IK, de Oliveira Rozino L, Zenato K, Cardozo T, Flores WH, Vargas VMF. Lowering the pH leads to the disaggregation of NiO and ZnO nanoparticles and modifies the mutagenic response. J Appl Toxicol 2024; 44:445-454. [PMID: 37828814 DOI: 10.1002/jat.4553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
In a changing environmental scenario, acid rain can have a significant impact on aquatic ecosystems. Acidification is known to produce corrosion in metals, hence increasing their harmful effects on the environment, organisms and human health. The prevalent use of metallic nanoparticles (NPs) in everyday products raises concerns regarding exposure and nanotoxicity even in these acidified conditions. We thus report on the cytotoxic and genotoxic potential of nickel oxide (NiO-NP) and zinc oxide (ZnO-NP) NPs when suspended in aqueous media in light of pH variations (7.5 and 5). A modified microsuspension method of the Salmonella/microsome assay was adopted, and strains (TA97a, TA98, TA100, TA102) were exposed to NPs (10-1280 μg/plate) with and without a metabolization fraction. The acidic condition favored disaggregation and caused a decrease in NPs size. Mutagenicity was observed in all samples and different strains, with greater DNA base pair substitution damage (TA100 and TA102), but extrinsic conditions (pH) suggest different action mechanisms of NiO-NP and ZnO-NP on genetic content. Mutagenic activity was found to increase upon metabolic activation (TA98, TA100, and TA102) demonstrating the bioactivity of NiO-NP and ZnO-NP in relation to metabolites generated by the mammalian p450 system in vitro. Modifications in the Salmonella assay methodology increased cell exposure time. The observed responses recommend this modified assay as one of the methodologies of choice for nanoecotoxicological evaluation. These findings emphasize the significance of incorporating the environmental context when evaluating the toxicity of metal-based NPs.
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Affiliation(s)
- Ismael Krüger Pescke
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Mutagênese Ambiental, Centro de Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Lívia de Oliveira Rozino
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Mutagênese Ambiental, Centro de Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Karoline Zenato
- Laboratório de Mutagênese Ambiental, Centro de Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Tatiane Cardozo
- Grupo de Materiais Nanoestruturados, Universidade Federal do Pampa (UNIPAMPA), Bagé, Brazil
| | | | - Vera Maria Ferrão Vargas
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Mutagênese Ambiental, Centro de Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Roy L, Pan N, Ghosh R, Hasan MN, Mondal S, Banerjee A, Das M, Sen O, Bhattacharya K, Chattopadhyay A, Pal SK. A Mutagen Acts as a Potent Reducing Agent of Glycated Hemoglobin: a Combined Ultrafast Electron Transfer and Computational Studies. Chembiochem 2024; 25:e202300721. [PMID: 38226959 DOI: 10.1002/cbic.202300721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
Glycated hemoglobin (GHb) found in mammals undergoes irreversible damage when exposed to external redox agents, which is much more vulnerable than its normal counterpart hemoglobin (Hb). Besides the oxygen regulation throughout the body, Hb plays a vital role in balancing immunological health and the redox cycle. Photoinduced ultra-fast electron transfer phenomena actively participate in regulation of various kind of homeostasis involved in such biomacromolecules. In the present study we have shown that a well-known mutagen Ethidium Bromide (EtBr) reduces GHb in femtosecond time scale (efficiently) upon photoexcitation after efficient recognition in the biomolecule. We have performed similar experiment by colocalizing EtBr and Iron (Fe(III)) on the micellar surface as Hb mimic in order to study the excited state EtBr dynamics to rationalize the time scale obtained from EtBr in GHb and Hb. While other experimental techniques including Dynamic Light Scattering (DLS), Zeta potential, absorbance and emission spectroscopy have been employed for the confirmation of structural perturbation of GHb compared to Hb, a detailed computational studies involving molecular docking and density functional theory (DFT) have been employed for the explanation of the experimental observations.
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Affiliation(s)
- Lopamudra Roy
- Department of Applied Optics and Photonics, University of Calcutta, JD-2, Sector-III, Salt Lake, Kolkata, West Bengal, 700 106, India
| | - Nivedita Pan
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700106
| | - Ria Ghosh
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700106
| | - Md Nur Hasan
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700106
| | - Susmita Mondal
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700106
| | - Amrita Banerjee
- Department of Physics, Jadavpur University, 188, Raja S.C. Mallick Rd, Kolkata, 700032, India
| | - Monojit Das
- Department of Zoology, Vidyasagar University Rangamati, Midnapore, 721102, India
- Department of Zoology, Uluberia College, University of Calcutta, Uluberia, Howrah, 711315, India
| | - Oyshi Sen
- Department of Biochemistry and Biophysics, University of Kalyani Nadia, Kalyani, West Bengal, 741245
| | - Kallol Bhattacharya
- Department of Applied Optics and Photonics, University of Calcutta, JD-2, Sector-III, Salt Lake, Kolkata, West Bengal, 700 106, India
| | - Arpita Chattopadhyay
- Department of Basic Science and Humanities, Techno International New Town Block, DG 1/1, Action Area 1 New Town, Rajarhat, Kolkata, 700156, India
| | - Samir Kumar Pal
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700106
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11
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Takimoto N, Ishii Y, Mitsumoto T, Takasu S, Namiki M, Shibutani M, Ogawa K. Formation of hepatocyte cytoplasmic inclusions and their contribution to methylcarbamate-induced hepatocarcinogenesis in F344 rats. Toxicol Sci 2024; 198:40-49. [PMID: 38230821 DOI: 10.1093/toxsci/kfad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Abstract
Methylcarbamate (MC), a reaction product between dimethyl dicarbonate and ammonia or ammonium ion, is a potent hepatocarcinogen in F344 rats. Various genotoxicity tests have shown negative results for MC. Although previous studies have described the effects of MC on the liver, including the formation of characteristic basophilic cytoplasmic inclusions (CIs) in hepatocytes, the toxicological significance of CIs and their involvement in hepatocarcinogenesis remain unclear. In the current study, to elucidate the mechanisms of MC hepatocarcinogenesis, we examined hepatotoxicity and genotoxicity after 4 weeks of administration of MC using gpt delta rats with an F344 genetic background as a reporter gene transgenic animal model. Histopathologically, single-cell necrosis, karyomegaly, and the formation of CIs positive for Feulgen staining were observed in hepatocytes at the carcinogenic dose, demonstrating the hepatotoxicity of MC. CIs were also detected as large micronuclei in liver micronucleus tests but not in the bone marrow, suggesting that MC could cause chromosomal instability specifically in the livers of rats. Reporter gene mutation assays demonstrated that MC did not induce mutagenicity even in the liver. Immunofluorescence analyses revealed that CIs exhibited loss of nuclear envelope integrity, increased heterochromatinization, and accumulation of DNA damage. An increase in liver STING protein levels suggested an effect on the cyclic GMP-AMP synthase/stimulator of interferon genes innate immune pathway. Overall, these data demonstrated the possible occurrence of chromothripsis-like chromosomal rearrangements via CIs. Thus, the formation of CIs could be a crucial event in the early stage of MC-induced hepatocarcinogenesis in F344 rats.
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Affiliation(s)
- Norifumi Takimoto
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
| | - Yuji Ishii
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Tatsuya Mitsumoto
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
- Faculty of Animal Health Technology, Yamazaki University of Animal Health Technology, Hachioji, Tokyo 192-0364, Japan
| | - Shinji Takasu
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Moeka Namiki
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Makoto Shibutani
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
| | - Kumiko Ogawa
- Division of Pathology, National Institute of Health Sciences, Kawasaki-shi, Kanagawa 210-9501, Japan
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12
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Verheijen BM, Chung C, Thompson B, Kim H, Nakahara A, Anink JJ, Mills JD, Lee JH, Aronica E, Oyanagi K, Kakita A, Gout JF, Vermulst M. The cycad genotoxin methylazoxymethanol, linked to Guam ALS/PDC, induces transcriptional mutagenesis. Acta Neuropathol Commun 2024; 12:30. [PMID: 38383591 PMCID: PMC10882831 DOI: 10.1186/s40478-024-01725-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 02/23/2024] Open
Affiliation(s)
- Bert M Verheijen
- School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Neuroscience, Maastricht University, Maastricht, The Netherlands.
| | - Claire Chung
- School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ben Thompson
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hyunjin Kim
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Asa Nakahara
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Jasper J Anink
- Department of Neuropathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - James D Mills
- Department of Neuropathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter, SL9 0RJ, UK
| | - Jeong H Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Eleonora Aronica
- Department of Neuropathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Kiyomitsu Oyanagi
- Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Jean-Francois Gout
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Marc Vermulst
- School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
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13
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Dubey S, Verma DK, Kumar M. Severe acute respiratory syndrome Coronavirus-2 GenoAnalyzer and mutagenic anomaly detector using FCMFI and NSCE. Int J Biol Macromol 2024; 258:129051. [PMID: 38159703 DOI: 10.1016/j.ijbiomac.2023.129051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 11/08/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
In order to deepen our understanding of the virus and help guide the creation of efficient therapies, this study uses artificial intelligence tools to thoroughly explore the genetic sequences of the SARS-CoV-2 virus. The process starts by using the Fuzzy Closure Miner for Frequent Itemsets (FCMFI) on a large corpus of SARS-CoV-2 genomic sequences to reveal hidden patterns, including nucleotides base sequences, repeating motifs, and corresponding interchanges. Then, using the Nucleotide Sequence Comprehension Engine (NSCE) technique, we were able to precisely define the genomic areas for mutation analysis. Structured and unstructured proteins are both strongly impacted by virus mutations, with spike proteins that are linked to the severity of COVID-19 pneumonia being particularly affected. Notably, the Mutagenic Anomaly Detector shows a 65 % efficiency boost in computing genome mutation rates compared to conventional point mutation analysis, while GenoAnalyzer offers a remarkable 93.33 % improvement over existing approaches in recognizing common genomic sequence patterns. These results highlight the potential of FCMFI to reveal complex genomic patterns and significant insights in COVID-19 genetic sequences when combined with mutation analysis. The Mutagenic Anomaly Detector and GenoAnalyzer show promise for revealing hidden genomic patterns and precisely estimating the SARS-CoV-2 mutation rate.
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Affiliation(s)
- Shivendra Dubey
- Department of Computer Science & Engineering, Jaypee University of Engineering & Technology, Guna, Madhya Pradesh Pin-473226, India.
| | - Dinesh Kumar Verma
- Department of Computer Science & Engineering, Jaypee University of Engineering & Technology, Guna, Madhya Pradesh Pin-473226, India.
| | - Mahesh Kumar
- Department of Computer Science & Engineering, Jaypee University of Engineering & Technology, Guna, Madhya Pradesh Pin-473226, India.
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14
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Tchernev G, Dimova D. EDUCATION FROM DERMATOLOGISTS: THE SIMULTANEOUSLY DEVELOPMENT OF 16 KERATINOCYTIC CANCERS AFTER USE OF METFORMIN IN COMBINATION WITH LOSARTAN/ HYDROCHLOROTHIAZIDE, METOPROLOL AND NIFEDIPINE- IMPORTANT LINKS TO DRUG RELATED (PHOTO)-NITROSO-CARCINOGENESIS AND ONCOPHARMACOGENESIS. Georgian Med News 2024:136-141. [PMID: 38609130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Oncopharmacogenesis and Drug-Induced Skin cancer related Nitrosogenesis are newly introduced concepts in the medical literature that owe their genesis or presence to the carcinogens/ mutagens, also known as nitrosamines/NDSRIs, which are present in a heterogeneous class of drugs. The contribution to the origin of these 2 concepts is entirely due to 1) the functions and efficacy of FDA in terms of control and identification of these carcinogens, and 2) the establishment of clinicopathological correlations by the dermatologists, occurring during drug intake. According to recent FDA data, the concentration of NDMA in just one metformin tablet could be up to more than 5-fold increased. The intake of 3 to 6 tablets per day should result in a carcinogen intake that is 15 to 30 times elevated within the day and within the monomedication alone. It is these circumstances that paraphrase/ ˝betonate˝ concepts such as Onco-Pharmacogenesis and Drug-mediated Nitrosogenesis of skin cancer. Although not officially declared, these mutagens are present and have been in forced tolerance mode for the last 30-40 years. And after their intake, multiple cancers have been found to develop. The concomitant use of other nitrosamine-contaminated drugs such as losartan/hydrochlorothiazide, metoprolol and nefidipine should certainly not be surprising when it could also be associated with the development of exactly 16 keratinocytic tumours as in the case presented by us. Recent evidence in medical literature has linked the nitrosamine N-nitrosomorpholine (NMOR) with the direct development of its subsequent mutagenic action in rodents following irradiation with UVA. This fact leaves open the question of the potentially available photocarcinogenic action of the other nitrosamines in humans found in medicinal preparations. This is what necessitates a clarification of the concept of Photo-Nitroso-Carcinogenesis/ Oncogenesis in humans and its relationship to skin cancer. The overlap of the mutational patterns of some of the nitrosamine-induced mutations in target genes such as p53 and RAS oncogenes, with those of UV light-induced mutations - or practically the same ones mentioned above, suggest a possible significant role of the Drug-Induced Photo-Nitroso-Carcinogenesis of keratinocyte cancer in the context of Onco-Pharmacogenesis. Future analyses should focus on elucidating the photocarcinogenic effect of nitrosamines in drug preparations and differentiating Skin cancer Nitrosogenesis from ˝pure˝ Photo-Carcinogenesis and Nitroso-Photo-Carcinogenesis. The localization of the tumors in the area of the UV-exposed sites within the potential/actual contamination of the 4 preparations (simultaneously) in the described patient are indicative of a possible pathogenetic influence in the context of the already mentioned Nitroso-(Photo)carcinogenesis. Polycontamination of polymedication remains a so far unresolvable problem.
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Affiliation(s)
- G Tchernev
- 1Onkoderma - Clinic for Dermatology, Venereology and Dermatologic Surgery, Sofia; 2Department of Dermatology and Venereology, Medical Institute of Ministry of Interior, Sofia, Bulgaria
| | - D Dimova
- 3Department of Ophtalmology, Medical Instittute of Ministry of Interior, Sofia, Bulgaria
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15
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Sriram S, Kumar MS, Shourie GK, Palukurthi A, Kadam S, Srikanth TM. Ninety-day toxicity and genotoxic effects of synthetically derived fully saturated forms of anacardic acid in mice. Regul Toxicol Pharmacol 2024; 147:105538. [PMID: 38151226 DOI: 10.1016/j.yrtph.2023.105538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/22/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023]
Abstract
Organically synthesized fully saturated form of Anacardic acid (AA) has previously shown to be effective in the treatment of inflammatory autoimmune disease. In this study, organically synthesized fully saturated form of AA was orally administered to male and female Swiss albino mice for 90 consecutive days at doses of 25, 50 and 100 mg/kg BW (n = 20 per sex/group). Administration of AA was well tolerated at all dose levels. The treated animals did not show a dose-response toxicity in their hematology, liver, or metabolic profile. Minimally significant changes in serum biochemistry and hematology parameters were noted, but these were not considered to be of biological or toxicological importance and were not outside the known accepted ranges. Sporadic differences in organ weights were observed between groups, but all were minimal (<10%) and unlikely to indicate toxicity. The incidence of histopathological lesions was comparable between treated and control groups across all tested organs. Based upon these findings, the no-observed-adverse-effect level was determined to be ≥ 100 mg/kg BW, which was the highest dose tested. There were no genotoxic (mutagenic and clastogenic) effects seen in In-vivo micronucleus test, In-vitro chromosomal aberration test and Bacterial reverse mutation test. These results support, no genotoxicity and no toxicity associated with oral consumption of AA in mice as a dietary supplement for beverages and food.
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Affiliation(s)
- S Sriram
- Department of Neurology, Vanderbilt University, Nashville, TN, 37212, USA; Department of Medicine Vanderbilt Medical Center, TN, 37212, USA.
| | - M Sai Kumar
- Vipragen Biosciences Pvt. Ltd., Mysore, KA, 570018, India
| | - G K Shourie
- Vipragen Biosciences Pvt. Ltd., Mysore, KA, 570018, India
| | - A Palukurthi
- Vipragen Biosciences Pvt. Ltd., Mysore, KA, 570018, India
| | - S Kadam
- Vipragen Biosciences Pvt. Ltd., Mysore, KA, 570018, India
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16
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Shah SM, Demidova EV, Ringenbach S, Faezov B, Andrake M, Gandhi A, Mur P, Viana-Errasti J, Xiu J, Swensen J, Valle L, Dunbrack RL, Hall MJ, Arora S. Exploring Co-occurring POLE Exonuclease and Non-exonuclease Domain Mutations and Their Impact on Tumor Mutagenicity. Cancer Res Commun 2024; 4:213-225. [PMID: 38282550 PMCID: PMC10812383 DOI: 10.1158/2767-9764.crc-23-0312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/05/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
POLE driver mutations in the exonuclease domain (ExoD driver) are prevalent in several cancers, including colorectal cancer and endometrial cancer, leading to dramatically ultra-high tumor mutation burden (TMB). To understand whether POLE mutations that are not classified as drivers (POLE Variant) contribute to mutagenesis, we assessed TMB in 447 POLE-mutated colorectal cancers, endometrial cancers, and ovarian cancers classified as TMB-high ≥10 mutations/Mb (mut/Mb) or TMB-low <10 mut/Mb. TMB was significantly highest in tumors with "POLE ExoD driver plus POLE Variant" (colorectal cancer and endometrial cancer, P < 0.001; ovarian cancer, P < 0.05). TMB increased with additional POLE variants (P < 0.001), but plateaued at 2, suggesting an association between the presence of these variants and TMB. Integrated analysis of AlphaFold2 POLE models and quantitative stability estimates predicted the impact of multiple POLE variants on POLE functionality. The prevalence of immunogenic neoepitopes was notably higher in the "POLE ExoD driver plus POLE Variant" tumors. Overall, this study reveals a novel correlation between POLE variants in POLE ExoD-driven tumors, and ultra-high TMB. Currently, only select pathogenic ExoD mutations with a reliable association with ultra-high TMB inform clinical practice. Thus, these findings are hypothesis-generating, require functional validation, and could potentially inform tumor classification, treatment responses, and clinical outcomes. SIGNIFICANCE Somatic POLE ExoD driver mutations cause proofreading deficiency that induces high TMB. This study suggests a novel modifier role for POLE variants in POLE ExoD-driven tumors, associated with ultra-high TMB. These data, in addition to future functional studies, may inform tumor classification, therapeutic response, and patient outcomes.
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Affiliation(s)
- Shreya M. Shah
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Science Scholars Program, Temple University, Philadelphia, Pennsylvania
| | - Elena V. Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Salena Ringenbach
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Lewis Katz School of Medicine, Temple University, Bethlehem, Pennsylvania
| | - Bulat Faezov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mark Andrake
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Arjun Gandhi
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- University College Dublin School of Medicine and Medical Science, Dublin, Ireland
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Julen Viana-Errasti
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | | | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Roland L. Dunbrack
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael J. Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
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17
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Hayran AB, Liabakk NB, Aas PA, Kusnierczyk A, Vågbø CB, Sarno A, Iveland TS, Chawla K, Zahn A, Di Noia JM, Slupphaug G, Kavli B. RPA guides UNG to uracil in ssDNA to facilitate antibody class switching and repair of mutagenic uracil at the replication fork. Nucleic Acids Res 2024; 52:784-800. [PMID: 38000394 PMCID: PMC10810282 DOI: 10.1093/nar/gkad1115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) interacts with replication protein A (RPA), the major ssDNA-binding protein, to promote deamination of cytosine to uracil in transcribed immunoglobulin (Ig) genes. Uracil-DNA glycosylase (UNG) acts in concert with AID during Ig diversification. In addition, UNG preserves genome integrity by base-excision repair (BER) in the overall genome. How UNG is regulated to support both mutagenic processing and error-free repair remains unknown. UNG is expressed as two isoforms, UNG1 and UNG2, which both contain an RPA-binding helix that facilitates uracil excision from RPA-coated ssDNA. However, the impact of this interaction in antibody diversification and genome maintenance has not been investigated. Here, we generated B-cell clones with targeted mutations in the UNG RPA-binding motif, and analysed class switch recombination (CSR), mutation frequency (5' Ig Sμ), and genomic uracil in clones representing seven Ung genotypes. We show that the UNG:RPA interaction plays a crucial role in both CSR and repair of AID-induced uracil at the Ig loci. By contrast, the interaction had no significant impact on total genomic uracil levels. Thus, RPA coordinates UNG during CSR and pre-replicative repair of mutagenic uracil in ssDNA but is not essential in post-replicative and canonical BER of uracil in dsDNA.
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Affiliation(s)
- Abdul B Hayran
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Nina B Liabakk
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Per A Aas
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Anna Kusnierczyk
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- PROMEC - Proteomics and Modomics Experimental Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Cathrine B Vågbø
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- PROMEC - Proteomics and Modomics Experimental Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Tobias S Iveland
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Konika Chawla
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- BioCore - Bioinformatics Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
- Département of Médicine, Université de Montréal H3C 3J7 Montréal, Québec, Canada
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- PROMEC - Proteomics and Modomics Experimental Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Bodil Kavli
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
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18
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Marple T, Son MY, Cheng X, Ko JH, Sung P, Hasty P. TREX2 deficiency suppresses spontaneous and genotoxin-associated mutagenesis. Cell Rep 2024; 43:113637. [PMID: 38175749 PMCID: PMC10883656 DOI: 10.1016/j.celrep.2023.113637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/15/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
TREX2, a 3'-5' exonuclease, is a part of the DNA damage tolerance (DDT) pathway that stabilizes replication forks (RFs) by ubiquitinating PCNA along with the ubiquitin E3 ligase RAD18 and other DDT factors. Mismatch repair (MMR) corrects DNA polymerase errors, including base mismatches and slippage. Here we demonstrate that TREX2 deletion reduces mutations in cells upon exposure to genotoxins, including those that cause base lesions and DNA polymerase slippage. Importantly, we show that TREX2 generates most of the spontaneous mutations in MMR-mutant cells derived from mice and people. TREX2-induced mutagenesis is dependent on the nuclease and DNA-binding attributes of TREX2. RAD18 deletion also reduces spontaneous mutations in MMR-mutant cells, albeit to a lesser degree. Inactivation of both MMR and TREX2 additively increases RF stalls, while it decreases DNA breaks, consistent with a synthetic phenotype.
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Affiliation(s)
- Teresa Marple
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Mi Young Son
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Xiaodong Cheng
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Jun Ho Ko
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; The Mays Cancer Center, University of Texas Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Paul Hasty
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; The Mays Cancer Center, University of Texas Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229, USA; Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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Kruchinin AA, Kamzeeva PN, Zharkov DO, Aralov AV, Makarova AV. 8-Oxoadenine: A «New» Player of the Oxidative Stress in Mammals? Int J Mol Sci 2024; 25:1342. [PMID: 38279342 PMCID: PMC10816367 DOI: 10.3390/ijms25021342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Numerous studies have shown that oxidative modifications of guanine (7,8-dihydro-8-oxoguanine, 8-oxoG) can affect cellular functions. 7,8-Dihydro-8-oxoadenine (8-oxoA) is another abundant paradigmatic ambiguous nucleobase but findings reported on the mutagenicity of 8-oxoA in bacterial and eukaryotic cells are incomplete and contradictory. Although several genotoxic studies have demonstrated the mutagenic potential of 8-oxoA in eukaryotic cells, very little biochemical and bioinformatics data about the mechanism of 8-oxoA-induced mutagenesis are available. In this review, we discuss dual coding properties of 8-oxoA, summarize historical and recent genotoxicity and biochemical studies, and address the main protective cellular mechanisms of response to 8-oxoA. We also discuss the available structural data for 8-oxoA bypass by different DNA polymerases as well as the mechanisms of 8-oxoA recognition by DNA repair enzymes.
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Affiliation(s)
- Alexander A. Kruchinin
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- National Research Center, Kurchatov Institute, Kurchatov sq. 2, 123182 Moscow, Russia
| | - Polina N. Kamzeeva
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia;
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Andrey V. Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Alena V. Makarova
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- National Research Center, Kurchatov Institute, Kurchatov sq. 2, 123182 Moscow, Russia
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20
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Lopez Chiloeches M, Bergonzini A, Martin OCB, Bergstein N, Erttmann SF, Aung KM, Gekara NO, Avila Cariño JF, Pateras IS, Frisan T. Genotoxin-producing Salmonella enterica induces tissue-specific types of DNA damage and DNA damage response outcomes. Front Immunol 2024; 14:1270449. [PMID: 38274797 PMCID: PMC10808668 DOI: 10.3389/fimmu.2023.1270449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Typhoid toxin-expressing Salmonella enterica causes DNA damage in the intestinal mucosa in vivo, activating the DNA damage response (DDR) in the absence of inflammation. To understand whether the tissue microenvironment constrains the infection outcome, we compared the immune response and DDR patterns in the colon and liver of mice infected with a genotoxigenic strain or its isogenic control strain. Methods In situ spatial transcriptomic and immunofluorescence have been used to assess DNA damage makers, activation of the DDR, innate immunity markers in a multiparametric analysis. Result The presence of the typhoid toxin protected from colonic bacteria-induced inflammation, despite nuclear localization of p53, enhanced co-expression of type-I interferons (IfnbI) and the inflammasome sensor Aim2, both classic features of DNA-break-induced DDR activation. These effects were not observed in the livers of either infected group. Instead, in this tissue, the inflammatory response and DDR were associated with high oxidative stress-induced DNA damage. Conclusions Our work highlights the relevance of the tissue microenvironment in enabling the typhoid toxin to suppress the host inflammatory response in vivo.
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Affiliation(s)
- Maria Lopez Chiloeches
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR) Umeå University, Umeå, Sweden
| | - Anna Bergonzini
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR) Umeå University, Umeå, Sweden
| | - Océane C. B. Martin
- Biological and Medical Sciences Department, University Bordeaux, Centre National de la Recherche Scientifique (CNRS), Institut de Biochimie et Génétique Cellulaires (IBGC), Unité Mixte de Recherche (UMR) 5095, Bordeaux, France
| | - Nicole Bergstein
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR) Umeå University, Umeå, Sweden
| | - Saskia F. Erttmann
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR) Umeå University, Umeå, Sweden
- Infection Oncology Unit, Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Kyaw Min Aung
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Nelson O. Gekara
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Institute of Medical Microbiology and Hygiene, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Javier F. Avila Cariño
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR) Umeå University, Umeå, Sweden
| | - Ioannis S. Pateras
- Second Department of Pathology, “Attikon” University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Teresa Frisan
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR) Umeå University, Umeå, Sweden
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21
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Shumega AR, Pavlov YI, Chirinskaite AV, Rubel AA, Inge-Vechtomov SG, Stepchenkova EI. CRISPR/Cas9 as a Mutagenic Factor. Int J Mol Sci 2024; 25:823. [PMID: 38255897 PMCID: PMC10815272 DOI: 10.3390/ijms25020823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
The discovery of the CRISPR/Cas9 microbial adaptive immune system has revolutionized the field of genetics, by greatly enhancing the capacity for genome editing. CRISPR/Cas9-based editing starts with DNA breaks (or other lesions) predominantly at target sites and, unfortunately, at off-target genome sites. DNA repair systems differing in accuracy participate in establishing desired genetic changes but also introduce unwanted mutations, that may lead to hereditary, oncological, and other diseases. New approaches to alleviate the risks associated with genome editing include attenuating the off-target activity of editing complex through the use of modified forms of Cas9 nuclease and single guide RNA (sgRNA), improving delivery methods for sgRNA/Cas9 complex, and directing DNA lesions caused by the sgRNA/Cas9 to non-mutagenic repair pathways. Here, we have described CRISPR/Cas9 as a new powerful mutagenic factor, discussed its mutagenic properties, and reviewed factors influencing the mutagenic activity of CRISPR/Cas9.
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Affiliation(s)
- Andrey R. Shumega
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Departments of Biochemistry and Molecular Biology, Pathology and Microbiology, Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Angelina V. Chirinskaite
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia;
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Sergey G. Inge-Vechtomov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
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22
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Arora S, Satija S, Mittal A, Solanki S, Mohanty SK, Srivastava V, Sengupta D, Rout D, Arul Murugan N, Borkar RM, Ahuja G. Unlocking The Mysteries of DNA Adducts with Artificial Intelligence. Chembiochem 2024; 25:e202300577. [PMID: 37874183 DOI: 10.1002/cbic.202300577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
Cellular genome is considered a dynamic blueprint of a cell since it encodes genetic information that gets temporally altered due to various endogenous and exogenous insults. Largely, the extent of genomic dynamicity is controlled by the trade-off between DNA repair processes and the genotoxic potential of the causative agent (genotoxins or potential carcinogens). A subset of genotoxins form DNA adducts by covalently binding to the cellular DNA, triggering structural or functional changes that lead to significant alterations in cellular processes via genetic (e. g., mutations) or non-genetic (e. g., epigenome) routes. Identification, quantification, and characterization of DNA adducts are indispensable for their comprehensive understanding and could expedite the ongoing efforts in predicting carcinogenicity and their mode of action. In this review, we elaborate on using Artificial Intelligence (AI)-based modeling in adducts biology and present multiple computational strategies to gain advancements in decoding DNA adducts. The proposed AI-based strategies encompass predictive modeling for adduct formation via metabolic activation, novel adducts' identification, prediction of biochemical routes for adduct formation, adducts' half-life predictions within biological ecosystems, and, establishing methods to predict the link between adducts chemistry and its location within the genomic DNA. In summary, we discuss some futuristic AI-based approaches in DNA adduct biology.
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Affiliation(s)
- Sakshi Arora
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Shiva Satija
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Aayushi Mittal
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Saveena Solanki
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Sanjay Kumar Mohanty
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry CBH School, Royal Institute of Technology (KTH) AlbaNova University Center, 10691, Stockholm, Sweden
| | - Debarka Sengupta
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Diptiranjan Rout
- Department of Transfusion Medicine National Cancer Institute, AIIMS, New Delhi, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110608, India
| | - Natarajan Arul Murugan
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Roshan M Borkar
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER)-Guwahati, Sila Katamur Halugurisuk P.O.: Changsari, Dist, Guwahati, Assam, 781101, India
| | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
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Habiballah S, Heath LS, Reisfeld B. A deep-learning approach for identifying prospective chemical hazards. Toxicology 2024; 501:153708. [PMID: 38104655 DOI: 10.1016/j.tox.2023.153708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
With the aim of helping to set safe exposure limits for the general population, various techniques have been implemented to conduct risk assessments for chemicals and other environmental stressors; however, none of these tools facilitate the identification of completely new chemicals that are likely hazardous and elicit an adverse biological effect. Here, we detail a novel in silico, deep-learning framework that is designed to systematically generate structures for new chemical compounds that are predicted to be chemical hazards. To assess the utility of the framework, we applied the tool to four endpoints related to environmental toxicants and their impacts on human and animal health: (i) toxicity to honeybees, (ii) immunotoxicity, (iii) endocrine disruption via ER-α antagonism, and (iv) mutagenicity. In addition, we characterized the predicted potency of these compounds and examined their structural relationship to existing chemicals of concern. As part of the array of emerging new approach methodologies (NAMs), we anticipate that such a framework will be a significant asset to risk assessors and other environmental scientists when planning and forecasting. Though not in the scope of the present study, we expect that the methodology detailed here could also be useful in the de novo design of more environmentally-friendly industrial chemicals.
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Affiliation(s)
- Sohaib Habiballah
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1370, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061-0106, USA
| | - Brad Reisfeld
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1370, USA; Colorado School of Public Health, Colorado State University, Fort Collins, CO 80523-1612, USA.
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24
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Li J, Dai L, Feng Y, Cao Z, Ding Y, Xu H, Xu A, Du H. Multigenerational effects and mutagenicity of three flame retardants on germ cells in Caenorhabditis elegans. Ecotoxicol Environ Saf 2024; 269:115815. [PMID: 38091675 DOI: 10.1016/j.ecoenv.2023.115815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/14/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024]
Abstract
Flame retardants (FRs) have raised public concerns because of their environmental persistence and negative impacts on human health. Recent evidence has revealed that many FRs exhibit reproductive toxicities and transgenerational impacts, whereas the toxic effects of FRs on germ cells remain barely explored. Here we investigated the multigenerational effects of three flame retardants (TBBPA, TCEP and TCPP) on germ cell development in Caenorhabditis elegans, and examined the germ cell mutagenicity of these FRs by using whole genome sequencing. Parental exposure to three FRs markedly increased germ cell apoptosis, and impeded oogenesis in F1-F6 offspring. In addition, the double-increased mutation frequencies observed in progeny genomes uncover the mutagenic actions of FRs on germ cells. Analysis of mutation spectra revealed that these FRs predominantly induced point mutations at A:T base pairs, whereas both small and large indels were almost unaffected. These results revealed the long-term effects of FRs on development and genomic stability of germ cells, which may pose risks to environmental organisms and human reproductive health. Taken together, our findings suggest that germ cell mutagenicity should be carefully examined for the environmental risk assessment of FRs and other emerging pollutants.
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Affiliation(s)
- Jiali Li
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, Anhui, China; Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China
| | - Linglong Dai
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Science Island Branch, Graduate School of USTC, Hefei 230026, Anhui, China
| | - Yu Feng
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Science Island Branch, Graduate School of USTC, Hefei 230026, Anhui, China
| | - Zhenxiao Cao
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Yuting Ding
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Hao Xu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, Anhui, China
| | - An Xu
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China.
| | - Hua Du
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China.
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25
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Haque MM, Hossen MN, Rahman A, Roy J, Talukder MR, Ahmed M, Ahiduzzaman M, Haque MA. Decolorization, degradation and detoxification of mutagenic dye Methyl orange by novel biofilm producing plant growth-promoting rhizobacteria. Chemosphere 2024; 346:140568. [PMID: 38303387 DOI: 10.1016/j.chemosphere.2023.140568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 10/10/2023] [Accepted: 10/26/2023] [Indexed: 02/03/2024]
Abstract
Discharge of untreated dyeing wastewater nearby water-bodies is one of major causes of water pollution. Generally, bacterial strains isolated from industrial effluents and/or contaminated soils are used for the bioremediation of Methyl orange (MO), a mutagenic recalcitrant mono-azo dye, used in textiles and biomedical. However, MO degradation by biofilm producing plant growth-promoting rhizobacteria (BPPGPR) was not studied yet. In this study, 19 out of 21 BPPGPR strains decolorized 96.3-99.9% and 89.5-96.3% MO under microaerophilic and aerobic conditions, respectively from Luria-Bertani broth (LBB) followed by yeast-extract peptone and salt-optimized broth plus glycerol media within 120 h of incubation at 28 °C. Only selected BPPGPR including Pseudomonas fluorescens ESR7, P. veronii ESR13, Stenotrophomonas maltophilia ESR20, Staphylococcus saprophyticus ESD8, and P. parafulva ESB18 were examined for process optimization of MO decolorization using a single factor optimization method. This study showed that under optimal conditions (e.g., LBB, 100 mg L-1 MO, pH 7, incubation of 96 h, 28 °C), these strains could remove 99.1-99.8% and 97.6-99.5% MO under microaerophilic and aerobic conditions, respectively. Total azoreductase and laccase activities responsible for biodegradation were also remarkably activated in the biodegraded samples under optimal conditions, while these activities were repressed under unfavorable conditions (e.g., 40 °C and 7.5% NaCl). This study confirmed that MO was degraded and detoxified by these bacterial strains through breakage of azo bond. So far, this is the first report on bioremediation of MO by the BPPGPR strains. These BPPGPR strains are highly promising to be utilized for the bioremediation of dyeing wastewater in future.
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Affiliation(s)
- Md Manjurul Haque
- Department of Environmental Science, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| | - Md Nayeem Hossen
- Department of Environmental Science, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Ashikur Rahman
- Department of Environmental Science, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Joty Roy
- Department of Environmental Science, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Raihan Talukder
- Department of Environmental Science, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Minhaz Ahmed
- Department of Agroforestry and Environment, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Ahiduzzaman
- Department of Agro-processing, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Amdadul Haque
- Department of Agro-processing, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
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Till BJ. Identification of Induced Copy Number Variation from Low Coverage Sequence Data. Methods Mol Biol 2024; 2787:141-152. [PMID: 38656487 DOI: 10.1007/978-1-0716-3778-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Induced mutations have been an important tool for plant breeding and functional genomics for more than 80 years. Novel mutations can be induced by treating seed or other plant cells with chemical mutagens or ionizing radiation. The majority of released mutant crop varieties were developed using ionizing radiation. This has been shown to create a variety of different DNA lesions including large (e.g., >=10,000 bps) copy number variations (CNV). Detection of induced DNA lesions from whole genome sequence data is useful for choosing a mutagen dosage prior to committing resources to develop a large mutant population for forward or reverse-genetic screening. Here I provide a method for detecting large induced CNV from mutant plants that utilizes a new tool to streamline the process of obtaining read coverage directly from BAM files, comparing non-mutagenized controls and mutagenized samples, and plotting the results for visual evaluation. Example data is provided from low coverage sequence data from gamma-irradiated vegetatively propagated triploid banana.
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Affiliation(s)
- Bradley J Till
- Veterinary Genetics Laboratory, University of California, Davis, CA, USA.
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27
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Macdonald Miller S, Abbriano RM, Herdean A, Banati R, Ralph PJ, Pernice M. Random mutagenesis of Phaeodactylum tricornutum using ultraviolet, chemical, and X-radiation demonstrates the need for temporal analysis of phenotype stability. Sci Rep 2023; 13:22385. [PMID: 38104215 PMCID: PMC10725415 DOI: 10.1038/s41598-023-45899-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/25/2023] [Indexed: 12/19/2023] Open
Abstract
We investigated two non-ionising mutagens in the form of ultraviolet radiation (UV) and ethyl methanosulfonate (EMS) and an ionising mutagen (X-ray) as methods to increase fucoxanthin content in the model diatom Phaeodactylum tricornutum. We implemented an ultra-high throughput method using fluorescence-activated cell sorting (FACS) and live culture spectral deconvolution for isolation and screening of potential pigment mutants, and assessed phenotype stability by measuring pigment content over 6 months using high-performance liquid chromatography (HPLC) to investigate the viability of long-term mutants. Both UV and EMS resulted in significantly higher fucoxanthin within the 6 month period after treatment, likely as a result of phenotype instability. A maximum fucoxanthin content of 135 ± 10% wild-type found in the EMS strain, a 35% increase. We found mutants generated using all methods underwent reversion to the wild-type phenotype within a 6 month time period. X-ray treatments produced a consistently unstable phenotype even at the maximum treatment of 1000 Grays, while a UV mutant and an EMS mutant reverted to wild-type after 4 months and 6 months, respectively, despite showing previously higher fucoxanthin than wild-type. This work provides new insights into key areas of microalgal biotechnology, by (i) demonstrating the use of an ionising mutagen (X-ray) on a biotechnologically relevant microalga, and by (ii) introducing temporal analysis of mutants which has substantial implications for strain creation and utility for industrial applications.
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Affiliation(s)
- Sean Macdonald Miller
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia.
| | - Raffaela M Abbriano
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Andrei Herdean
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Richard Banati
- Australian Nuclear Science and Technology Organisation (ANSTO), Kirrawee DC, NSW, 2232, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Peter J Ralph
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Mathieu Pernice
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
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Speer RM, Nandi SP, Cooper KL, Zhou X, Yu H, Guo Y, Hudson LG, Alexandrov LB, Liu KJ. Arsenic is a potent co-mutagen of ultraviolet light. Commun Biol 2023; 6:1273. [PMID: 38104187 PMCID: PMC10725444 DOI: 10.1038/s42003-023-05659-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
Arsenic enhances the carcinogenicity of ultraviolet radiation (UVR). However, the mechanisms of arsenic-driven oncogenesis are not well understood. Here, we utilize experimental systems to investigate the carcinogenic and mutagenic properties of co-exposure to arsenic and UVR. In vitro and in vivo exposures indicate that, by itself, arsenic is not mutagenic. However, in combination with UVR, arsenic exposure has a synergistic effect leading to an accelerated mouse skin carcinogenesis and to more than 2-fold enrichment of UVR mutational burden. Notably, mutational signature ID13, previously found only in UVR-associated human skin cancers, is observed exclusively in mouse skin tumors and cell lines jointly exposed to arsenic and UVR. This signature was not observed in any model system exposed purely to arsenic or purely to UVR, making ID13, to the best of our knowledge, the first co-exposure signature to be reported using controlled experimental conditions. Analysis of existing skin cancer genomics data reveals that only a subset of cancers harbor ID13 and these exhibit an elevated UVR mutagenesis. Our results report a unique mutational signature caused by a co-exposure to two environmental carcinogens and provide comprehensive evidence that arsenic is a potent co-mutagen and co-carcinogen of UVR.
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Affiliation(s)
- Rachel M Speer
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Shuvro P Nandi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
| | - Karen L Cooper
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Xixi Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Hui Yu
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA
| | - Yan Guo
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA
| | - Laurie G Hudson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA.
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.
| | - Ke Jian Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA.
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, 11794, USA.
- Department of Pathology, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA.
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Diniz RR, Domingos TFS, Pinto GR, Cabral LM, de Pádula M, de Souza AMT. Use of in silico and in vitro methods as a potential new approach methodologies (NAMs) for (photo)mutagenicity and phototoxicity risk assessment of agrochemicals. Sci Total Environ 2023; 904:167320. [PMID: 37748613 DOI: 10.1016/j.scitotenv.2023.167320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
The increased use of agrochemicals raises concerns about environmental, animal, and mainly human toxicology. The development of New Approach Methodologies (NAMs) for toxicological risk assessment including new in vitro tests and in silico protocols is encouraged. Although agrochemical mutagenicity testing is well established, a complementary alternative approach may contribute to increasing reliability, with the consequent reduction of false-positive results that lead to unnecessary use of animals in follow-up in vivo testing. Additionally, it is unreasonable to underestimate the phototoxic effects of an accidental dermal exposure to agrochemicals during agricultural work or domestic application in the absence of adequate personal protection equipment, especially in terms of photomutagenicity. In this scenario, we addressed the integration of in vitro and in silico techniques as NAMs to assess the mutagenic and phototoxic potential of agrochemicals. In the present study we used the yno1 S. cerevisiae strain as a biomodel for in vitro assessment of agrochemical mutagenicity, both in the absence and in the presence of simulated sunlight. In parallel, in silico predictions were performed using a combination of expert rule-based and statistical-based models to assess gene mutations and phototoxicity. None of the tested agrochemicals showed mutagenic potential in the two proposed approaches. The Gly and 2,4D herbicides were photomutagenic in the in vitro yeast test despite the negative in silico prediction of phototoxicity. Herein, we demonstrated a novel experimental approach combining both in silico and in vitro experiments to address the complementary investigation of the phototoxicity and (photo)mutagenicity of agrochemicals. These findings shed light on the importance of investigating and reconsidering the photosafety assessment of these products, using not only photocytotoxicity assays but also photomutagenicity assays, which should be encouraged.
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Affiliation(s)
- Raiane R Diniz
- Universidade Federal do Rio de Janeiro, Faculdade de Farmácia, Laboratório de Modelagem Molecular & QSAR (ModMolQSAR), Rio de Janeiro, RJ, Brazil; Universidade Federal do Rio de Janeiro, Faculdade de Farmácia, Laboratório de Microbiologia e Avaliação Genotóxica (LAMIAG), Rio de Janeiro, RJ, Brazil
| | | | - Gabriel R Pinto
- Universidade Federal do Rio de Janeiro, Faculdade de Farmácia, Laboratório de Microbiologia e Avaliação Genotóxica (LAMIAG), Rio de Janeiro, RJ, Brazil
| | - Lucio M Cabral
- Universidade Federal do Rio de Janeiro, Faculdade de Farmácia, Laboratório de Tecnologia Industrial Farmacêutica (LabTIF), Rio de Janeiro, RJ, Brazil
| | - Marcelo de Pádula
- Universidade Federal do Rio de Janeiro, Faculdade de Farmácia, Laboratório de Microbiologia e Avaliação Genotóxica (LAMIAG), Rio de Janeiro, RJ, Brazil
| | - Alessandra M T de Souza
- Universidade Federal do Rio de Janeiro, Faculdade de Farmácia, Laboratório de Modelagem Molecular & QSAR (ModMolQSAR), Rio de Janeiro, RJ, Brazil.
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Keir JLA, Papas W, Wawrzynczak A, Aranda-Rodriguez R, Blais JM, White PA. Use of silicone wristbands to measure firefighters' exposures to polycyclic aromatic hydrocarbons (PAHs) during live fire training. Environ Res 2023; 239:117306. [PMID: 37797669 DOI: 10.1016/j.envres.2023.117306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023]
Abstract
Firefighters experience exposures to carcinogenic and mutagenic substances, including polycyclic aromatic hydrocarbons (PAHs). Silicone wristbands (SWBs) have been used as passive samplers to assess firefighters' exposures over the course of a shift but their utility in measuring short term exposures, source of exposure, and correlations with other measurements of exposure have not yet been investigated. In this study, SWBs were used to measure the concentrations of 16 priority PAHs inside and outside of firefighters' personal protective equipment (PPE) while firefighting. SWBs were placed on the wrist and jacket of 20 firefighters conducting live fire training. Correlations were made with matching data from a sister project that measured urinary concentrations of PAH metabolites and PAH concentrations from personal air samples from the same participants. Naphthalene, acenaphthylene and phenanthrene had the highest geometric mean concentrations in both jacket and wrist SWB, with 1040, 320, 180 ng/g SWB for jacket and 55.0, 4.9, and 6.0 ng/g SWB for wrist, respectively. Ratios of concentrations between the jacket and wrist SWBs were calculated as worker protection factors (WPFs) and averaged 40.1 for total PAHs and ranged from 2.8 to 214 for individual PAHs, similar to previous studies. Several significant correlations were observed between PAHs in jacket SWBs and air samples (e.g., total and low molecular weight PAHs, r = 0.55 and 0.59, p < 0.05, respectively). A few correlations were found between PAHs from SWBs worn on the wrist and jacket, and urinary concentrations of PAH metabolites and PAH concentrations in air samples. The ability of the SWBs to accurately capture exposures to various PAHs was likely influenced by short sampling time, high temperatures, and high turbulence. Future work should further examine the limitations of SWBs for PAH exposures in firefighting, and other extreme environments.
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Affiliation(s)
- Jennifer L A Keir
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada; Environmental Health Science and Research Bureau, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, K1A 0K9, Canada
| | - William Papas
- Environmental Health Science and Research Bureau, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, K1A 0K9, Canada
| | - Adam Wawrzynczak
- Environmental Health Science and Research Bureau, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, K1A 0K9, Canada
| | - Rocio Aranda-Rodriguez
- Environmental Health Science and Research Bureau, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, K1A 0K9, Canada.
| | - Jules M Blais
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada.
| | - Paul A White
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada; Environmental Health Science and Research Bureau, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, K1A 0K9, Canada
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Dolan M, St. John N, Zaidi F, Doyle F, Fasullo M. High-throughput screening of the Saccharomyces cerevisiae genome for 2-amino-3-methylimidazo [4,5-f] quinoline resistance identifies colon cancer-associated genes. G3 (Bethesda) 2023; 13:jkad219. [PMID: 37738679 PMCID: PMC11025384 DOI: 10.1093/g3journal/jkad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 10/25/2022] [Accepted: 09/15/2023] [Indexed: 09/24/2023]
Abstract
Heterocyclic aromatic amines (HAAs) are potent carcinogenic agents found in charred meats and cigarette smoke. However, few eukaryotic resistance genes have been identified. We used Saccharomyces cerevisiae (budding yeast) to identify genes that confer resistance to 2-amino-3-methylimidazo[4,5-f] quinoline (IQ). CYP1A2 and NAT2 activate IQ to become a mutagenic nitrenium compound. Deletion libraries expressing human CYP1A2 and NAT2 or no human genes were exposed to either 400 or 800 µM IQ for 5 or 10 generations. DNA barcodes were sequenced using the Illumina HiSeq 2500 platform and statistical significance was determined for exactly matched barcodes. We identified 424 ORFs, including 337 genes of known function, in duplicate screens of the "humanized" collection for IQ resistance; resistance was further validated for a select group of 51 genes by growth curves, competitive growth, or trypan blue assays. Screens of the library not expressing human genes identified 143 ORFs conferring resistance to IQ per se. Ribosomal protein and protein modification genes were identified as IQ resistance genes in both the original and "humanized" libraries, while nitrogen metabolism, DNA repair, and growth control genes were also prominent in the "humanized" library. Protein complexes identified included the casein kinase 2 (CK2) and histone chaperone (HIR) complex. Among DNA Repair and checkpoint genes, we identified those that function in postreplication repair (RAD18, UBC13, REV7), base excision repair (NTG1), and checkpoint signaling (CHK1, PSY2). These studies underscore the role of ribosomal protein genes in conferring IQ resistance, and illuminate DNA repair pathways for conferring resistance to activated IQ.
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Affiliation(s)
- Michael Dolan
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Nick St. John
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Faizan Zaidi
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Francis Doyle
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Michael Fasullo
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
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Colomer-Castell S, Gregori J, Garcia-Cehic D, Riveiro-Barciela M, Buti M, Rando-Segura A, Vico-Romero J, Campos C, Ibañez-Lligoña M, Adombi CM, Cortese MF, Tabernero D, Esteban JI, Rodriguez-Frias F, Quer J. In-Host HEV Quasispecies Evolution Shows the Limits of Mutagenic Antiviral Treatments. Int J Mol Sci 2023; 24:17185. [PMID: 38139013 PMCID: PMC10743355 DOI: 10.3390/ijms242417185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
Here, we report the in-host hepatitis E virus (HEV) quasispecies evolution in a chronically infected patient who was treated with three different regimens of ribavirin (RBV) for nearly 6 years. Sequential plasma samples were collected at different time points and subjected to RNA extraction and deep sequencing using the MiSeq Illumina platforms. Specifically, we RT-PCR amplified a single amplicon from the core region located in the open-reading frame 2 (ORF2). At the nucleotide level (genotype), our analysis showed an increase in the number of rare haplotypes and a drastic reduction in the frequency of the master (most represented) sequence during the period when the virus was found to be insensitive to RBV treatment. Contrarily, at the amino acid level (phenotype), our study revealed conservation of the amino acids, which is represented by a high prevalence of the master sequence. Our findings suggest that using mutagenic antivirals concomitant with high viral loads can lead to the selection and proliferation of a rich set of synonymous haplotypes that express the same phenotype. This can also lead to the selection and proliferation of conservative substitutions that express fitness-enhanced phenotypes. These results have important clinical implications, as they suggest that using mutagenic agents as a monotherapy treatment regimen in the absence of sufficiently effective viral inhibitors can result in diversification and proliferation of a highly diverse quasispecies resistant to further treatment. Therefore, such approaches should be avoided whenever possible.
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Affiliation(s)
- Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (D.G.-C.); (M.R.-B.); (M.B.); (J.V.-R.); (C.C.); (M.I.-L.); (C.M.A.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (A.R.-S.); (M.F.C.); (D.T.); (F.R.-F.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (D.G.-C.); (M.R.-B.); (M.B.); (J.V.-R.); (C.C.); (M.I.-L.); (C.M.A.); (J.I.E.)
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (D.G.-C.); (M.R.-B.); (M.B.); (J.V.-R.); (C.C.); (M.I.-L.); (C.M.A.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (A.R.-S.); (M.F.C.); (D.T.); (F.R.-F.)
| | - Mar Riveiro-Barciela
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (D.G.-C.); (M.R.-B.); (M.B.); (J.V.-R.); (C.C.); (M.I.-L.); (C.M.A.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (A.R.-S.); (M.F.C.); (D.T.); (F.R.-F.)
- Medicine Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Maria Buti
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (D.G.-C.); (M.R.-B.); (M.B.); (J.V.-R.); (C.C.); (M.I.-L.); (C.M.A.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (A.R.-S.); (M.F.C.); (D.T.); (F.R.-F.)
- Medicine Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Ariadna Rando-Segura
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (A.R.-S.); (M.F.C.); (D.T.); (F.R.-F.)
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Judit Vico-Romero
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (D.G.-C.); (M.R.-B.); (M.B.); (J.V.-R.); (C.C.); (M.I.-L.); (C.M.A.); (J.I.E.)
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (D.G.-C.); (M.R.-B.); (M.B.); (J.V.-R.); (C.C.); (M.I.-L.); (C.M.A.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (A.R.-S.); (M.F.C.); (D.T.); (F.R.-F.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Marta Ibañez-Lligoña
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (D.G.-C.); (M.R.-B.); (M.B.); (J.V.-R.); (C.C.); (M.I.-L.); (C.M.A.); (J.I.E.)
- Medicine Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Caroline Melanie Adombi
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (D.G.-C.); (M.R.-B.); (M.B.); (J.V.-R.); (C.C.); (M.I.-L.); (C.M.A.); (J.I.E.)
- Institute of Agropastoral Management, University Peleforo Gon Coulibaly, Korhogo BP 1328, Côte d’Ivoire
| | - Maria Francesca Cortese
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (A.R.-S.); (M.F.C.); (D.T.); (F.R.-F.)
- Biochemistry Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (A.R.-S.); (M.F.C.); (D.T.); (F.R.-F.)
- Biochemistry Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (D.G.-C.); (M.R.-B.); (M.B.); (J.V.-R.); (C.C.); (M.I.-L.); (C.M.A.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (A.R.-S.); (M.F.C.); (D.T.); (F.R.-F.)
- Medicine Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (A.R.-S.); (M.F.C.); (D.T.); (F.R.-F.)
- Biochemistry Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (D.G.-C.); (M.R.-B.); (M.B.); (J.V.-R.); (C.C.); (M.I.-L.); (C.M.A.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (A.R.-S.); (M.F.C.); (D.T.); (F.R.-F.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
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Wu-Baer F, Wong M, Tschoe L, Lin CS, Jiang W, Zha S, Baer R. ATM/ATR Phosphorylation of CtIP on Its Conserved Sae2-like Domain Is Required for Genotoxin-Induced DNA Resection but Dispensable for Animal Development. Cells 2023; 12:2762. [PMID: 38067190 PMCID: PMC10706839 DOI: 10.3390/cells12232762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/09/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Homology-directed repair (HDR) of double-strand DNA breaks (DSBs) is dependent on enzymatic resection of DNA ends by the Mre11/Rad50/Nbs1 complex. DNA resection is triggered by the CtIP/Sae2 protein, which allosterically promotes Mre11-mediated endonuclease DNA cleavage at a position internal to the DSB. Although the mechanics of resection, including the initial endonucleolytic step, are largely conserved in eucaryotes, CtIP and its functional counterpart in Saccharomyces cerevisiae (Sae2) share only a modest stretch of amino acid homology. Nonetheless, this stretch contains two highly conserved phosphorylation sites for cyclin-dependent kinases (T843 in mouse) and the damage-induced ATM/ATR kinases (T855 in mouse), both of which are required for DNA resection. To explore the function of ATM/ATR phosphorylation at Ctip-T855, we generated and analyzed mice expressing the Ctip-T855A mutant. Surprisingly, unlike Ctip-null mice and Ctip-T843A-expressing mice, both of which undergo embryonic lethality, homozygous CtipT855A/T855A mice develop normally. Nonetheless, they are hypersensitive to ionizing radiation, and CtipT855A/T855A mouse embryo fibroblasts from these mice display marked defects in DNA resection, chromosomal stability, and HDR-mediated repair of DSBs. Thus, although ATM/ATR phosphorylation of CtIP-T855 is not required for normal animal development, it enhances CtIP-mediated DNA resection in response to acute stress, such as genotoxin exposure.
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Affiliation(s)
- Foon Wu-Baer
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Madeline Wong
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Lydia Tschoe
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Chyuan-Sheng Lin
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shan Zha
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Richard Baer
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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34
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Seplyarskiy V, Koch EM, Lee DJ, Lichtman JS, Luan HH, Sunyaev SR. A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription. Nat Genet 2023; 55:2235-2242. [PMID: 38036792 DOI: 10.1038/s41588-023-01562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/06/2023] [Indexed: 12/02/2023]
Abstract
De novo mutations occur at substantially different rates depending on genomic location, sequence context and DNA strand. The success of methods to estimate selection intensity, infer demographic history and map rare disease genes, depends strongly on assumptions about the local mutation rate. Here we present Roulette, a genome-wide mutation rate model at basepair resolution that incorporates known determinants of local mutation rate. Roulette is shown to be more accurate than existing models. We use Roulette to refine the estimates of population growth within Europe by incorporating the full range of human mutation rates. The analysis of significant deviations from the model predictions revealed a tenfold increase in mutation rate in nearly all genes transcribed by polymerase III (Pol III), suggesting a new mutagenic mechanism. We also detected an elevated mutation rate within transcription factor binding sites restricted to sites actively used in testis and residing in promoters.
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Affiliation(s)
- Vladimir Seplyarskiy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA
| | - Evan M Koch
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA
| | - Daniel J Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua S Lichtman
- NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
- Soleil Labs, South San Francisco, CA, USA
| | - Harding H Luan
- NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
- Soleil Labs, South San Francisco, CA, USA
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA.
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35
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Ayres LCG, Dos Santos MAL, da Mota Santana LA, Avanci LDS, Souza DVD, Lima BNS, Soares AF, Sousa SFD, Trento CL, Ribeiro DA, Takeshita WM. Comparative evaluation of mutagenic effects of two cone-beam computed tomography in oral mucosa cells. Diagn Cytopathol 2023; 51:729-734. [PMID: 37533363 DOI: 10.1002/dc.25206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/05/2023] [Accepted: 07/23/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND This pilot study aimed to evaluate the mutagenic effects in cells of the oral mucosa after exposure to two different cone beam computed tomography (CBCT). METHODS Eighteen adults were submitted to the different CBCT (Carestream CS8100 3D and I-CAT). The cells were collected immediately before the CBCT exposure and 10 days later, when the material was placed on a slide and stained using the Feulgen/Fast Green technique. Microscopic analysis counted micronuclei and other nuclear alterations, which are indicative of cytotoxicity such as pyknosis, karyolysis, karyorrhexis, and binucletion. 2000 cells were analyzed. The statistical analysis was performed with the Wilcoxon Signed-Rank test to compare the frequency of cellular alterations, and the Mann-Whitney U test to compare different CBCTs, both with a significance level of 5%. RESULTS There was no statistically significant difference in the micronucleated cell count before and after the exposition to the ionizing radiation from I-CAT (p = .298) and CS8100 3D (p = .203) A significate increase of pyknosis (p < .001), karyolysis (p < .001), karyorrhexis (p < .001), and binucletion (p < .001) were noted on I-CAT CBCT. There was no statistically significant difference in cellular alterations in CS8100 3D CBCT. CONCLUSION Despite the increase in micronuclei after exposure, this study indicates that there is no evidence of genotoxicity. On the other hand, the I-CAT CBCT produced cytotoxic effects.
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Affiliation(s)
| | | | | | | | - Daniel Vitor de Souza
- Department of Biosciences, Federal University of Sao Paulo (UNIFESP), Santos, Brazil
| | | | | | - Sílvia Ferreira de Sousa
- Oral Surgery and Pathology Department, School of Dentistry, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Daniel Araki Ribeiro
- Department of Biosciences, Federal University of Sao Paulo (UNIFESP), Santos, Brazil
| | - Wilton Mitsunari Takeshita
- Department of Diagnosis and Surgery, São Paulo State University (UNESP), School of Dentistry, Araçatuba, Brazil
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36
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Ruis C, Weimann A, Tonkin-Hill G, Pandurangan AP, Matuszewska M, Murray GGR, Lévesque RC, Blundell TL, Floto RA, Parkhill J. Mutational spectra are associated with bacterial niche. Nat Commun 2023; 14:7091. [PMID: 37925514 PMCID: PMC10625568 DOI: 10.1038/s41467-023-42916-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
As observed in cancers, individual mutagens and defects in DNA repair create distinctive mutational signatures that combine to form context-specific spectra within cells. We reasoned that similar processes must occur in bacterial lineages, potentially allowing decomposition analysis to detect both disruption of DNA repair processes and exposure to niche-specific mutagens. Here we reconstruct mutational spectra for 84 clades from 31 diverse bacterial species and find distinct mutational patterns. We extract signatures driven by specific DNA repair defects using hypermutator lineages, and further deconvolute the spectra into multiple signatures operating within different clades. We show that these signatures are explained by both bacterial phylogeny and replication niche. By comparing mutational spectra of clades from different environmental and biological locations, we identify niche-associated mutational signatures, and then employ these signatures to infer the predominant replication niches for several clades where this was previously obscure. Our results show that mutational spectra may be associated with sites of bacterial replication when mutagen exposures differ, and can be used in these cases to infer transmission routes for established and emergent human bacterial pathogens.
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Affiliation(s)
- Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Aaron Weimann
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gemma G R Murray
- Parasites and Microbes Programme, Wellcome Sanger Institute; Wellcome Genome Campus, Cambridge, UK
| | - Roger C Lévesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Tom L Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK.
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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37
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da Silva Mirowski P, da Silva Coutinho de Araújo Bueno G, Elsner Rodrigues V, Fernandes Barros T, da Costa AG, Yoshida NC, da Rosa Guterres Z, Trentin DS, Rodrigues Garcez F. Chemical Composition and Evaluation of Antibacterial, Antibiofilm, and Mutagenic Potentials of a Propolis Sample from the Atlantic Forest of Midwest Brazil. Chem Biodivers 2023; 20:e202301238. [PMID: 37769153 DOI: 10.1002/cbdv.202301238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Sixteen triterpenoids with various skeletal types, five phenylpropanoid derivatives, and two flavonoids were isolated from a propolis sample produced by Apis mellifera collected in the Atlantic Forest of Midwest Brazil. Among these compounds, six triterpenes, namely 3β,20R-dihydroxylanost-24-en-3-yl-palmitate, (23E)-25-methoxycycloartan-23-en-3-one, 24-methylenecycloartenone, epi-lupeol, epi-α-amyrin, and epi-β-amyrin are being reported for the first time in propolis, while cycloartenone, (E)-cinnamyl benzoate, and (E)-cinnamyl cinnamate are new findings in Brazilian propolis. The presence of cycloartane- and lanostane-type triterpenoids, the latter being a class of compounds of restricted distribution in propolis worldwide, has not been reported in propolis from Midwest Brazil until now. The ethyl acetate phase obtained from the ethanol extract was effective in preventing biofilm formation by Staphylococcus aureus, with an inhibition rate of about 96 % at 0.5 mg.mL-1 , and with quercetin isolated as one of its active constituents. In contrast, the hexane phase exhibited notable antibacterial activity against Pseudomonas aeruginosa, inhibiting bacterial growth by 92 % at 0.5 mg.mL-1 ; however, none of the triterpenoids isolated from this phase proved active against this pathogen. The ethanol extract was neither toxic nor mutagenic at the concentrations tested, as determined by the in vivo SMART assay on Drosophila melanogaster, even under conditions of high metabolic activation.
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Affiliation(s)
- Patrick da Silva Mirowski
- Bioactive Natural Products Research Laboratory, Institute of Chemistry, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, 79074-460, Brazil
| | | | - Vitória Elsner Rodrigues
- Laboratório de Bacteriologia & Modelos Experimentais Alternativos, Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, 90050-170, Brazil
| | - Thayná Fernandes Barros
- Laboratório de Bacteriologia & Modelos Experimentais Alternativos, Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, 90050-170, Brazil
| | - Alberto Grangeiro da Costa
- Bioactive Natural Products Research Laboratory, Institute of Chemistry, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, 79074-460, Brazil
| | - Nídia Cristiane Yoshida
- Bioactive Natural Products Research Laboratory, Institute of Chemistry, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, 79074-460, Brazil
| | - Zaira da Rosa Guterres
- Bioactive Natural Products Research Laboratory, Institute of Chemistry, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, 79074-460, Brazil
| | - Danielle Silva Trentin
- Laboratório de Bacteriologia & Modelos Experimentais Alternativos, Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, 90050-170, Brazil
| | - Fernanda Rodrigues Garcez
- Bioactive Natural Products Research Laboratory, Institute of Chemistry, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, 79074-460, Brazil
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Attia SM, Ahmad SF, Nadeem A, Attia MSM, Ansari MA, Ashour AE, Albekairi NA, Al-Hamamah MA, Alshamrani AA, Bakheet SA. Saxagliptin, a selective dipeptidyl peptidase-4 inhibitor, alleviates somatic cell aneugenicity and clastogenicity in diabetic mice. Mutat Res Genet Toxicol Environ Mutagen 2023; 892:503707. [PMID: 37973297 DOI: 10.1016/j.mrgentox.2023.503707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Diabetes-related complications are becoming increasingly common as the global prevalence of diabetes increases. Diabetes is also linked to a high risk of developing cancer. This raises the question of whether cancer vulnerability is caused by diabetes itself or the use of antidiabetic drugs. Chromosomal instability, a source of genetic modification involving either an altered chromosomal number or structure, is a hallmark of cancer. Saxagliptin has been approved by the FDA for diabetes treatment. However, the detailed in vivo effects of prolonged saxagliptin treatment on chromosomal instability have not yet been reported. In this study, streptozotocin was used to induce diabetes in mice, and both diabetic and non-diabetic mice received saxagliptin for five weeks. Fluorescence in situ hybridization was conducted in combination with a bone marrow micronucleus test for measuring chromosomal instability. Our results indicated that saxagliptin is neither mutagenic nor cytotoxic, under the given treatment regimen. Diabetic mice had a much higher incidence of micronuclei formation, and a centromeric DNA probe was present inside the majority of the induced micronuclei, indicating that most of these were caused by chromosome nondisjunction. Conversely, diabetic mice treated with saxagliptin exhibited a significant decrease in micronuclei induction, which were centromeric-positive and centromeric-negative. Diabetes also causes significant biochemical changes indicative of oxidative stress, such as increased lipid peroxidation and decreased reduced/oxidized glutathione ratio, which was reversed by saxagliptin administration. Overall, saxagliptin, the non-mutagenic antidiabetic drug, maintains chromosomal integrity in diabetes and reduces micronuclei formation by restoring redox imbalance, further indicating its usefulness in diabetic patients.
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Affiliation(s)
- Sabry M Attia
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia.
| | - Sheikh F Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Ahmed Nadeem
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Mohamed S M Attia
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Mushtaq A Ansari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Abdelkader E Ashour
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Norah A Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Mohammed A Al-Hamamah
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Ali A Alshamrani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Saleh A Bakheet
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
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Zhao Y, Sun H, Lin F, Yang H. Acute, repeated inhalation toxicity, respiratory system irritation, and mutagenicity studies of 1,1,2,2-tetrafluoroethane (HFC-134) as the impurity in the pharmaceutical propellant 1,1,1,2-tetrafluoroethane (HFA-134a). Drug Chem Toxicol 2023; 46:841-850. [PMID: 35920286 DOI: 10.1080/01480545.2022.2104866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/05/2022] [Accepted: 07/17/2022] [Indexed: 11/03/2022]
Abstract
HFC-134 is the main impurity of HFA-134a. In order to verify the rationality of HFC-134 limits in HFA-134a and ensure the safety of HFA-134a as propellant in pharmaceutical metered-dose inhalers, acute inhalation toxicity, seven-day repeat dose inhalation irritation study, 21-day repeat dose inhalation toxicity study and reverse mutation assay of HFC-134 were tested to evaluate its inhalation safety. In acute inhalation studies, Sprague-Dawley rats were exposed nose-only to HFC-134 at levels of 100 000, 200 000, 400 000, 600 000, and 800 000 ppm for 4 h. Based on the mortality incidence, the calculated four-hour LC50 value for HFC-134 is 532 069 ppm for males and 502 058 ppm for females and acute inhalation toxicity is manifested as the lung lobes turn dark red. Exposures to 836 ± 67 ppm for 4 hours/day 7 days/week continuously did not induce local irritation of the respiratory system in Sprague-Dawley rats. Sprague-Dawley rats were exposed nose-only to HFC-134 at levels of 0 (control), 203 929 ppm and 394 871 ppm 2 h/day for 21 consecutive days, no significant treatment-related adverse effects was noted. Results from Ames studies demonstrated that HFC-134 was not mutagenic. Although HFC-134 has a very low acute inhalation toxicity, considering that its acute inhalation toxicity is higher than that of HFA-134a, and due to the high frequency of use of MDI by asthma patients, acceptance criteria of HFC-134 as the impurity in aerosol propellant HFA-134a should be lower than 8-h TWA WEEL value of 1000 ppm to ensure the safety of the MDI.
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Affiliation(s)
- Yanjun Zhao
- NMPA Key Laboratory for Quality Research and Evaluation of Pharmaceutical Excipients, Beijing, China
- National Institutes for Food and Drug Control, Beijing, China
| | - Huimin Sun
- NMPA Key Laboratory for Quality Research and Evaluation of Pharmaceutical Excipients, Beijing, China
- National Institutes for Food and Drug Control, Beijing, China
| | - Fei Lin
- NMPA Key Laboratory for Quality Research and Evaluation of Pharmaceutical Excipients, Beijing, China
- National Institutes for Food and Drug Control, Beijing, China
| | - Huiying Yang
- NMPA Key Laboratory for Quality Research and Evaluation of Pharmaceutical Excipients, Beijing, China
- National Institutes for Food and Drug Control, Beijing, China
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40
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Stanfill SB, Hecht SS, Joerger AC, González PJ, Maia LB, Rivas MG, Moura JJG, Gupta AK, Le Brun NE, Crack JC, Hainaut P, Sparacino-Watkins C, Tyx RE, Pillai SD, Zaatari GS, Henley SJ, Blount BC, Watson CH, Kaina B, Mehrotra R. From cultivation to cancer: formation of N-nitrosamines and other carcinogens in smokeless tobacco and their mutagenic implications. Crit Rev Toxicol 2023; 53:658-701. [PMID: 38050998 DOI: 10.1080/10408444.2023.2264327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/20/2023] [Indexed: 12/07/2023]
Abstract
Tobacco use is a major cause of preventable morbidity and mortality globally. Tobacco products, including smokeless tobacco (ST), generally contain tobacco-specific N-nitrosamines (TSNAs), such as N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-butanone (NNK), which are potent carcinogens that cause mutations in critical genes in human DNA. This review covers the series of biochemical and chemical transformations, related to TSNAs, leading from tobacco cultivation to cancer initiation. A key aim of this review is to provide a greater understanding of TSNAs: their precursors, the microbial and chemical mechanisms that contribute to their formation in ST, their mutagenicity leading to cancer due to ST use, and potential means of lowering TSNA levels in tobacco products. TSNAs are not present in harvested tobacco but can form due to nitrosating agents reacting with tobacco alkaloids present in tobacco during certain types of curing. TSNAs can also form during or following ST production when certain microorganisms perform nitrate metabolism, with dissimilatory nitrate reductases converting nitrate to nitrite that is then released into tobacco and reacts chemically with tobacco alkaloids. When ST usage occurs, TSNAs are absorbed and metabolized to reactive compounds that form DNA adducts leading to mutations in critical target genes, including the RAS oncogenes and the p53 tumor suppressor gene. DNA repair mechanisms remove most adducts induced by carcinogens, thus preventing many but not all mutations. Lastly, because TSNAs and other agents cause cancer, previously documented strategies for lowering their levels in ST products are discussed, including using tobacco with lower nornicotine levels, pasteurization and other means of eliminating microorganisms, omitting fermentation and fire-curing, refrigerating ST products, and including nitrite scavenging chemicals as ST ingredients.
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Affiliation(s)
- Stephen B Stanfill
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen S Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Andreas C Joerger
- Structural Genomics Consortium (SGC), Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pablo J González
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - Luisa B Maia
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | - Maria G Rivas
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - José J G Moura
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | | | - Nick E Le Brun
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Jason C Crack
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Grenoble Alpes University, Grenoble, France
| | - Courtney Sparacino-Watkins
- University of Pittsburgh, School of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Vascular Medicine Institute, PA, USA
| | - Robert E Tyx
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suresh D Pillai
- Department of Food Science & Technology, National Center for Electron Beam Research, Texas A&M University, College Station, TX, USA
| | - Ghazi S Zaatari
- Department of Pathology and Laboratory Medicine, American University of Beirut, Beirut, Lebanon
| | - S Jane Henley
- Division of Cancer Prevention and Control, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Benjamin C Blount
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clifford H Watson
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bernd Kaina
- Institute of Toxicology, University Medical Center, Mainz, Germany
| | - Ravi Mehrotra
- Centre for Health, Innovation and Policy Foundation, Noida, India
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41
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Baadu R, Chong KP, Gansau JA, Mohamed Zin MR, Dayou J. A systematic review on physical mutagens in rice breeding in Southeast Asia. PeerJ 2023; 11:e15682. [PMID: 37868055 PMCID: PMC10590103 DOI: 10.7717/peerj.15682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 06/14/2023] [Indexed: 10/24/2023] Open
Abstract
In the 1920s, Lewis Stadler initiated the introduction of permanent improvements to the genetic makeup of irradiated plants. Since then, studies related to breeding mutations have grown, as efforts have been made to expand and improve crop productivity and quality. Stadler's discovery began with x-rays on corn and barley and later extended to the use of gamma-rays, thermal, and fast neutrons in crops. Radiation has since been shown to be an effective and unique method for increasing the genetic variability of species, including rice. Numerous systematic reviews have been conducted on the impact of physical mutagens on the production and grain quality of rice in Southeast Asia. However, the existing literature still lacks information on the type of radiation used, the rice planting materials used, the dosage of physical mutagens, and the differences in mutated characteristics. Therefore, this article aims to review existing literature on the use of physical mutagens in rice crops in Southeast Asian countries. Guided by the PRISMA Statement review method, 28 primary studies were identified through a systematic review of the Scopus, Science Direct, Emerald Insight, Multidisciplinary Digital Publishing, and MDPI journal databases published between 2016 and 2020. The results show that 96% of the articles used seeds as planting materials, and 80% of the articles focused on gamma-rays as a source of physical mutagens. The optimal dosage of gamma-rays applied was around 100 to 250 Gy to improve plant development, abiotic stress, biochemical properties, and nutritional and industrial quality of rice.
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Affiliation(s)
- Rosina Baadu
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Khim Phin Chong
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Jualang Azlan Gansau
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | | | - Jedol Dayou
- Energy, Vibration and Sound Research Group (e-VIBS), Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Sabah, Malaysia
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42
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Olaniyi OO, Ajulo AS, Lawal OT, Olatunji VK. Engineered Alcaligenes sp. by chemical mutagen produces thermostable and acido-alkalophilic endo-1,4-β-mannanases for improved industrial biocatalyst. Prep Biochem Biotechnol 2023; 53:1120-1136. [PMID: 36752611 DOI: 10.1080/10826068.2023.2172038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
This study reported physicochemical properties of purified endo-1,4-β-mannanase from the wild type, Alcaligenes sp. and its most promising chemical mutant. The crude enzymes from fermentation of wild and mutant bacteria were purified by ammonium sulfate precipitation, ion exchange and gel-filtration chromatography followed by an investigation of the physicochemical properties of purified wild and mutant enzymes. β-mannanase from wild and mutant Alcaligenes sp. exhibited 1.75 and 1.6 purification-folds with percentage recoveries of 2.6 and 2.5% and molecular weights of 61.6 and 80 kDa respectively. The wild and mutant β-mannanase were most active at 40 and 50 °C with optimum pH 6.0 for both and were thermostable with very high percentage activity but the wild-type β-mannanase showed better stability over a broad pH activity. The β-mannanase activity from the parent strain was stimulated in the presence of Mn2+, Co2+, Zn2+, Mg2+ and Na+. Vmax and Km for the wild type and its mutant were found to be 0.747 U//mL/min and 5.2 × 10-4 mg/mL, and 0.247 U/mL/min and 2.47 × 10-4 mg/mL, respectively. Changes that occurred in the nucleotide sequences of the most improved mutant may be attributed to its thermo-stability, thermo-tolerant and high substrate affinity- desired properties for improved bioprocesses.
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Affiliation(s)
| | | | - Olusola Tosin Lawal
- Department of Biochemistry, Federal University of Technology, Akure, Nigeria
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Barathi S, J G, Rathinasamy G, Sabapathi N, Aruljothi KN, Lee J, Kandasamy S. Recent trends in polycyclic aromatic hydrocarbons pollution distribution and counteracting bio-remediation strategies. Chemosphere 2023; 337:139396. [PMID: 37406936 DOI: 10.1016/j.chemosphere.2023.139396] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/21/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are distributed worldwide due to long-term anthropogenic pollution sources. PAHs are recalcitrant and highly persistent in the environment due to their inherent properties, such as heterocyclic aromatic ring structures, thermostability, and hydrophobicity. They are highly toxic, carcinogenic, immunotoxic, teratogenic, and mutagenic to various life systems. This review focuses on the unique data of PAH sources, exposure routes, detection techniques, and harmful effects on the environment and human health. This review provides a comprehensive and systematic compilation of eco-friendly biological treatment solutions for PAH remediation, such as microbial remediation approaches utilizing microbial cultures. In situ and Ex situ bioremediation of PAH methods, including composting land farming, biopiles, bioreactors bioaugmentation, and phytoremediation processes, are discussed in detail, as is a summary of the factors affecting and limiting PAH bioremediation. This review provides an overview of emerging technologies that use multi-process combinatorial treatment approaches and answers to generating value-added by-products during PAH remediation.
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Affiliation(s)
- Selvaraj Barathi
- School of Chemical Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
| | - Gitanjali J
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, 63014, Tamil Nadu, India
| | - Gandhimathi Rathinasamy
- Department of Pharmaceutical Chemistry and Analysis, School of Pharmaceutical Sciences, Vels Institute of Science, Technology & Advanced Studies (VISTAS), Pallavaram, Chennai, 600117, Tamilnadu, India
| | - Nadana Sabapathi
- Centre of Translational Research, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518107, China
| | - K N Aruljothi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, 603 203, India
| | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Sabariswaran Kandasamy
- Department of Biotechnology, PSGR Krishnammal College for Women, Peelamedu, Coimbatore, 641004, India.
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Zhang Q, Tretyakova N. Incorporation of inosine into DNA by human polymerase eta (Polη): kinetics of nucleotide misincorporation and structural basis for the mutagenicity. Biochem J 2023; 480:1479-1483. [PMID: 37746864 PMCID: PMC10586757 DOI: 10.1042/bcj20230159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Inosine, a purine nucleoside containing the hypoxanthine (HX) nucleobase, can form in DNA via hydrolytic deamination of adenine. Due to its structural similarity to guanine and the geometry of Watson-Crick base pairs, inosine can mispair with cytosine upon catalysis by DNA polymerases, leading to AT → GC mutations. Additionally, inosine plays an essential role in purine nucleotide biosynthesis, and inosine triphosphate is present in living cells. In a recent publication, Averill and Jung examined the possibility of polη catalyzed incorporation of deoxyinosine triphosphate (dITP) across dC and dT in a DNA template. They found that dITP can be incorporated across C or T, with the ratio of 13.7. X ray crystallography studies revealed that the mutagenic incorporation of dITP by human polη was affected by several factors including base pair geometry in the active site of the polymerase, tautomerization of nucleobases, and the interaction of the incoming dITP nucleotide with active site residues of polη. This study demonstrates that TLS incorporation of inosine monophosphate (IMP) into growing DNA chains contributes to its mutagenic potential in cells.
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Affiliation(s)
- Qi Zhang
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, U.S.A
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, U.S.A
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Li X, Lu K, Chen X, Tu K, Xie D. capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements. Commun Biol 2023; 6:974. [PMID: 37741908 PMCID: PMC10517987 DOI: 10.1038/s42003-023-05349-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Transposable elements (TEs) serve as both insertional mutagens and regulatory elements in cells, and their aberrant activity is increasingly being revealed to contribute to diseases and cancers. However, measuring the transcriptional consequences of nonreference and young TEs at individual loci remains challenging with current methods, primarily due to technical limitations, including short read lengths generated and insufficient coverage in target regions. Here, we introduce a long-read targeted RNA sequencing method, Cas9-assisted profiling TE expression sequencing (capTEs), for quantitative analysis of transcriptional outputs for individual TEs, including transcribed nonreference insertions, noncanonical transcripts from various transcription patterns and their correlations with expression changes in related genes. This method selectively identified TE-containing transcripts and outputted data with up to 90% TE reads, maintaining a comparable data yield to whole-transcriptome sequencing. We applied capTEs to human cancer cells and found that internal and inserted Alu elements may employ distinct regulatory mechanisms to upregulate gene expression. We expect that capTEs will be a critical tool for advancing our understanding of the biological functions of individual TEs at the locus level, revealing their roles as both mutagens and regulators in biological and pathogenic processes.
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Affiliation(s)
- Xuemei Li
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Keying Lu
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiao Chen
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kailing Tu
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Dan Xie
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Bacurio JHT, Gao S, Yang H, Basu AK, Greenberg MM. Synergistic effects on mutagenicity of tandem lesions containing 8-oxo-7,8-dihydro-2'-deoxyguanosine or Fapy•dG flanked by a 3' 5-formyl-2'-deoxyuridine in human cells. DNA Repair (Amst) 2023; 129:103527. [PMID: 37467631 PMCID: PMC10528826 DOI: 10.1016/j.dnarep.2023.103527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/10/2023] [Accepted: 06/18/2023] [Indexed: 07/21/2023]
Abstract
Modified nucleotides often hinder and/or decrease the fidelity of DNA polymerases. Tandem lesions, which are comprised of DNA modifications at two contiguous nucleotide positions, can be even more detrimental to genome stability. Recently, tandem lesions containing 5-formyl-2'-deoxyuridine (5fdU) flanked at the 5'-position by 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo) or N-(2-deoxy-α,β-D-erythropentofuranosyl)-N-(2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy•dG) were discovered. We examined the replication of 5'- 8-OxodGuo-5fdU and 5'-Fapy•dG-5fdU tandem lesions in HEK 293T cells and several polymerase deficient variants by transfecting single-stranded vectors containing them. The local sequence of the tandem lesions encompasses the 273 codon of the p53 gene, a mutational hot-spot. The bypass efficiency and mutation spectra of the tandem lesions were compared to those of the isolated lesions. Replication of weakly mutagenic 5-fdU is little changed when part of the 5'- 8-OxodGuo-5fdU tandem lesion. G → T transversions attributable to 8-OxodGuo increase > 10-fold when the tandem lesion is bypassed. 5'-Fapy•dG-5fdU has a synergistic effect on the error-prone bypass of both lesions. The mutation frequency (MF) of 5'-Fapy•dG-5fdU increases 3-fold compared to isolated Fapy•dG. In addition, a 5'-adjacent Fapy•dG significantly increases the MF of 5fdU. The major mutation, G → T transversions, decrease by almost a third in hPol κ- cells, which is the opposite effect when isolated Fapy•dG in the same sequence context is replicated in HEK 293T cells in the same sequence. Steady-state kinetics indicate that hPol κ contributes to greater G → T transversions by decreasing the specificity constant for dCTP compared to an isolated Fapy•dG. The greater conformational freedom of Fapy•dG compared to 8-OxodGuo and its unusual ability to epimerize at the anomeric center is believed to be the source of the complex effects of 5'-Fapy•dG-5fdU on replication.
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Affiliation(s)
| | - Shijun Gao
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Haozhe Yang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Respiratory and Critical Care Medicine Targeted Tracer Research and Development Laboratory West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA.
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.
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Tchernev G. NITROSAMINES IN COMMONLY PRESCRIBED ANTIHYPERTENSIVES AND THE (UN)CONTROLLED DRUG-INDUCED SKIN CANCER: SIMULTANEOUS DEVELOPMENT OF CUTANEOUS MELANOMA AND MULTIPLE BCC AFTER CONCOMITANT ADMINISTRATION OF BISOPROLOL AND FUROSEMIDE. Georgian Med News 2023:149-151. [PMID: 37991971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
The era of nitrosogenesis is the era that is conditioned by the permanent and prolonged intake of carcinogens/mutagens, also known as nitrosamines/NDSRIs in the context of polymedication/polycontamination in polymorbid patients. Until recently, the favoured and universally accepted thesis by the scientific community that polymorbidity determines the risk of developing cancer has been shown to be weakly substantiated and superseded by the more modern notion that: it is the polycontamination with carcinogens in the context of concomitant medication/ polymorbidity that determines to a large extent the risk of developing heterogeneous cancers, including skin cancer: keratinocytic and melanocytic. The FDA is the organization that first pulled back the curtain on the backstage back in 2018 on this topic. It was not until 2023 that the FDA again catalogued over 250 drugs that are affected by contamination with carcinogens/mutagens/NDSRIs having varying carcinogenic potencies graded between 1 to 5. The expectations of clinicians and patients globally at the moment remain hopeful that the diplomatic recommendations of regulators will soon be replaced by more restrictive regimes and sanctions. The reason for the need to clarify this issue quickly is due to the following circumstances: 1) The reassuring calls and analyses of the regulators that the minimum intake of carcinogens ( nitrosamines or intake within reference values) , could not become a threat to the health of patients even after 70 years of intake, appear to be rather inconsistent; 2) Lack of any official data on any drug batch that has at least been declared by the FDA/EMA (if declared at all) as potentially contaminated; 3) Another not insignificant reason is that a number of scientific publications are indicative of exactly the opposite: short-term concomitant intake of polycontaminated drugs leads to short-term cancer development while shortening cumulative survival and quality of life for those affected. Only the transparency of the results of checks carried out on the presence of carcinogens in drug batches can guarantee peace of mind, and this in turn can be guaranteed by the regulatory authorities. 4) In parallel, the number of clinical data indicating an association between the intake of potentially nitrosamine-contaminated drugs (mainly for high blood pressure, but not only) and - in particular - keratinocytic and/or melanocytic skin cancer is growing avalanche-like. The dramatic increase in skin cancer in general/ worldwide is in absolute contradiction to the continuous explanations that the most important factor in the generation of skin cancer is ultraviolet light and sunburn: the incidence of skin cancer is increasing despite the widespread intensive use of sunscreen protection creams, the lack of any sun exposure in certain groups of patients, and its occurrence in areas not exposed to solar radiation. It follows only that solar radiation is not the only and perhaps not the most important factor determining the occurrence and progression of skin cancer. We report another concomitant intake of potentially nitrosamine contaminated blood pressure medications: bisoprolol and furosemide, taken over a period of 7 years that resulted in the concurrent occurrence of a medium-thickness cutaneous melanoma and 2 basal cell carcinomas. Successful surgical treatment of the tumors was performed, and the role of concurrent administration of ˝hypothetical˝ class 4 carcinogens within the framework of polymedication, polycontamination, and polymorbidity is discussed.
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Affiliation(s)
- G Tchernev
- Onkoderma - Clinic for Dermatology, Venereology and Dermatologic Surgery, Sofia; Department of Dermatology and Venereology, Medical Institute of Ministry of Interior, Sofia, Bulgaria
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de Sousa JT, Dihl RR, Menezes Boaretto FB, Garcia ALH, Grivicich I, da Silva J, Picada JN. Morphine decreases cytotoxicity and mutagenicity of doxorubicin in vitro: Implications for cancer chemotherapy. Chem Biol Interact 2023; 382:110652. [PMID: 37524295 DOI: 10.1016/j.cbi.2023.110652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 07/21/2023] [Accepted: 07/29/2023] [Indexed: 08/02/2023]
Abstract
Morphine is the most common opioid analgesic administered to treat pain in patients undergoing cancer chemotherapy. This study aimed to evaluate the cytotoxic and mutagenic effects of morphine alone and in combination with doxorubicin (Dox), an antineoplastic agent largely used in patients with solid cancers. Cytotoxicity was evaluated in neuroblastoma (SH-SY5Y) and fibroblast (V79) cells using 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide (MTT) colorimetric assay while mutagenicity was assessed using the Salmonella/microsome assay in the absence and in the presence of S9 mix. Morphine showed a cytotoxic effect mainly on SH-SY5Y cells and reduced the cytotoxic effects of Dox when evaluated in a co-treatment procedure. In the Salmonella/microsome assay, it was observed that morphine did not induce mutations and, in fact, decreased the mutagenic effects induced by Dox in TA98 and TA102 strains in the absence of metabolic activation. Furthermore, in the presence of metabolic activation, no induction of mutations was observed with morphine. In conclusion, morphine decreased Dox cytotoxicity in both neuronal and non-neuronal cells and showed antimutagenic effects in the TA102 strain which detects mutagens inducing DNA oxidative damages. However, morphine decreased frameshift mutations induced by Dox in non-cytotoxic concentrations, an effect suggesting interference of Dox intercalation activity that could decrease its chemotherapeutic efficacy. These compelling findings highlight the importance of conducting further studies to explore the potential implications of co-administering morphine and Dox during cancer chemotherapy.
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Affiliation(s)
- Jayne Torres de Sousa
- Laboratory of Genetic Toxicology, Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil, Av. Farroupilha 8001, 92425-900, Canoas, RS, Brazil; Laboratory of Genetic Toxicity and Cellular Toxic-Genetic Analysis, Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil, Av. Farroupilha 8001, 92425-900, Canoas, Brazil
| | - Rafael Rodrigues Dihl
- Laboratory of Genetic Toxicity and Cellular Toxic-Genetic Analysis, Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil, Av. Farroupilha 8001, 92425-900, Canoas, Brazil
| | - Fernanda Brião Menezes Boaretto
- Laboratory of Genetic Toxicology, Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil, Av. Farroupilha 8001, 92425-900, Canoas, RS, Brazil
| | - Ana Leticia Hilário Garcia
- Laboratory of Genetic Toxicology, Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil, Av. Farroupilha 8001, 92425-900, Canoas, RS, Brazil; Laboratory of Genetics Toxicology, La Salle University, Av. Victor Barreto, 2288, 92010-000, Canoas, RS, Brazil
| | - Ivana Grivicich
- Laboratory of Cancer Biology, Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil, Av. Farroupilha 8001, 92425-900, Canoas, RS, Brazil
| | - Juliana da Silva
- Laboratory of Genetic Toxicology, Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil, Av. Farroupilha 8001, 92425-900, Canoas, RS, Brazil; Laboratory of Genetics Toxicology, La Salle University, Av. Victor Barreto, 2288, 92010-000, Canoas, RS, Brazil
| | - Jaqueline Nascimento Picada
- Laboratory of Genetic Toxicology, Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil, Av. Farroupilha 8001, 92425-900, Canoas, RS, Brazil.
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Ghosh I, De Benedetti A. Untousling the Role of Tousled-like Kinase 1 in DNA Damage Repair. Int J Mol Sci 2023; 24:13369. [PMID: 37686173 PMCID: PMC10487508 DOI: 10.3390/ijms241713369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
DNA damage repair lies at the core of all cells' survival strategy, including the survival strategy of cancerous cells. Therefore, targeting such repair mechanisms forms the major goal of cancer therapeutics. The mechanism of DNA repair has been tousled with the discovery of multiple kinases. Recent studies on tousled-like kinases have brought significant clarity on the effectors of these kinases which stand to regulate DSB repair. In addition to their well-established role in DDR and cell cycle checkpoint mediation after DNA damage or inhibitors of replication, evidence of their suspected involvement in the actual DSB repair process has more recently been strengthened by the important finding that TLK1 phosphorylates RAD54 and regulates some of its activities in HRR and localization in the cell. Earlier findings of its regulation of RAD9 during checkpoint deactivation, as well as defined steps during NHEJ end processing, were earlier hints of its broadly important involvement in DSB repair. All this has opened up new avenues to target cancer cells in combination therapy with genotoxins and TLK inhibitors.
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Affiliation(s)
| | - Arrigo De Benedetti
- Department of Medicine, Department of Biochemistry, Louisiana Health Science Center-Shreveport, Shreveport, LA 71103, USA;
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Lynch AM, Zanoni TB, Salk JJ, Martincorena I, Young RR, Kucab J, Valentine CC, Yauk C, Escobar PA, Witt KL, Frötschl R, Reed SH, Ashford A. Next Generation Sequencing Workshop at the Royal Society of Medicine (London, May 2022): how genomics is on the path to modernizing genetic toxicology. Mutagenesis 2023; 38:192-200. [PMID: 37300447 PMCID: PMC10687350 DOI: 10.1093/mutage/gead012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Indexed: 06/12/2023] Open
Abstract
The use of error-corrected Next Generation Sequencing (ecNG) to determine mutagenicity has been a subject of growing interest and potentially a disruptive technology that could supplement, and in time, replace current testing paradigms in preclinical safety assessment. Considering this, a Next Generation Sequencing Workshop was held at the Royal Society of Medicine in London in May 2022, supported by the United Kingdom Environmental Mutagen Society (UKEMS) and TwinStrand Biosciences (WA, USA), to discuss progress and future applications of this technology. In this meeting report, the invited speakers provide an overview of the Workshop topics covered and identify future directions for research. In the area of somatic mutagenesis, several speakers reviewed recent progress made with correlating ecNGS to classic in vivo transgenic rodent mutation assays as well as exploring the use of this technology directly in humans and animals, and in complex organoid models. Additionally, ecNGS has been used for detecting off-target effects of gene editing tools and emerging data suggest ecNGS potential to measure clonal expansion of cells carrying mutations in cancer driver genes as an early marker of carcinogenic potential and for direct human biomonitoring. As such, the workshop demonstrated the importance of raising awareness and support for advancing the science of ecNGS for mutagenesis, gene editing, and carcinogenesis research. Furthermore, the potential of this new technology to contribute to advances in drug and product development and improve safety assessment was extensively explored.
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Affiliation(s)
- Anthony M Lynch
- GSK R&D, Stevenage, United Kingdom
- School of Medicine, Swansea University, Swansea, United Kingdom
| | | | - Jesse J Salk
- TwinStrand Biosciences, Seattle, WA, United States
- Division of Medical Oncology, University of Washington, Seattle, WA, United States
- Fred Hutch Cancer Center, Seattle, WA, United States
| | - Inigo Martincorena
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Jill Kucab
- Genetic and Environmental Toxicology, King’s College, London, United Kingdom
| | | | - Carole Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | | | - Kristine L Witt
- National Institute of Environmental Health Sciences, Division of Translational Toxicology, Research Triangle Park, NC, United States
| | - Roland Frötschl
- Federal Institute for Drugs and Medical Devices (Bundesinstitiut für Arzneimittel und Medizinprodukte), Bonn, Germany
| | - Simon H Reed
- School of Medicine, Division of Cancer and Genetics, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Anne Ashford
- Safety Innovation, Safety Sciences, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
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