1
|
Rath S, Das S. Oxidative stress-induced DNA damage and DNA repair mechanisms in mangrove bacteria exposed to climatic and heavy metal stressors. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 339:122722. [PMID: 37863253 DOI: 10.1016/j.envpol.2023.122722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/25/2023] [Accepted: 10/08/2023] [Indexed: 10/22/2023]
Abstract
Bacteria thriving in the mangrove ecosystem are major drivers of elemental cycles. Climate change and environmental stressors (heavy metals) influence the performance of these microorganisms, thereby affecting the biogeochemical cycle. The present study reports the genotoxic effect of climatic and heavy metal stressors on mangrove bacteria and their adaptation strategies. Comparative analysis between two bacterial strains, Bacillus stercoris GST-03 and Pseudomonas balearica DST-02 isolated from the Bhitarkanika mangrove ecosystem, Odisha, India, showed cellular injuries in response to various stressors as evident by declined growth, elevated levels of reactive oxygen species (ROS) and resulted DNA damage. B. stercoris GST-03 showed more tolerance towards acidic pH, whereas P. balearica DST-02 showed higher tolerance towards UV exposure and heavy metals (Lead and Cadmium). The adaptation strategies of the strains revealed a significant role of GST in ROS scavenging activity and the involvement of Nucleotide excision repair or SOS response pathways. However, irreparable DNA damage was observed at pH 9 and 200 ppm Cd in B. stercoris GST-03, and at pH 4, 1000 ppm of Pb and 200 ppm of Cd in P. balearica DST-02. The current findings provide a broad overview of bacterial response and adaptability concerning future climate and environmental changes.
Collapse
Affiliation(s)
- Sonalin Rath
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
| |
Collapse
|
2
|
Lapa BS, Costa MI, Figueiredo D, Jorge J, Alves R, Monteiro AR, Serambeque B, Laranjo M, Botelho MF, Carreira IM, Sarmento-Ribeiro AB, Gonçalves AC. AZD-7648, a DNA-PK Inhibitor, Induces DNA Damage, Apoptosis, and Cell Cycle Arrest in Chronic and Acute Myeloid Leukemia Cells. Int J Mol Sci 2023; 24:15331. [PMID: 37895013 PMCID: PMC10607085 DOI: 10.3390/ijms242015331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The non-homologous end joining pathway is vital for repairing DNA double-strand breaks (DSB), with DNA-dependent protein kinase (DNA-PK) playing a critical role. Altered DNA damage response (DDR) in chronic (CML) and acute myeloid leukemia (AML) offers potential therapeutic opportunities. We studied the therapeutic potential of AZD-7648 (DNA-PK inhibitor) in CML and AML cell lines. This study used two CML (K-562 and LAMA-84) and five AML (HEL, HL-60, KG-1, NB-4, and THP-1) cell lines. DDR gene mutations were obtained from the COSMIC database. The copy number and methylation profile were evaluated using MS-MLPA and DDR genes, and telomere length using qPCR. p53 protein expression was assessed using Western Blot, chromosomal damage through cytokinesis-block micronucleus assay, and γH2AX levels and DSB repair kinetics using flow cytometry. Cell density and viability were analyzed using trypan blue assay after treatment with AZD-7648 in concentrations ranging from 10 to 200 µM. Cell death, cell cycle distribution, and cell proliferation rate were assessed using flow cytometry. The cells displayed different DNA baseline damage, DDR gene expressions, mutations, genetic/epigenetic changes, and p53 expression. Only HEL cells displayed inefficient DSB repair. The LAMA-84, HEL, and KG-1 cells were the most sensitive to AZD-7648, whereas HL-60 and K-562 showed a lower effect on density and viability. Besides the reduction in cell proliferation, AZD-7648 induced apoptosis, cell cycle arrest, and DNA damage. In conclusion, these results suggest that AZD-7648 holds promise as a potential therapy for myeloid leukemias, however, with variations in drug sensitivity among tested cell lines, thus supporting further investigation to identify the specific factors influencing sensitivity to this DNA-PK inhibitor.
Collapse
Affiliation(s)
- Beatriz Santos Lapa
- Laboratory of Oncobiology and Hematology (LOH), University Clinics of Hematology and Oncology, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.L.); (M.I.C.); (J.J.); (R.A.); (A.R.M.); (A.B.S.-R.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Group of Environmental Genetics of Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.); (I.M.C.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
| | - Maria Inês Costa
- Laboratory of Oncobiology and Hematology (LOH), University Clinics of Hematology and Oncology, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.L.); (M.I.C.); (J.J.); (R.A.); (A.R.M.); (A.B.S.-R.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Group of Environmental Genetics of Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.); (I.M.C.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
| | - Diana Figueiredo
- Laboratory of Oncobiology and Hematology (LOH), University Clinics of Hematology and Oncology, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.L.); (M.I.C.); (J.J.); (R.A.); (A.R.M.); (A.B.S.-R.)
| | - Joana Jorge
- Laboratory of Oncobiology and Hematology (LOH), University Clinics of Hematology and Oncology, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.L.); (M.I.C.); (J.J.); (R.A.); (A.R.M.); (A.B.S.-R.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Group of Environmental Genetics of Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.); (I.M.C.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3000-061 Coimbra, Portugal
| | - Raquel Alves
- Laboratory of Oncobiology and Hematology (LOH), University Clinics of Hematology and Oncology, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.L.); (M.I.C.); (J.J.); (R.A.); (A.R.M.); (A.B.S.-R.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Group of Environmental Genetics of Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.); (I.M.C.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3000-061 Coimbra, Portugal
| | - Ana Raquel Monteiro
- Laboratory of Oncobiology and Hematology (LOH), University Clinics of Hematology and Oncology, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.L.); (M.I.C.); (J.J.); (R.A.); (A.R.M.); (A.B.S.-R.)
| | - Beatriz Serambeque
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Group of Environmental Genetics of Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.); (I.M.C.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Institute of Biophysics, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Mafalda Laranjo
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Group of Environmental Genetics of Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.); (I.M.C.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3000-061 Coimbra, Portugal
- Institute of Biophysics, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Maria Filomena Botelho
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Group of Environmental Genetics of Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.); (I.M.C.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3000-061 Coimbra, Portugal
- Institute of Biophysics, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Isabel Marques Carreira
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Group of Environmental Genetics of Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.); (I.M.C.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3000-061 Coimbra, Portugal
- Cytogenetics and Genomics Laboratory, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ana Bela Sarmento-Ribeiro
- Laboratory of Oncobiology and Hematology (LOH), University Clinics of Hematology and Oncology, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.L.); (M.I.C.); (J.J.); (R.A.); (A.R.M.); (A.B.S.-R.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Group of Environmental Genetics of Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.); (I.M.C.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3000-061 Coimbra, Portugal
- Hematology Service, Centro Hospitalar e Universitário de Coimbra (CHUC), 3000-061 Coimbra, Portugal
| | - Ana Cristina Gonçalves
- Laboratory of Oncobiology and Hematology (LOH), University Clinics of Hematology and Oncology, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.L.); (M.I.C.); (J.J.); (R.A.); (A.R.M.); (A.B.S.-R.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Group of Environmental Genetics of Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal; (B.S.); (I.M.C.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3000-061 Coimbra, Portugal
| |
Collapse
|
3
|
Panessa GM, Tassoni-Tsuchida E, Pires MR, Felix RR, Jekabson R, de Souza-Pinto NC, da Cunha FM, Brandman O, Cussiol JRR. Opi1-mediated transcriptional modulation orchestrates genotoxic stress response in budding yeast. Genetics 2023; 225:iyad130. [PMID: 37440469 PMCID: PMC10691878 DOI: 10.1093/genetics/iyad130] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
In budding yeast, the transcriptional repressor Opi1 regulates phospholipid biosynthesis by repressing expression of genes containing inositol-sensitive upstream activation sequences. Upon genotoxic stress, cells activate the DNA damage response to coordinate a complex network of signaling pathways aimed at preserving genomic integrity. Here, we reveal that Opi1 is important to modulate transcription in response to genotoxic stress. We find that cells lacking Opi1 exhibit hypersensitivity to genotoxins, along with a delayed G1-to-S-phase transition and decreased gamma-H2A levels. Transcriptome analysis using RNA sequencing reveals that Opi1 plays a central role in modulating essential biological processes during methyl methanesulfonate (MMS)-associated stress, including repression of phospholipid biosynthesis and transduction of mating signaling. Moreover, Opi1 induces sulfate assimilation and amino acid metabolic processes, such as arginine and histidine biosynthesis and glycine catabolism. Furthermore, we observe increased mitochondrial DNA instability in opi1Δ cells upon MMS treatment. Notably, we show that constitutive activation of the transcription factor Ino2-Ino4 is responsible for genotoxin sensitivity in Opi1-deficient cells, and the production of inositol pyrophosphates by Kcs1 counteracts Opi1 function specifically during MMS-induced stress. Overall, our findings highlight Opi1 as a critical sensor of genotoxic stress in budding yeast, orchestrating gene expression to facilitate appropriate stress responses.
Collapse
Affiliation(s)
- Giovanna Marques Panessa
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Eduardo Tassoni-Tsuchida
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Marina Rodrigues Pires
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Rodrigo Rodrigues Felix
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Rafaella Jekabson
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | | | - Fernanda Marques da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - José Renato Rosa Cussiol
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| |
Collapse
|
4
|
Kamat A, Badrinarayanan A. SOS-independent bacterial DNA damage responses: diverse mechanisms, unifying function. Curr Opin Microbiol 2023; 73:102323. [PMID: 37148591 DOI: 10.1016/j.mib.2023.102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/23/2023] [Accepted: 04/06/2023] [Indexed: 05/08/2023]
Abstract
Cells across domains of life have dedicated pathways to sense and respond to DNA damage. These responses are broadly termed as DNA damage responses (DDRs). In bacteria, the best studied DDR is the Save our Soul (SOS) response. More recently, several SOS-independent DDRs have also been discovered. Studies further report diversity in the types of repair proteins present across bacterial species as well as differences in their mechanisms of action. Although the primary function of DDRs is preservation of genome integrity, the diverse organization, conservation, and function of bacterial DDRs raises important questions about how genome error correction mechanisms could influence or be influenced by the genomes that encode them. In this review, we discuss recent insights on three SOS-independent bacterial DDRs. We consider open questions in our understanding of how diversity in response and repair mechanisms is generated, and how action of these pathways is regulated in cells to ensure maintenance of genome integrity.
Collapse
Affiliation(s)
- Aditya Kamat
- National Centre for Biological Sciences (TIFR), Bengaluru 560065, India
| | | |
Collapse
|
5
|
Nanotechnology as a Tool for Optimizing Topical Photoprotective Formulations Containing Buriti Oil (Mauritia flexuosa) and Dry Aloe vera Extracts: Stability and Cytotoxicity Evaluations. Pharmaceuticals (Basel) 2023. [DOI: 10.3390/ph16020292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Human beings are actively exposed to ultraviolet (UV) radiation, which is associated with skin cancer. This has encouraged the continuous search for more effective and safer photoprotective formulations. Along with the application of traditional organic sunscreens, there is a growing interest in “green products” containing natural compounds such as plant extracts and oils. This trend is combined with the use of nanotechnology as a tool for optimizing the vehicles of such compounds. Nanoemulsions (NEs) are suitable for the encapsulation of natural compounds, which improves topical treatment. Therefore, we have developed oil-in-water (O/W) nanoemulsions containing 3% buriti oil (BO), incorporated in a 10% vegetal extract of Aloe vera (AV) by means of ultrasonic processing to improve the chemical characteristics of this component and, consequently, its efficacy and safety in pharmaceutical and cosmetic formulations. The composition of the formulation was initially defined in a preliminary study on surfactants where the concentrations of Tween® 80 and Span® 20 were evaluated in relation to particle size and the polydispersity index (PDI). The nanoemulsion was prepared and then chemical sunscreens were incorporated with the aim of developing a sunscreen nanoemulsion called NE-A19. This nanoemulsion was found to be the best formulation due to its stability, droplet size (146.80 ± 2.74), and PDI (0.302 ± 0.088), with a monomodal size distribution. The stability was evaluated over 90 days and showed a low growth in particle size at the end of the study. NE-A19 exhibited good viscosity and organoleptic properties, in addition to an occlusion factor indicating an interesting and higher water holding capacity when compared with a NE without AV (p < 0.05). The in vitro efficacy and safety studies of NE-19A were promising. Its average in vitro sun protection factor value was 49, with a critical wavelength (λc) of 369.7 nm, satisfactory UVA protection, and a UVA/UVB ratio of 0.40, indicating broad spectrum protection against UVA and UVB radiation. Furthermore, NE-19A displayed a good safety profile in dermal keratinocytes. It can be concluded that NE-19A is a promising formulation for carrying natural products, such as buriti oil and AV, associated with synthetic filters in lower concentrations.
Collapse
|
6
|
Camus A, Espinosa E, Zapater Baras P, Singh P, Quenech’Du N, Vickridge E, Modesti M, Barre FX, Espéli O. The SMC-like RecN protein is at the crossroads of several genotoxic stress responses in Escherichia coli. Front Microbiol 2023; 14:1146496. [PMID: 37168111 PMCID: PMC10165496 DOI: 10.3389/fmicb.2023.1146496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/04/2023] [Indexed: 05/13/2023] Open
Abstract
Introduction DNA damage repair (DDR) is an essential process for living organisms and contributes to genome maintenance and evolution. DDR involves different pathways including Homologous recombination (HR), Nucleotide Excision Repair (NER) and Base excision repair (BER) for example. The activity of each pathway is revealed with particular drug inducing lesions, but the repair of most DNA lesions depends on concomitant or subsequent action of the multiple pathways. Methods In the present study, we used two genotoxic antibiotics, mitomycin C (MMC) and Bleomycin (BLM), to decipher the interplays between these different pathways in E. coli. We combined genomic methods (TIS and Hi-SC2) and imaging assays with genetic dissections. Results We demonstrate that only a small set of DDR proteins are common to the repair of the lesions induced by these two drugs. Among them, RecN, an SMC-like protein, plays an important role by controlling sister chromatids dynamics and genome morphology at different steps of the repair processes. We further demonstrate that RecN influence on sister chromatids dynamics is not equivalent during the processing of the lesions induced by the two drugs. We observed that RecN activity and stability requires a pre-processing of the MMC-induced lesions by the NER but not for BLM-induced lesions. Discussion Those results show that RecN plays a major role in rescuing toxic intermediates generated by the BER pathway in addition to its well-known importance to the repair of double strand breaks by HR.
Collapse
Affiliation(s)
- Adrien Camus
- CIRB, Collège de France, INSERM U1050, CNRS UMR 7241, Université PSL, Paris, France
| | - Elena Espinosa
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | | | - Parul Singh
- CIRB, Collège de France, INSERM U1050, CNRS UMR 7241, Université PSL, Paris, France
| | - Nicole Quenech’Du
- CIRB, Collège de France, INSERM U1050, CNRS UMR 7241, Université PSL, Paris, France
| | - Elise Vickridge
- CIRB, Collège de France, INSERM U1050, CNRS UMR 7241, Université PSL, Paris, France
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Mauro Modesti
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR 7258, INSERM U1068, Institut Paoli-Calmettes, Aix Marseille University, Marseille, France
| | - François Xavier Barre
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Olivier Espéli
- CIRB, Collège de France, INSERM U1050, CNRS UMR 7241, Université PSL, Paris, France
- *Correspondence: Olivier Espéli,
| |
Collapse
|
7
|
Islam MZ, Shen X, Pardue S, Kevil CG, Shackelford RE. The ataxia-telangiectasia mutated gene product regulates the cellular acid-labile sulfide fraction. DNA Repair (Amst) 2022; 116:103344. [PMID: 35696854 PMCID: PMC11118069 DOI: 10.1016/j.dnarep.2022.103344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/30/2022] [Accepted: 05/11/2022] [Indexed: 11/03/2022]
Abstract
The ataxia-telangiectasia mutated (ATM) protein regulates cell cycle checkpoints, the cellular redox state, and double-stranded DNA break repair. ATM loss causes the disorder ataxia-telangiectasia (A-T), distinguished by ataxia, telangiectasias, dysregulated cellular redox and iron responses, and an increased cancer risk. We examined the sulfur pool in A-T cells, with and without an ATM expression vector. While free and bound sulfide levels were not changed with ATM expression, the acid-labile sulfide faction was significantly increased. ATM expression also increased cysteine desulfurase (NFS1), NFU1 iron-sulfur cluster scaffold homolog protein, and several mitochondrial complex I proteins' expression. Additionally, ATM expression suppressed cystathionine β-synthase and cystathionine γ-synthase protein expression, cystathionine γ-synthase enzymatic activity, and increased the reduced to oxidized glutathione ratio. This last observation is interesting, as dysregulated glutathione is implicated in A-T pathology. As ATM expression increases the expression of proteins central in initiating 2Fe-2S and 4Fe-4S cluster formation (NFS1 and NFU1, respectively), and the acid-labile sulfide faction is composed of sulfur incorporated into Fe-S clusters, our data indicates that ATM regulates aspects of Fe-S cluster biosynthesis, the transsulfuration pathway, and glutathione redox cycling. Thus, our data may explain some of the redox- and iron-related pathologies seen in A-T.
Collapse
Affiliation(s)
- Mohammad Z Islam
- Department of Pathology & Translational Pathobiology, LSU Health Sciences Center Shreveport, Shreveport, LA 71130, United States
| | - Xinggui Shen
- Department of Pathology & Translational Pathobiology, LSU Health Sciences Center Shreveport, Shreveport, LA 71130, United States
| | - Sibile Pardue
- Department of Pathology & Translational Pathobiology, LSU Health Sciences Center Shreveport, Shreveport, LA 71130, United States
| | - Christopher G Kevil
- Department of Pathology & Translational Pathobiology, LSU Health Sciences Center Shreveport, Shreveport, LA 71130, United States
| | - Rodney E Shackelford
- Department of Pathology & Translational Pathobiology, LSU Health Sciences Center Shreveport, Shreveport, LA 71130, United States.
| |
Collapse
|
8
|
Masłowska KH, Villafañez F, Laureti L, Iwai S, Pagès V. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2074-2080. [PMID: 35104879 PMCID: PMC8887424 DOI: 10.1093/nar/gkac044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 12/04/2022] Open
Abstract
The DNA damage response (DDR) preserves the genetic integrity of the cell by sensing and repairing damages after a genotoxic stress. Translesion Synthesis (TLS), an error-prone DNA damage tolerance pathway, is controlled by PCNA ubiquitination. In this work, we raise the question whether TLS is controlled locally or globally. Using a recently developed method that allows to follow the bypass of a single lesion inserted into the yeast genome, we show that (i) TLS is controlled locally at each individual lesion by PCNA ubiquitination, (ii) a single lesion is enough to induce PCNA ubiquitination and (iii) PCNA ubiquitination is imperative for TLS to occur. More importantly, we show that the activation of the DDR that follows a genotoxic stress does not increase TLS at individual lesions. We conclude that unlike the SOS response in bacteria, the eukaryotic DDR does not promote TLS and mutagenesis.
Collapse
Affiliation(s)
- Katarzyna H Masłowska
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille 13009, France
| | - Florencia Villafañez
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille 13009, France
| | - Luisa Laureti
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille 13009, France
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, Osaka 560-8531, Japan
| | - Vincent Pagès
- To whom correspondence should be addressed. Tel: +33 4 86 977 384;
| |
Collapse
|
9
|
Shackelford RE, Li Y, Ghali GE, Kevil CG. Bad Smells and Broken DNA: A Tale of Sulfur-Nucleic Acid Cooperation. Antioxidants (Basel) 2021; 10:1820. [PMID: 34829691 PMCID: PMC8614844 DOI: 10.3390/antiox10111820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 12/19/2022] Open
Abstract
Hydrogen sulfide (H2S) is a gasotransmitter that exerts numerous physiologic and pathophysiologic effects. Recently, a role for H2S in DNA repair has been identified, where H2S modulates cell cycle checkpoint responses, the DNA damage response (DDR), and mitochondrial and nuclear genomic stability. In addition, several DNA repair proteins modulate cellular H2S concentrations and cellular sulfur metabolism and, in turn, are regulated by cellular H2S concentrations. Many DDR proteins are now pharmacologically inhibited in targeted cancer therapies. As H2S and the enzymes that synthesize it are increased in many human malignancies, it is likely that H2S synthesis inhibition by these therapies is an underappreciated aspect of these cancer treatments. Moreover, both H2S and DDR protein activities in cancer and cardiovascular diseases are becoming increasingly apparent, implicating a DDR-H2S signaling axis in these pathophysiologic processes. Taken together, H2S and DNA repair likely play a central and presently poorly understood role in both normal cellular function and a wide array of human pathophysiologic processes. Here, we review the role of H2S in DNA repair.
Collapse
Affiliation(s)
- Rodney E. Shackelford
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA; (Y.L.); (C.G.K.)
| | - Yan Li
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA; (Y.L.); (C.G.K.)
| | - Ghali E. Ghali
- Head & Neck Oncologic/Microvascular Reconstructive Surgery Department of Oral & Maxillofacial/Head & Neck Surgery, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA;
| | - Christopher G. Kevil
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA; (Y.L.); (C.G.K.)
| |
Collapse
|
10
|
He L, Lomberk G. Collateral Victim or Rescue Worker?-The Role of Histone Methyltransferases in DNA Damage Repair and Their Targeting for Therapeutic Opportunities in Cancer. Front Cell Dev Biol 2021; 9:735107. [PMID: 34869318 PMCID: PMC8636273 DOI: 10.3389/fcell.2021.735107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/01/2021] [Indexed: 01/25/2023] Open
Abstract
Disrupted DNA damage signaling greatly threatens cell integrity and plays significant roles in cancer. With recent advances in understanding the human genome and gene regulation in the context of DNA damage, chromatin biology, specifically biology of histone post-translational modifications (PTMs), has emerged as a popular field of study with great promise for cancer therapeutics. Here, we discuss how key histone methylation pathways contribute to DNA damage repair and impact tumorigenesis within this context, as well as the potential for their targeting as part of therapeutic strategies in cancer.
Collapse
Affiliation(s)
- Lishu He
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Gwen Lomberk
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States,LaBahn Pancreatic Cancer Program, Medical College of Wisconsin, Milwaukee, WI, United States,*Correspondence: Gwen Lomberk,
| |
Collapse
|
11
|
Tromans-Coia C, Sanchi A, Moeller GK, Timinszky G, Lopes M, Ahel I. TARG1 protects against toxic DNA ADP-ribosylation. Nucleic Acids Res 2021; 49:10477-10492. [PMID: 34508355 PMCID: PMC8501950 DOI: 10.1093/nar/gkab771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/16/2021] [Accepted: 09/09/2021] [Indexed: 01/15/2023] Open
Abstract
ADP-ribosylation is a modification that targets a variety of macromolecules and regulates a diverse array of important cellular processes. ADP-ribosylation is catalysed by ADP-ribosyltransferases and reversed by ADP-ribosylhydrolases. Recently, an ADP-ribosyltransferase toxin termed 'DarT' from bacteria, which is distantly related to human PARPs, was shown to modify thymidine in single-stranded DNA in a sequence specific manner. The antitoxin of DarT is the macrodomain containing ADP-ribosylhydrolase DarG, which shares striking structural homology with the human ADP-ribosylhydrolase TARG1. Here, we show that TARG1, like DarG, can reverse thymidine-linked DNA ADP-ribosylation. We find that TARG1-deficient human cells are extremely sensitive to DNA ADP-ribosylation. Furthermore, we also demonstrate the first detection of reversible ADP-ribosylation on genomic DNA in vivo from human cells. Collectively, our results elucidate the impact of DNA ADP-ribosylation in human cells and provides a molecular toolkit for future studies into this largely unknown facet of ADP-ribosylation.
Collapse
Affiliation(s)
- Callum Tromans-Coia
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Giuliana K Moeller
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Gyula Timinszky
- Lendület Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), 6276 Szeged, Hungary
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| |
Collapse
|
12
|
Sheng DH, Wang Y, Wu SG, Duan RQ, Li YZ. The Regulation of LexA on UV-Induced SOS Response in Myxococcus xanthus Based on Transcriptome Analysis. J Microbiol Biotechnol 2021; 31:912-920. [PMID: 34024894 PMCID: PMC9705874 DOI: 10.4014/jmb.2103.03047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/15/2022]
Abstract
SOS response is a conserved response to DNA damage in prokaryotes and is negatively regulated by LexA protein, which recognizes specifically an "SOS-box" motif present in the promoter region of SOS genes. Myxococcus xanthus DK1622 possesses a lexA gene, and while the deletion of lexA had no significant effect on either bacterial morphology, UV-C resistance, or sporulation, it did delay growth. UV-C radiation resulted in 651 upregulated genes in M. xanthus, including the typical SOS genes lexA, recA, uvrA, recN and so on, mostly enriched in the pathways of DNA replication and repair, secondary metabolism, and signal transduction. The UV-irradiated lexA mutant also showed the induced expression of SOS genes and these SOS genes enriched into a similar pathway profile to that of wild-type strain. Without irradiation treatment, the absence of LexA enhanced the expression of 122 genes that were not enriched in any pathway. Further analysis of the promoter sequence revealed that in the 122 genes, only the promoters of recA2, lexA and an operon composed of three genes (pafB, pafC and cyaA) had SOS box sequence to which the LexA protein is bound directly. These results update our current understanding of SOS response in M. xanthus and show that UV induces more genes involved in secondary metabolism and signal transduction in addition to DNA replication and repair; and while the canonical LexA-dependent regulation on SOS response has shrunk, only 5 SOS genes are directly repressed by LexA.
Collapse
Affiliation(s)
- Duo-hong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China,
D-h. Sheng Phone: +86-532-58631538 E-mail:
| | - Ye Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Shu-ge Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Rui-qin Duan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China,Corresponding authors Y.Z. Li Phone: +86-532-58631539 E-mail:
| |
Collapse
|
13
|
Huang R, Zhou PK. DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy. Signal Transduct Target Ther 2021; 6:254. [PMID: 34238917 PMCID: PMC8266832 DOI: 10.1038/s41392-021-00648-7] [Citation(s) in RCA: 288] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/28/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Genomic instability is the hallmark of various cancers with the increasing accumulation of DNA damage. The application of radiotherapy and chemotherapy in cancer treatment is typically based on this property of cancers. However, the adverse effects including normal tissues injury are also accompanied by the radiotherapy and chemotherapy. Targeted cancer therapy has the potential to suppress cancer cells' DNA damage response through tailoring therapy to cancer patients lacking specific DNA damage response functions. Obviously, understanding the broader role of DNA damage repair in cancers has became a basic and attractive strategy for targeted cancer therapy, in particular, raising novel hypothesis or theory in this field on the basis of previous scientists' findings would be important for future promising druggable emerging targets. In this review, we first illustrate the timeline steps for the understanding the roles of DNA damage repair in the promotion of cancer and cancer therapy developed, then we summarize the mechanisms regarding DNA damage repair associated with targeted cancer therapy, highlighting the specific proteins behind targeting DNA damage repair that initiate functioning abnormally duo to extrinsic harm by environmental DNA damage factors, also, the DNA damage baseline drift leads to the harmful intrinsic targeted cancer therapy. In addition, clinical therapeutic drugs for DNA damage and repair including therapeutic effects, as well as the strategy and scheme of relative clinical trials were intensive discussed. Based on this background, we suggest two hypotheses, namely "environmental gear selection" to describe DNA damage repair pathway evolution, and "DNA damage baseline drift", which may play a magnified role in mediating repair during cancer treatment. This two new hypothesis would shed new light on targeted cancer therapy, provide a much better or more comprehensive holistic view and also promote the development of new research direction and new overcoming strategies for patients.
Collapse
Affiliation(s)
- Ruixue Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China.
| |
Collapse
|
14
|
Gabriel BM, Zierath JR. Zeitgebers of skeletal muscle and implications for metabolic health. J Physiol 2021; 600:1027-1036. [PMID: 33963554 DOI: 10.1113/jp280884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/04/2021] [Indexed: 12/25/2022] Open
Abstract
Metabolic health is a crucial area of current research, and is an outcome of innate physiology, and interactions with the environment. Environmental cues, such as the Earth's day-night rhythm, partly regulate diurnal hormones and metabolites. Circadian physiology consists of highly conserved biological processes over ∼24-h cycles, which are influenced by external cues (Zeitgebers - 'time-keepers'). Skeletal muscle has diurnal variations of a large magnitude, owing in part to the strong nature of physical activity throughout the day and other external Zeitgebers. The orchestration of whole-body and skeletal muscle metabolism is a complex, finely tuned process, and molecular diurnal variations are regulated by a transcription-translation feedback loop controlled by the molecular clock, as well as non-transcriptional metabolic processes. The mitochondrion may play an important role in regulating diurnal metabolites within skeletal muscle, given its central role in the regulation of NAD+ /NADH, O2 , reactive oxygen species and redox metabolism. These molecular pathways display diurnal variation and illustrate the complex orchestration of circadian metabolism in skeletal muscle. Probably the most robust Zeitgeber of skeletal muscle is exercise, which alters glucose metabolism and flux, in addition to a range of other diurnal metabolic pathways. Indeed, performing exercise at different times of the day may alter metabolism and health outcomes in some cohorts. The objective of this Symposium Review is to briefly cover the current literature, and to speculate regarding future areas of research. Thus, we postulate that metabolic health may be optimized by altering the timing of external cues such as diet and exercise.
Collapse
Affiliation(s)
- Brendan M Gabriel
- Aberdeen Cardiovascular & Diabetes Centre, The Rowett Institute, University of Aberdeen, Aberdeen, UK.,Department of Physiology and Pharmacology, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Juleen R Zierath
- Department of Physiology and Pharmacology, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
15
|
Zell J, Rota Sperti F, Britton S, Monchaud D. DNA folds threaten genetic stability and can be leveraged for chemotherapy. RSC Chem Biol 2021; 2:47-76. [PMID: 35340894 PMCID: PMC8885165 DOI: 10.1039/d0cb00151a] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022] Open
Abstract
Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an anticancer target, and the manipulation of DDR pathways as a valuable anticancer strategy. We describe in detail the DDR signalling and repair pathways activated in response to DNA damage. We then summarise the current understanding of non-B DNA folds, such as G-quadruplexes and DNA junctions, when they are formed and why they can offer a more specific therapeutic target compared to that of canonical B-DNA. Finally, we merge these subjects to depict the new and highly promising chemotherapeutic strategy which combines enhanced-specificity DNA damaging and DDR targeting agents. This review thus highlights how chemical biology has given rise to significant scientific advances thanks to resolutely multidisciplinary research efforts combining molecular and cell biology, chemistry and biophysics. We aim to provide the non-specialist reader a gateway into this exciting field and the specialist reader with a new perspective on the latest results achieved and strategies devised.
Collapse
Affiliation(s)
- Joanna Zell
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS Toulouse France
- Équipe Labellisée la Ligue Contre le Cancer 2018 Toulouse France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| |
Collapse
|
16
|
The interaction of DNA repair factors ASCC2 and ASCC3 is affected by somatic cancer mutations. Nat Commun 2020; 11:5535. [PMID: 33139697 PMCID: PMC7608686 DOI: 10.1038/s41467-020-19221-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023] Open
Abstract
The ASCC3 subunit of the activating signal co-integrator complex is a dual-cassette Ski2-like nucleic acid helicase that provides single-stranded DNA for alkylation damage repair by the α-ketoglutarate-dependent dioxygenase AlkBH3. Other ASCC components integrate ASCC3/AlkBH3 into a complex DNA repair pathway. We mapped and structurally analyzed interacting ASCC2 and ASCC3 regions. The ASCC3 fragment comprises a central helical domain and terminal, extended arms that clasp the compact ASCC2 unit. ASCC2–ASCC3 interfaces are evolutionarily highly conserved and comprise a large number of residues affected by somatic cancer mutations. We quantified contributions of protein regions to the ASCC2–ASCC3 interaction, observing that changes found in cancers lead to reduced ASCC2–ASCC3 affinity. Functional dissection of ASCC3 revealed similar organization and regulation as in the spliceosomal RNA helicase Brr2. Our results delineate functional regions in an important DNA repair complex and suggest possible molecular disease principles. The DNA helicase ASCC3 is the largest subunit of the activating signal co-integrator complex (ASCC), and its DNA unwinding activity is required for the AlkBH3/ASCC-dependent DNA de-alkylation repair pathway. Here, the authors identify a minimal stable complex of the two ASCC subunits ASCC2 and ASCC3, determine the complex crystal structure and further show that cancer-related mutations at the interface between both proteins reduce ASCC2–ASCC3 affinity.
Collapse
|
17
|
Shackelford R, Ozluk E, Islam MZ, Hopper B, Meram A, Ghali G, Kevil CG. Hydrogen sulfide and DNA repair. Redox Biol 2020; 38:101675. [PMID: 33202302 PMCID: PMC7677119 DOI: 10.1016/j.redox.2020.101675] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/12/2020] [Accepted: 08/02/2020] [Indexed: 12/28/2022] Open
Abstract
Recent evidence has revealed that exposing cells to exogenous H 2 S or inhibiting cellular H 2 S synthesis can modulate cell cycle checkpoints, DNA damage and repair, and the expression of proteins involved in the maintenance of genomic stability, all suggesting that H 2 S plays an important role in the DNA damage response (DDR). Here we review the role of H 2 S in the DRR and maintenance of genomic stability. Treatment of various cell types with pharmacologic H 2 S donors or cellular H 2 S synthesis inhibitors modulate the G 1 checkpoint, inhibition of DNA synthesis, and cause p21, and p53 induction. Moreover, in some cell models H 2 S exposure induces PARP-1 and g-H2AX foci formation, increases PCNA, CHK2, Ku70, Ku80, and DNA polymerase-d protein expression, and maintains mitochondrial genomic stability. Our group has also revealed that H 2 S bioavailability and the ATR kinase regulate each other with ATR inhibition lowering cellular H 2 S concentrations, whereas intracellular H 2 S concentrations regulate ATR kinase activity via ATR serine 435 phosphorylation. In summary, these findings have many implications for the DDR, for cancer chemotherapy, and fundamental biochemical metabolic pathways involving H 2 S. Inhibition of the ATR kinase lowers intracellular H2S concentrations. Inhibition of H2S synthesis activates the ATR kinase and increases its kinase activity. Inhibition of H2S synthesis combined with low-level oxidative stress increases genomic instability. These findings may have applications the cancer chemotherapeutics.
Collapse
Affiliation(s)
- Rodney Shackelford
- LSU Health Shreveport, Department of Pathology, Shreveport, LA, United States.
| | - Ekin Ozluk
- Department of Pathology & Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, LA, 71130, United States
| | - Mohammad Z Islam
- Department of Pathology & Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, LA, 71130, United States
| | - Brian Hopper
- Department of Pathology & Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, LA, 71130, United States
| | - Andrew Meram
- Head & Neck Oncologic/Microvascular Reconstructive Surgery Department of Oral & Maxillofacial/Head & Neck Surgery, Louisiana State University Health Sciences Center, Shreveport, LA, 71130, United States
| | - Ghali Ghali
- Head & Neck Oncologic/Microvascular Reconstructive Surgery Department of Oral & Maxillofacial/Head & Neck Surgery, Louisiana State University Health Sciences Center, Shreveport, LA, 71130, United States
| | - Christopher G Kevil
- Department of Pathology & Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, LA, 71130, United States
| |
Collapse
|
18
|
Cipolla L, Bertoletti F, Maffia A, Liang CC, Lehmann AR, Cohn MA, Sabbioneda S. UBR5 interacts with the replication fork and protects DNA replication from DNA polymerase η toxicity. Nucleic Acids Res 2020; 47:11268-11283. [PMID: 31586398 PMCID: PMC6868395 DOI: 10.1093/nar/gkz824] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 09/06/2019] [Accepted: 09/25/2019] [Indexed: 11/26/2022] Open
Abstract
Accurate DNA replication is critical for the maintenance of genome integrity and cellular survival. Cancer-associated alterations often involve key players of DNA replication and of the DNA damage-signalling cascade. Post-translational modifications play a fundamental role in coordinating replication and repair and central among them is ubiquitylation. We show that the E3 ligase UBR5 interacts with components of the replication fork, including the translesion synthesis (TLS) polymerase polη. Depletion of UBR5 leads to replication problems, such as slower S-phase progression, resulting in the accumulation of single stranded DNA. The effect of UBR5 knockdown is related to a mis-regulation in the pathway that controls the ubiquitylation of histone H2A (UbiH2A) and blocking this modification is sufficient to rescue the cells from replication problems. We show that the presence of polη is the main cause of replication defects and cell death when UBR5 is silenced. Finally, we unveil a novel interaction between polη and H2A suggesting that UbiH2A could be involved in polη recruitment to the chromatin and the regulation of TLS.
Collapse
Affiliation(s)
- Lina Cipolla
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Federica Bertoletti
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Antonio Maffia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Chih-Chao Liang
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Martin A Cohn
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| |
Collapse
|
19
|
Núñez FJ, Mendez FM, Kadiyala P, Alghamri MS, Savelieff MG, Garcia-Fabiani MB, Haase S, Koschmann C, Calinescu AA, Kamran N, Saxena M, Patel R, Carney S, Guo MZ, Edwards M, Ljungman M, Qin T, Sartor MA, Tagett R, Venneti S, Brosnan-Cashman J, Meeker A, Gorbunova V, Zhao L, Kremer DM, Zhang L, Lyssiotis CA, Jones L, Herting CJ, Ross JL, Hambardzumyan D, Hervey-Jumper S, Figueroa ME, Lowenstein PR, Castro MG. IDH1-R132H acts as a tumor suppressor in glioma via epigenetic up-regulation of the DNA damage response. Sci Transl Med 2020; 11:11/479/eaaq1427. [PMID: 30760578 DOI: 10.1126/scitranslmed.aaq1427] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 08/08/2018] [Accepted: 12/28/2018] [Indexed: 01/01/2023]
Abstract
Patients with glioma whose tumors carry a mutation in isocitrate dehydrogenase 1 (IDH1R132H) are younger at diagnosis and live longer. IDH1 mutations co-occur with other molecular lesions, such as 1p/19q codeletion, inactivating mutations in the tumor suppressor protein 53 (TP53) gene, and loss-of-function mutations in alpha thalassemia/mental retardation syndrome X-linked gene (ATRX). All adult low-grade gliomas (LGGs) harboring ATRX loss also express the IDH1R132H mutation. The current molecular classification of LGGs is based, partly, on the distribution of these mutations. We developed a genetically engineered mouse model harboring IDH1R132H, TP53 and ATRX inactivating mutations, and activated NRAS G12V. Previously, we established that ATRX deficiency, in the context of wild-type IDH1, induces genomic instability, impairs nonhomologous end-joining DNA repair, and increases sensitivity to DNA-damaging therapies. In this study, using our mouse model and primary patient-derived glioma cultures with IDH1 mutations, we investigated the function of IDH1R132H in the context of TP53 and ATRX loss. We discovered that IDH1R132H expression in the genetic context of ATRX and TP53 gene inactivation (i) increases median survival in the absence of treatment, (ii) enhances DNA damage response (DDR) via epigenetic up-regulation of the ataxia-telangiectasia-mutated (ATM) signaling pathway, and (iii) elicits tumor radioresistance. Accordingly, pharmacological inhibition of ATM or checkpoint kinases 1 and 2, essential kinases in the DDR, restored the tumors' radiosensitivity. Translation of these findings to patients with IDH1132H glioma harboring TP53 and ATRX loss could improve the therapeutic efficacy of radiotherapy and, consequently, patient survival.
Collapse
Affiliation(s)
- Felipe J Núñez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Flor M Mendez
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Padma Kadiyala
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mahmoud S Alghamri
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Masha G Savelieff
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria B Garcia-Fabiani
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Santiago Haase
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Carl Koschmann
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Neha Kamran
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Meghna Saxena
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rohin Patel
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Stephen Carney
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Marissa Z Guo
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Marta Edwards
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Environmental Health Science, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rebecca Tagett
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sriram Venneti
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Alan Meeker
- Departments of Pathology, Oncology and Urology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Lili Zhao
- Department of Biostatistics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Daniel M Kremer
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.,Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Costas A Lyssiotis
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lindsey Jones
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cameron J Herting
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA.,Graduate Division of Molecular and Systems Pharmacology, Emory University, Atlanta, GA 30322, USA
| | - James L Ross
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA.,Graduate Division of Cancer Biology, Emory University, Atlanta, GA 30322, USA
| | - Dolores Hambardzumyan
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shawn Hervey-Jumper
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria E Figueroa
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136-1000, USA
| | - Pedro R Lowenstein
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA. .,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria G Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA. .,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
20
|
Zhang Z, Zheng L, Yu Y, Wu J, Yang F, Xu Y, Guo Q, Wu X, Cao S, Cao L, Song X. Involvement of SAMHD1 in dNTP homeostasis and the maintenance of genomic integrity and oncotherapy (Review). Int J Oncol 2020; 56:879-888. [PMID: 32319570 DOI: 10.3892/ijo.2020.4988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 02/07/2020] [Indexed: 11/06/2022] Open
Abstract
Sterile alpha motif and histidine/aspartic acid domain‑containing protein 1 (SAMHD1), the only deoxynucleotide triphosphate (dNTP) hydrolase in eukaryotes, plays a crucial role in regulating the dynamic balance and ratio of cellular dNTP pools. Furthermore, SAMHD1 has been reported to be involved in the pathological process of several diseases. Homozygous SAMHD1 mutations have been identified in immune system disorders, such as autoimmune disease Aicardi‑Goutières syndrome (AGS), whose primary pathogenesis is associated with the abnormal accumulation and disproportion of dNTPs. SAMHD1 is also considered to be an intrinsic virus‑restriction factor by suppressing the viral infection process, including reverse transcription, replication, packaging and transmission. In addition, SAMHD1 has been shown to promote genome integrity during homologous recombination following DNA damage, thus being considered a promising candidate for oncotherapy applications. The present review summarizes the molecular mechanisms of SAMHD1 regarding the regulation of dNTP homeostasis and DNA damage response. Additionally, its potential effects on tumorigenesis and oncotherapy are reported.
Collapse
Affiliation(s)
- Zhou Zhang
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Lixia Zheng
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Yang Yu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Jinying Wu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Fan Yang
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Yingxi Xu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Qiqiang Guo
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Xuan Wu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Sunrun Cao
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Liu Cao
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Xiaoyu Song
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| |
Collapse
|
21
|
Choi BK, Fujiwara K, Dayaram T, Darlington Y, Dickerson J, Goodell MA, Donehower LA. WIP1 dephosphorylation of p27 Kip1 Serine 140 destabilizes p27 Kip1 and reverses anti-proliferative effects of ATM phosphorylation. Cell Cycle 2020; 19:479-491. [PMID: 31959038 PMCID: PMC7100888 DOI: 10.1080/15384101.2020.1717025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/22/2019] [Accepted: 11/07/2019] [Indexed: 01/07/2023] Open
Abstract
The phosphoinositide-3-kinase like kinases (PIKK) such as ATM and ATR play a key role in initiating the cellular DNA damage response (DDR). One key ATM target is the cyclin-dependent kinase inhibitor p27Kip1 that promotes G1 arrest. ATM activates p27Kip1-induced arrest in part through phosphorylation of p27Kip1 at Serine 140. Here we show that this site is dephosphorylated by the type 2C serine/threonine phosphatase, WIP1 (Wildtype p53-Induced Phosphatase-1), encoded by the PPM1D gene. WIP1 has been shown to dephosphorylate numerous ATM target sites in DDR proteins, and its overexpression and/or mutation has often been associated with oncogenesis. We demonstrate that wildtype, but not phosphatase-dead WIP1, efficiently dephosphorylates p27Kip1 Ser140 both in vitro and in cells and that this dephosphorylation is sensitive to the WIP1-specific inhibitor GSK 2830371. Increased expression of wildtype WIP1 reduces stability of p27Kip1 while increased expression of similar amounts of phosphatase-dead WIP1 has no effect on p27Kip1 protein stability. Overexpression of wildtype p27Kip1 reduces cell proliferation and colony forming capability relative to the S140A (constitutively non-phosphorylated) form of p27. Thus, WIP1 plays a significant role in homeostatic modulation of p27Kip1 activity following activation by ATM.
Collapse
Affiliation(s)
- Byung-Kwon Choi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kenichiro Fujiwara
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Tajhal Dayaram
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Yolanda Darlington
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joshua Dickerson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A. Goodell
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lawrence A. Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
22
|
Kültz D. Evolution of cellular stress response mechanisms. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2020; 333:359-378. [PMID: 31970941 DOI: 10.1002/jez.2347] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 12/16/2022]
Abstract
The cellular stress response (CSR) is pervasive to all domains of life. It has shaped the interaction between organisms and their environment since the origin of the first cell. Although the CSR has been subject to a myriad of nuanced modifications in the various branches of life present today, its core features remain preserved. The scientific literature covering the CSR is enormous and the broad scope of this brief overview was challenging. However, it is critical to conceptually understand how cells respond to stress in a holistic sense and to point out how fundamental aspects of the CSR framework are integrated. It was necessary to be extremely selective and not feasible to even mention many interesting and important developments in this expansive field. The purpose of this overview is to sketch out general and emerging CSR concepts with an emphasis on the initial cellular strain resulting from stress (macromolecular damage) and the evolutionarily most highly conserved elements of the CSR. Examples emphasize fish and aquatic invertebrates to highlight what is known in organisms beyond mammals, yeast, and other common models. Nonetheless, select pioneering studies using canonical models are also considered and the concepts discussed are applicable to all cells. More detail on important aspects of the CSR in aquatic animals is provided in the accompanying articles of this special issue.
Collapse
Affiliation(s)
- Dietmar Kültz
- Department of Animal Sciences, University of California Davis, Davis, California
| |
Collapse
|
23
|
Hanawalt P, Sweasy J. Mechanistic understanding of cellular responses to genomic stress. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:25-33. [PMID: 31793074 DOI: 10.1002/em.22349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Within the past half century we have learned of multiple pathways for repairing damaged DNA, based upon the intrinsic redundancy of information in its complementary double strands. Mechanistic details of these pathways have provided insights into environmental and endogenous threats to genomic stability. Studies on bacterial responses to ultraviolet light led to the discovery of excision repair, as well as the inducible SOS response to DNA damage. Similar responses in eukaryotes promote upregulation of error-prone translesion DNA polymerases. Recent advances in this burgeoning field include duplex DNA sequencing to provide strikingly accurate profiling of mutational signatures, analyses of gene expression patterns in single cells, CRISPR/Cas9 to generate changes at precise genomic positions, novel roles for RNA in gene expression and DNA repair, phase-separated aqueous environments for specialized cellular transactions, and DNA lesions as epigenetic signals for gene expression. The Environmental Mutagenesis and Genomics Society (EMGS), through the broad range of expertise in its membership, stands at the crossroad of basic understanding of mechanisms for genomic maintenance and the field of genetic toxicology, with the need for regulation of exposures to toxic substances. Our future challenges include devising strategies and technologies to identify individuals who are susceptible to specific genomic stresses, along with basic research on the underlying mechanisms of cellular stress responses that promote disease-causing mutations. As the science moves forward it should also be a responsibility for the EMGS to expand its outreach programs for the enlightenment and benefit of all humans and the biosphere. Environ. Mol. Mutagen. 61:25-33, 2020. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Philip Hanawalt
- Department of Biology, Stanford University, Stanford, California
| | - Joann Sweasy
- University of Arizona Cancer Center, Tucson, Arizona
| |
Collapse
|
24
|
Kuhns KJ, Lopez-Bertoni H, Coulter JB, Bressler JP. TET1 regulates DNA repair in human glial cells. Toxicol Appl Pharmacol 2019; 380:114646. [PMID: 31278917 DOI: 10.1016/j.taap.2019.114646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 06/26/2019] [Accepted: 07/01/2019] [Indexed: 12/21/2022]
Abstract
Glioblastomas are the most aggressive of malignant brain cancers with a median patient survival of approximately 18 months. We recently demonstrated that Tet methylcytosine dioxygenase 1(TET1) is involved in cellular responses to ionizing radiation (IR) in glial-, glioblastoma-, and non-tumor-derived cells. This study used a lentiviral-mediated knockdown of TET1 to further dissect the contribution of TET1 to the DNA damage response in glial cell lines by evaluating its role in DNA repair. TET1-deficient glial cell lines displayed attenuated cytotoxicity compared to non-targeted knockdown after treatment with IR but these differences were not observed between control and TET1 deficient in response to inhibitors of Na+/K+-ATPase. Additionally, the percentage of glial cells displaying γH2A.x foci was greatly reduced in TET1-deficient glial cells compared to non-targeted knockdown conditions in response to IR and topoisomerase inhibitors. We also observed a lower percentage and a delay in 53BP1 foci formation, a marker of non-homologous end-joining, in response to IR and topoisomerase inhibitors in TET1-deficient glial cells. DNA-PK, another marker of non-homologous end-joining, was also lower in TET1-deficient glial cell lines. Interestingly, TET1-deficient glial cells displayed higher numbers of DNA strand breaks compared to control cells and repaired DNA breaks less efficiently in Comet assays. We suggest that attenuated DNA repair in TET1 deficient gliomas leads to genomic instability, which underlies poor patient survival.
Collapse
Affiliation(s)
- Katherine J Kuhns
- Environmental Health Sciences, The Johns Hopkins University Bloomberg School of Public Health, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | - Hernando Lopez-Bertoni
- Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | - Jonathan B Coulter
- Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD 21205, USA; Environmental Health Sciences, The Johns Hopkins University Bloomberg School of Public Health, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | - Joseph P Bressler
- Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD 21205, USA; Environmental Health Sciences, The Johns Hopkins University Bloomberg School of Public Health, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD 21287, USA.
| |
Collapse
|
25
|
Reis-Mansur MCPP, Cardoso-Rurr JS, Silva JVMA, de Souza GR, Cardoso VDS, Mansoldo FRP, Pinheiro Y, Schultz J, Lopez Balottin LB, da Silva AJR, Lage C, Dos Santos EP, Rosado AS, Vermelho AB. Carotenoids from UV-resistant Antarctic Microbacterium sp. LEMMJ01. Sci Rep 2019; 9:9554. [PMID: 31266976 PMCID: PMC6606617 DOI: 10.1038/s41598-019-45840-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022] Open
Abstract
The Microbacterium sp. LEMMJ01 isolated from Antarctic soil does not belong to any of the nearest species identified in the RDP database. Under UV radiation (A, B and C wavebands) the survival fractions of Microbacterium sp. cells were much higher compared with wild-type E. coli K12A15. Especially remarkable for an Antarctic bacterium, an expressive resistance against high UV-B doses was observed. The increased survival of DNA repair-proficient E. coli grown overnight added of 0.1 mg/ml or 1 mg/ml of the whole pigment extract produced by Microbacterium sp. revealed that part of the resistance of Microbacterium sp. against UV-B radiation seems to be connected with photoprotection by its pigments. Scanning electron microscopy revealed that UV-A and UV-B ensued membrane alterations only in E. coli. The APCI-MS fingerprints revealed the diagnostic ions for neurosporene (m/z 580, 566, 522, 538, and 524) synergism for the first time in this bacterium by HPLC-MS/MS analysis. Carotenoids also were devoid of phototoxicity and cytotoxicity effects in mouse cells and in human keratinocytes and fibroblasts.
Collapse
Affiliation(s)
- Maria Cristina P P Reis-Mansur
- BIOINOVAR - Biocatalysis, Bioproducts and Bioenergy, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Janine S Cardoso-Rurr
- LaRBio - Radiations and Biology Laboratory, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Josemar V Maiworm Abreu Silva
- Labio/Dimav/Inmetro - Laboratory of Tissue Bioengineering/Directorate of Metrology Applied to Life Sciences/National Institute of Metrology, Quality and Technology, Duque de Caxias, Brazil
| | - Gabriela Rodrigues de Souza
- Research Institute for Natural Products, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Verônica da Silva Cardoso
- BIOINOVAR - Biocatalysis, Bioproducts and Bioenergy, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Felipe Raposo Passos Mansoldo
- BIOINOVAR - Biocatalysis, Bioproducts and Bioenergy, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Yuri Pinheiro
- LEMM - Laboratory of Microbial Molecular Ecology, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Júnia Schultz
- LEMM - Laboratory of Microbial Molecular Ecology, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Luciene B Lopez Balottin
- Labio/Dimav/Inmetro - Laboratory of Tissue Bioengineering/Directorate of Metrology Applied to Life Sciences/National Institute of Metrology, Quality and Technology, Duque de Caxias, Brazil
| | | | - Claudia Lage
- LaRBio - Radiations and Biology Laboratory, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Elisabete Pereira Dos Santos
- Faculty of Pharmacy, Galenico Development Laboratory, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Alexandre Soares Rosado
- LEMM - Laboratory of Microbial Molecular Ecology, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Alane Beatriz Vermelho
- BIOINOVAR - Biocatalysis, Bioproducts and Bioenergy, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| |
Collapse
|
26
|
Impact of solar UV radiation on amphibians: focus on genotoxic stress. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2019; 842:14-21. [DOI: 10.1016/j.mrgentox.2019.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 03/04/2019] [Accepted: 03/08/2019] [Indexed: 11/22/2022]
|
27
|
Meas R, Wyrick JJ, Smerdon MJ. Nucleosomes Regulate Base Excision Repair in Chromatin. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2019; 780:29-36. [PMID: 31388331 PMCID: PMC6684245 DOI: 10.1016/j.mrrev.2017.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chromatin is a significant barrier to many DNA damage response (DDR) factors, such as DNA repair enzymes, that process DNA lesions to reduce mutations and prevent cell death; yet, paradoxically, chromatin also has a critical role in many signaling pathways that regulate the DDR. The primary level of DNA packaging in chromatin is the nucleosome core particle (NCP), consisting of DNA wrapped around an octamer of the core histones H2A, H2B, H3 and H4. Here, we review recent studies characterizing how the packaging of DNA into nucleosomes modulates the activity of the base excision repair (BER) pathway and dictates BER subpathway choice. We also review new evidence indicating that the histone amino-terminal tails coordinately regulate multiple DDR pathways during the repair of alkylation damage in the budding yeast Saccharomyces cerevisiae.
Collapse
Affiliation(s)
- Rithy Meas
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520
| | - Michael J. Smerdon
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520
| |
Collapse
|
28
|
Rosina M, Langone F, Giuliani G, Cerquone Perpetuini A, Reggio A, Calderone A, Fuoco C, Castagnoli L, Gargioli C, Cesareni G. Osteogenic differentiation of skeletal muscle progenitor cells is activated by the DNA damage response. Sci Rep 2019; 9:5447. [PMID: 30931986 PMCID: PMC6443689 DOI: 10.1038/s41598-019-41926-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/19/2019] [Indexed: 12/27/2022] Open
Abstract
Heterotopic ossification (HO) is a pathological condition characterized by the deposition of mineralized tissue in ectopic locations such as the skeletal muscle. The precise cellular origin and molecular mechanisms underlying HO are still debated. In our study we focus on the differentiation of mesoangioblasts (MABs), a population of multipotent skeletal muscle precursors. High-content screening for small molecules that perturb MAB differentiation decisions identified Idoxuridine (IdU), an antiviral and radiotherapy adjuvant, as a molecule that promotes MAB osteogenic differentiation while inhibiting myogenesis. IdU-dependent osteogenesis does not rely on the canonical BMP-2/SMADs osteogenic pathway. At pro-osteogenic conditions IdU induces a mild DNA Damage Response (DDR) that activates ATM and p38 eventually promoting the phosphorylation of the osteogenesis master regulator RUNX2. By interfering with this pathway IdU-induced osteogenesis is severely impaired. Overall, our study suggests that induction of the DDR promotes osteogenesis in muscle resident MABs thereby offering a new mechanism that may be involved in the ectopic deposition of mineralized tissue in the muscle.
Collapse
Affiliation(s)
- M Rosina
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - F Langone
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - G Giuliani
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | | | - A Reggio
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - A Calderone
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - C Fuoco
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - L Castagnoli
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - C Gargioli
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
| | - G Cesareni
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
- Fondazione Santa Lucia Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy.
| |
Collapse
|
29
|
Review of the evidence for thresholds for DNA-Reactive and epigenetic experimental chemical carcinogens. Chem Biol Interact 2019; 301:88-111. [DOI: 10.1016/j.cbi.2018.11.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/06/2018] [Accepted: 11/22/2018] [Indexed: 01/01/2023]
|
30
|
Wang H, Huang Y, Shi J, Zhi Y, Yuan F, Yu J, Chen Z, Yang J. XPC deficiency leads to centrosome amplification by inhibiting BRCA1 expression upon cisplatin-mediated DNA damage in human bladder cancer. Cancer Lett 2018; 444:136-146. [PMID: 30579971 DOI: 10.1016/j.canlet.2018.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/03/2018] [Accepted: 12/11/2018] [Indexed: 12/15/2022]
Abstract
Xeroderma pigmentosum group C (XPC) is a well-known DNA damage recognition protein. Defects in XPC lead to carcinogenesis and progression of many human cancers. In the current study, we defined a novel, important role of XPC in preventing centrosome amplification during cisplatin-mediated DNA damage response. From experiments with human bladder cancer tissue, urothelial tissue from Xpc knockout mice and XPC-silenced cell lines, we found that attenuated XPC expression was associated with increased centrosome amplification in human bladder cancer. A significant increase in centrosome amplification was observed in XPC-silenced cells upon cisplatin treatment. XPC deficiency leads to reduced BRCA1 expression via upregulating its transcriptional repressor, Pit-1. The BRCA1 downregulation results in more DNA double strand breaks accumulation and persistent activation of the ATM-Chk1/Chk2 signaling, resulting in a prolonged G2/M arrest during which centrosome can over-duplicate and lead to centrosome amplification. XPC complementation in silenced cells could reduce Pit-1 expression, increase BRCA1 expression and recover the status of centrosome amplification. Our study reveals a new function for XPC in preventing chromosomal instability, providing new information on cancer chemotherapy and potential clinical significance for cancer management.
Collapse
Affiliation(s)
- Huanhuan Wang
- Department of Cell Biology, The Third Military Medical University, Chongqing, PR China
| | - Yaqin Huang
- Department of Cell Biology, The Third Military Medical University, Chongqing, PR China
| | - Jiazhong Shi
- Department of Cell Biology, The Third Military Medical University, Chongqing, PR China
| | - Yi Zhi
- Department of Urology, Third Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Fang Yuan
- Chongqing University Cancer Hospital, Chongqing, PR China
| | - Jin Yu
- Department of Cell Biology, The Third Military Medical University, Chongqing, PR China
| | - Zhiwen Chen
- Urology Institute of People's Liberation Army, Southwest Hospital, The Third Military Medical University, Chongqing, PR China; Southwest Cancer Center, Southwest Hospital, The Third Military Medical University, Chongqing, China.
| | - Jin Yang
- Department of Cell Biology, The Third Military Medical University, Chongqing, PR China.
| |
Collapse
|
31
|
Chen J, Shen X, Pardue S, Meram AT, Rajendran S, Ghali GE, Kevil CG, Shackelford RE. The Ataxia telangiectasia-mutated and Rad3-related protein kinase regulates cellular hydrogen sulfide concentrations. DNA Repair (Amst) 2018; 73:55-63. [PMID: 30470507 DOI: 10.1016/j.dnarep.2018.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 12/16/2022]
Abstract
The ataxia telangiectasia-mutated and Rad3-related (ATR) serine/threonine kinase plays a central role in the repair of replication-associated DNA damage, the maintenance of S and G2/M-phase genomic stability, and the promotion of faithful mitotic chromosomal segregation. A number of stimuli activate ATR, including persistent single-stranded DNA at stalled replication folks, R loop formation, hypoxia, ultraviolet light, and oxidative stress, leading to ATR-mediated protein phosphorylation. Recently, hydrogen sulfide (H2S), an endogenous gasotransmitter, has been found to regulate multiple cellular processes through complex redox reactions under similar cell stress environments. Three enzymes synthesize H2S: cystathionine-β-synthase, cystathionine γ-lyase, and 3-mercaptopyruvate sulfurtransferase. Since H2S can under some conditions cause DNA damage, we hypothesized that ATR activity may regulate cellular H2S concentrations and H2S-syntheszing enzymes. Here we show that human colorectal cancer cells carrying biallelic knock-in hypomorphic ATR mutations have lower cellular H2S concentrations than do syngeneic ATR wild-type cells, and all three H2S-synthesizing enzymes show lower protein expression in the ATR hypomorphic mutant cells. Additionally, ATR serine 428 phosphorylation is altered by H2S donor and H2S synthesis enzyme inhibition, while the oxidative-stress induced phosphorylation of the ATR-regulated protein CHK1 on serine 345 is increased by H2S synthesis enzyme inhibition. Lastly, inhibition of H2S production potentiated oxidative stress-induced double-stranded DNA breaks in the ATR hypomorphic mutant compared to ATR wild-type cells. Our findings demonstrate that the ATR kinase regulates and is regulated by H2S.
Collapse
Affiliation(s)
- Jie Chen
- Department of Pathology & Translational Pathobiology, LSU Health Sciences Center Shreveport, Shreveport, Louisiana, 71130, United States
| | - Xinggui Shen
- Department of Pathology & Translational Pathobiology, LSU Health Sciences Center Shreveport, Shreveport, Louisiana, 71130, United States
| | - Sibile Pardue
- Department of Cell Biology & Anatomy, LSU Health Sciences Center Shreveport, Shreveport, Louisiana, 71130, United States
| | - Andrew T Meram
- Head & Neck Oncologic/Microvascular Reconstructive Surgery Department of Oral & Maxillofacial/Head & Neck Surgery, Louisiana State University Health Sciences Center, Shreveport, LA, United States
| | - Saranya Rajendran
- Department of Cell Biology & Anatomy, LSU Health Sciences Center Shreveport, Shreveport, Louisiana, 71130, United States
| | - Ghali E Ghali
- Head & Neck Oncologic/Microvascular Reconstructive Surgery Department of Oral & Maxillofacial/Head & Neck Surgery, Louisiana State University Health Sciences Center, Shreveport, LA, United States
| | - Christopher G Kevil
- Department of Pathology & Translational Pathobiology, LSU Health Sciences Center Shreveport, Shreveport, Louisiana, 71130, United States; Department of Cell Biology & Anatomy, LSU Health Sciences Center Shreveport, Shreveport, Louisiana, 71130, United States.
| | - Rodney E Shackelford
- Department of Pathology & Translational Pathobiology, LSU Health Sciences Center Shreveport, Shreveport, Louisiana, 71130, United States.
| |
Collapse
|
32
|
Belotserkovskii BP, Tornaletti S, D'Souza AD, Hanawalt PC. R-loop generation during transcription: Formation, processing and cellular outcomes. DNA Repair (Amst) 2018; 71:69-81. [PMID: 30190235 PMCID: PMC6340742 DOI: 10.1016/j.dnarep.2018.08.009] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
R-loops are structures consisting of an RNA-DNA duplex and an unpaired DNA strand. They can form during transcription upon nascent RNA "threadback" invasion into the DNA duplex to displace the non-template strand. Although R-loops occur naturally in all kingdoms of life and serve regulatory roles, they are often deleterious and can cause genomic instability. Of particular importance are the disastrous consequences when replication forks or transcription complexes collide with R-loops. The appropriate processing of R-loops is essential to avoid a number of human neurodegenerative and other clinical disorders. We provide a perspective on mechanistic aspects of R-loop formation and their resolution learned from studies in model systems. This should contribute to improved understanding of R-loop biological functions and enable their practical applications. We propose the novel employment of artificially-generated stable R-loops to selectively inactivate tumor cells.
Collapse
Affiliation(s)
- Boris P Belotserkovskii
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Silvia Tornaletti
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Alicia D D'Souza
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Philip C Hanawalt
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States.
| |
Collapse
|
33
|
Abstract
From bacteria to humans, ancient stress responses enable organisms to contend with damage to both the genome and the proteome. These pathways have long been viewed as fundamentally separate responses. Yet recent discoveries from multiple fields have revealed surprising links between the two. Many DNA-damaging agents also target proteins, and mutagenesis induced by DNA damage produces variant proteins that are prone to misfolding, degradation, and aggregation. Likewise, recent studies have observed pervasive engagement of a p53-mediated response, and other factors linked to maintenance of genomic integrity, in response to misfolded protein stress. Perhaps most remarkably, protein aggregation and self-assembly has now been observed in multiple proteins that regulate the DNA damage response. The importance of these connections is highlighted by disease models of both cancer and neurodegeneration, in which compromised DNA repair machinery leads to profound defects in protein quality control, and vice versa.
Collapse
|
34
|
Li J, Lu L, Zhang YH, Liu M, Chen L, Huang T, Cai YD. Identification of synthetic lethality based on a functional network by using machine learning algorithms. J Cell Biochem 2018; 120:405-416. [PMID: 30125975 DOI: 10.1002/jcb.27395] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 07/09/2018] [Indexed: 12/27/2022]
Abstract
Synthetic lethality is the synthesis of mutations leading to cell death. Tumor-specific synthetic lethality has been targeted in research to improve cancer therapy. With the advances of techniques in molecular biology, such as RNAi and CRISPR/Cas9 gene editing, efforts have been made to systematically identify synthetic lethal interactions, especially for frequently mutated genes in cancers. However, elucidating the mechanism of synthetic lethality remains a challenge because of the complexity of its influencing conditions. In this study, we proposed a new computational method to identify critical functional features that can accurately predict synthetic lethal interactions. This method incorporates several machine learning algorithms and encodes protein-coding genes by an enrichment system derived from gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways to represent their functional features. We built a random forest-based prediction engine by using 2120 selected features and obtained a Matthews correlation coefficient of 0.532. We examined the top 15 features and found that most of them have potential roles in synthetic lethality according to previous studies. These results demonstrate the ability of our proposed method to predict synthetic lethal interactions and provide a basis for further characterization of these particular genetic combinations.
Collapse
Affiliation(s)
- JiaRui Li
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Lin Lu
- Department of Radiology, Columbia University Medical Center, New York
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Min Liu
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
| |
Collapse
|
35
|
Negelspach DC, Kaladchibachi S, Fernandez F. The circadian activity rhythm is reset by nanowatt pulses of ultraviolet light. Proc Biol Sci 2018; 285:20181288. [PMID: 30068685 PMCID: PMC6111179 DOI: 10.1098/rspb.2018.1288] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
The circadian pacemaker synchronizes to the Earth's rotation by tracking step-by-step changes in illumination that occur as the sun passes the horizon. While twilight progressions of irradiance and colour are considered important stimuli in this process, comparably less thought has been given to the possibility that ultraviolet A (UVA) radiation might actually play a more formative role given its evolutionary significance in shaping 24 h timekeeping. Here, we show that Drosophila activity rhythms can be phase-shifted by UVA light at an energy range seated well below that of the visible spectrum. Because the energy threshold for this resetting matches the incident amount of UVA on the human retina at twilight, our results suggest that UVA light has the potential to function as a similar time cue in people.
Collapse
Affiliation(s)
| | | | - Fabian Fernandez
- Department of Psychology, University of Arizona, Tucson, AZ, USA
- Department of Neurology, University of Arizona, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
36
|
Evaluation of Genotoxic and DNA Photo-Protective Activity of Bryothamnion triquetrum and Halimeda incrassata Seaweeds Extracts. COSMETICS 2017. [DOI: 10.3390/cosmetics4030023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
37
|
Morio T. Recent advances in the study of immunodeficiency and DNA damage response. Int J Hematol 2017; 106:357-365. [PMID: 28550350 DOI: 10.1007/s12185-017-2263-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 05/17/2017] [Indexed: 12/13/2022]
Abstract
DNA breaks can be induced by exogenous stimuli or by endogenous stress, but are also generated during recombination of V, D, and J genes (V(D)J recombination), immunoglobulin class switch recombination (CSR). Among various DNA breaks generated, DNA double strand break (DSB) is the most deleterious one. DNA damage response (DDR) is initiated when DSBs are detected, leading to DNA break repair by non-homologous end joining (NHEJ). The process is critically important for the generation of diversity for foreign antigens; and failure to exert DNA repair leads to immunodeficiency such as severe combined immunodeficiency and hyper-IgM syndrome. In V(D)J recombination, DSBs are induced by RAG1/2; and generated post-cleavage hairpins are resolved by Artemis/DNA-PKcs/KU70/KU80. DDR is initiated by ataxia-telangiectasia mutated as a master regulator together with MRE11/RAD50/NBS1 complex. Finally, DSBs are repaired by NHEJ. The defect of one of the molecules shows various degree of immunodeficiency and radiosensitivity. Upon CSR inducing signal, DSBs induced by activation-induced cytidine deaminase and endonucleases elicit DDR. Broken ends are repaired either by NHEJ or by mismatch repair system. Patients with radiosensitive SCID require hematopoietic cell transplantation as a curative therapy; but the procedures for eradication of recipient hematopoietic cells are often associated with severe toxicity.
Collapse
Affiliation(s)
- Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| |
Collapse
|
38
|
|
39
|
Lieberman HB, Panigrahi SK, Hopkins KM, Wang L, Broustas CG. p53 and RAD9, the DNA Damage Response, and Regulation of Transcription Networks. Radiat Res 2017; 187:424-432. [PMID: 28140789 DOI: 10.1667/rr003cc.1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The way cells respond to DNA damage is important since inefficient repair or misrepair of lesions can have deleterious consequences, including mutation, genomic instability, neurodegenerative disorders, premature aging, cancer or death. Whether damage occurs spontaneously as a byproduct of normal metabolic processes, or after exposure to exogenous agents, cells muster a coordinated, complex DNA damage response (DDR) to mitigate potential harmful effects. A variety of activities are involved to promote cell survival, and include DNA repair, DNA damage tolerance, as well as transient cell cycle arrest to provide time for repair before entry into critical cell cycle phases, an event that could be lethal if traversal occurs while damage is present. When such damage is prolonged or not repairable, senescence, apoptosis or autophagy is induced. One major level of DDR regulation occurs via the orchestrated transcriptional control of select sets of genes encoding proteins that mediate the response. p53 is a transcription factor that transactivates specific DDR downstream genes through binding DNA consensus sequences usually in or near target gene promoter regions. The profile of p53-regulated genes activated at any given time varies, and is dependent upon type of DNA damage or stress experienced, exact composition of the consensus DNA binding sequence, presence of other DNA binding proteins, as well as cell context. RAD9 is another protein critical for the response of cells to DNA damage, and can also selectively regulate gene transcription. The limited studies addressing the role of RAD9 in transcription regulation indicate that the protein transactivates at least one of its target genes, p21/waf1/cip1, by binding to DNA sequences demonstrated to be a p53 response element. NEIL1 is also regulated by RAD9 through a similar DNA sequence, though not yet directly verified as a bonafide p53 response element. These findings suggest a novel pathway whereby p53 and RAD9 control the DDR through a shared mechanism involving an overlapping network of downstream target genes. Details and unresolved questions about how these proteins coordinate or compete to execute the DDR through transcriptional reprogramming, as well as biological implications, are discussed.
Collapse
Affiliation(s)
- Howard B Lieberman
- a Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032; and.,b Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032
| | - Sunil K Panigrahi
- a Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032; and
| | - Kevin M Hopkins
- a Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032; and
| | - Li Wang
- a Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032; and
| | - Constantinos G Broustas
- a Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032; and
| |
Collapse
|
40
|
Hu J, Adar S. The Cartography of UV-induced DNA Damage Formation and DNA Repair. Photochem Photobiol 2017; 93:199-206. [PMID: 27861959 DOI: 10.1111/php.12668] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/23/2016] [Indexed: 12/29/2022]
Abstract
DNA damage presents a barrier to DNA-templated biochemical processes, including gene expression and faithful DNA replication. Compromised DNA repair leads to mutations, enhancing the risk for genetic diseases and cancer development. Conventional experimental approaches to study DNA damage required a researcher to choose between measuring bulk damage over the entire genome, with little or no resolution regarding a specific location, and obtaining data specific to a locus of interest, without a global perspective. Recent advances in high-throughput genomic tools overcame these limitations and provide high-resolution measurements simultaneously across the genome. In this review, we discuss the available methods for measuring DNA damage and their repair, focusing on genomewide assays for pyrimidine photodimers, the major types of damage induced by ultraviolet irradiation. These new genomic assays will be a powerful tool in identifying key components of genome stability and carcinogenesis.
Collapse
Affiliation(s)
- Jinchuan Hu
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Sheera Adar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
| |
Collapse
|
41
|
Adam S, Dabin J, Chevallier O, Leroy O, Baldeyron C, Corpet A, Lomonte P, Renaud O, Almouzni G, Polo SE. Real-Time Tracking of Parental Histones Reveals Their Contribution to Chromatin Integrity Following DNA Damage. Mol Cell 2016; 64:65-78. [PMID: 27642047 PMCID: PMC5065526 DOI: 10.1016/j.molcel.2016.08.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/20/2016] [Accepted: 08/11/2016] [Indexed: 12/22/2022]
Abstract
Chromatin integrity is critical for cell function and identity but is challenged by DNA damage. To understand how chromatin architecture and the information that it conveys are preserved or altered following genotoxic stress, we established a system for real-time tracking of parental histones, which characterize the pre-damage chromatin state. Focusing on histone H3 dynamics after local UVC irradiation in human cells, we demonstrate that parental histones rapidly redistribute around damaged regions by a dual mechanism combining chromatin opening and histone mobilization on chromatin. Importantly, parental histones almost entirely recover and mix with new histones in repairing chromatin. Our data further define a close coordination of parental histone dynamics with DNA repair progression through the damage sensor DDB2 (DNA damage-binding protein 2). We speculate that this mechanism may contribute to maintaining a memory of the original chromatin landscape and may help preserve epigenome stability in response to DNA damage. Parental H3 histones redistribute to the periphery of UVC-damaged regions The redistribution involves histone mobilization on chromatin and chromatin opening Parental histones recover massively during repair progression Parental histone dynamics may help coordinate DNA repair with epigenome integrity
Collapse
Affiliation(s)
- Salomé Adam
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France; Laboratory of Nuclear Dynamics, UMR3664 CNRS, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Juliette Dabin
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France
| | - Odile Chevallier
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France
| | - Olivier Leroy
- Plateforme Imagerie Cellulaire et Tissulaire-Infrastructure en Biologie Santé et Agronomie, UMR3215 CNRS/U934 INSERM, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Céline Baldeyron
- Laboratory of Nuclear Dynamics, UMR3664 CNRS, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Armelle Corpet
- Team Chromatin Assembly, Nuclear Domains, Virus, Institut NeuroMyoGène, LabEx DEVweCAN, Université Claude Bernard Lyon 1, UMR5310 CNRS/U1217 INSERM, F-69100 Lyon, France
| | - Patrick Lomonte
- Team Chromatin Assembly, Nuclear Domains, Virus, Institut NeuroMyoGène, LabEx DEVweCAN, Université Claude Bernard Lyon 1, UMR5310 CNRS/U1217 INSERM, F-69100 Lyon, France
| | - Olivier Renaud
- Plateforme Imagerie Cellulaire et Tissulaire-Infrastructure en Biologie Santé et Agronomie, UMR3215 CNRS/U934 INSERM, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Geneviève Almouzni
- Laboratory of Nuclear Dynamics, UMR3664 CNRS, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Sophie E Polo
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France.
| |
Collapse
|
42
|
DNA Replication Stress Phosphoproteome Profiles Reveal Novel Functional Phosphorylation Sites on Xrs2 in Saccharomyces cerevisiae. Genetics 2016; 203:353-68. [PMID: 27017623 DOI: 10.1534/genetics.115.185231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/21/2016] [Indexed: 01/11/2023] Open
Abstract
In response to replication stress, a phospho-signaling cascade is activated and required for coordination of DNA repair and replication of damaged templates (intra-S-phase checkpoint) . How phospho-signaling coordinates the DNA replication stress response is largely unknown. We employed state-of-the-art liquid chromatography tandem-mass spectrometry (LC-MS/MS) approaches to generate high-coverage and quantitative proteomic and phospho-proteomic profiles during replication stress in yeast, induced by continuous exposure to the DNA alkylating agent methyl methanesulfonate (MMS) . We identified 32,057 unique peptides representing the products of 4296 genes and 22,061 unique phosphopeptides representing the products of 3183 genes. A total of 542 phosphopeptides (mapping to 339 genes) demonstrated an abundance change of greater than or equal to twofold in response to MMS. The screen enabled detection of nearly all of the proteins known to be involved in the DNA damage response, as well as many novel MMS-induced phosphorylations. We assessed the functional importance of a subset of key phosphosites by engineering a panel of phosphosite mutants in which an amino acid substitution prevents phosphorylation. In total, we successfully mutated 15 MMS-responsive phosphorylation sites in seven representative genes including APN1 (base excision repair); CTF4 and TOF1 (checkpoint and sister-chromatid cohesion); MPH1 (resolution of homologous recombination intermediates); RAD50 and XRS2 (MRX complex); and RAD18 (PRR). All of these phosphorylation site mutants exhibited MMS sensitivity, indicating an important role in protecting cells from DNA damage. In particular, we identified MMS-induced phosphorylation sites on Xrs2 that are required for MMS resistance in the absence of the MRX activator, Sae2, and that affect telomere maintenance.
Collapse
|