1
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Gu S, Al-Hashimi HM. Direct Measurement of 8OG Syn-Anti Flips in Mutagenic 8OG·A and Long-Range Damage-Dependent Hoogsteen Breathing Dynamics Using 1H CEST NMR. J Phys Chem B 2024; 128:4087-4096. [PMID: 38644782 DOI: 10.1021/acs.jpcb.4c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Elucidating how damage impacts DNA dynamics is essential for understanding the mechanisms of damage recognition and repair. Many DNA lesions alter their propensities to form low-populated and short-lived conformational states. However, NMR methods to measure these dynamics require isotopic enrichment, which is difficult for damaged nucleotides. Here, we demonstrate the utility of the 1H chemical exchange saturation transfer (CEST) NMR experiment in measuring the dynamics of oxidatively damaged 8-oxoguanine (8OG) in the mutagenic 8OGsyn·Aanti mismatch. Using 8OG-H7 as an NMR probe of the damaged base, we directly measured 8OG syn-anti flips to form a lowly populated (pop. ∼ 5%) and short-lived (lifetime ∼50 ms) nonmutagenic 8OGanti·Aanti. These exchange parameters were in quantitative agreement with values from 13C off-resonance R1ρ and CEST on the labeled partner adenine. The Watson-Crick-like 8OGsyn·Aanti mismatch also rescued the kinetics of Hoogsteen motions at distant A-T base pairs, which the G·A mismatch had slowed down. The results lend further support for 8OGanti·Aanti as a minor conformational state of 8OG·A, reveal that 8OG damage can impact Hoogsteen dynamics at a distance, and demonstrate the utility of 1H CEST for measuring damage-dependent dynamics in unlabeled DNA.
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Affiliation(s)
- Stephanie Gu
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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2
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Navarro-Carrasco E, Monte-Serrano E, Campos-Díaz A, Rolfs F, de Goeij-de Haas R, Pham TV, Piersma SR, González-Alonso P, Jiménez CR, Lazo PA. VRK1 Regulates Sensitivity to Oxidative Stress by Altering Histone Epigenetic Modifications and the Nuclear Phosphoproteome in Tumor Cells. Int J Mol Sci 2024; 25:4874. [PMID: 38732093 PMCID: PMC11084957 DOI: 10.3390/ijms25094874] [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: 03/21/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
The chromatin organization and its dynamic remodeling determine its accessibility and sensitivity to DNA damage oxidative stress, the main source of endogenous DNA damage. We studied the role of the VRK1 chromatin kinase in the response to oxidative stress. which alters the nuclear pattern of histone epigenetic modifications and phosphoproteome pathways. The early effect of oxidative stress on chromatin was studied by determining the levels of 8-oxoG lesions and the alteration of the epigenetic modification of histones. Oxidative stress caused an accumulation of 8-oxoG DNA lesions that were increased by VRK1 depletion, causing a significant accumulation of DNA strand breaks detected by labeling free 3'-DNA ends. In addition, oxidative stress altered the pattern of chromatin epigenetic marks and the nuclear phosphoproteome pathways that were impaired by VRK1 depletion. Oxidative stress induced the acetylation of H4K16ac and H3K9 and the loss of H3K4me3. The depletion of VRK1 altered all these modifications induced by oxidative stress and resulted in losses of H4K16ac and H3K9ac and increases in the H3K9me3 and H3K4me3 levels. All these changes were induced by the oxidative stress in the epigenetic pattern of histones and impaired by VRK1 depletion, indicating that VRK1 plays a major role in the functional reorganization of chromatin in the response to oxidative stress. The analysis of the nuclear phosphoproteome in response to oxidative stress detected an enrichment of the phosphorylated proteins associated with the chromosome organization and chromatin remodeling pathways, which were significantly decreased by VRK1 depletion. VRK1 depletion alters the histone epigenetic pattern and nuclear phosphoproteome pathways in response to oxidative stress. The enzymes performing post-translational epigenetic modifications are potential targets in synthetic lethality strategies for cancer therapies.
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Affiliation(s)
- Elena Navarro-Carrasco
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Eva Monte-Serrano
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Aurora Campos-Díaz
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Frank Rolfs
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Richard de Goeij-de Haas
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Thang V. Pham
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Sander R. Piersma
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Paula González-Alonso
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Connie R. Jiménez
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Pedro A. Lazo
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
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3
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Dash M, Meher P, Aditya Kumar, Satapathy SS, Namsa ND. High frequency of transition to transversion ratio in the stem region of RNA secondary structure of untranslated region of SARS-CoV-2. PeerJ 2024; 12:e16962. [PMID: 38666080 PMCID: PMC11044879 DOI: 10.7717/peerj.16962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/26/2024] [Indexed: 04/28/2024] Open
Abstract
Introduction The propensity of nucleotide bases to form pairs, causes folding and the formation of secondary structure in the RNA. Therefore, purine (R): pyrimidine (Y) base-pairing is vital to maintain uniform lateral dimension in RNA secondary structure. Transversions or base substitutions between R and Y bases, are more detrimental to the stability of RNA secondary structure, than transitions derived from substitutions between A and G or C and T. The study of transversion and transition base substitutions is important to understand evolutionary mechanisms of RNA secondary structure in the 5' and 3' untranslated (UTR) regions of SARS-CoV-2. In this work, we carried out comparative analysis of transition and transversion base substitutions in the stem and loop regions of RNA secondary structure of SARS-CoV-2. Methods We have considered the experimentally determined and well documented stem and loop regions of 5' and 3' UTR regions of SARS-CoV-2 for base substitution analysis. The secondary structure comprising of stem and loop regions were visualized using the RNAfold web server. The GISAID repository was used to extract base sequence alignment of the UTR regions. Python scripts were developed for comparative analysis of transversion and transition frequencies in the stem and the loop regions. Results The results of base substitution analysis revealed a higher transition (ti) to transversion (tv) ratio (ti/tv) in the stem region of UTR of RNA secondary structure of SARS-CoV-2 reported during the early stage of the pandemic. The higher ti/tv ratio in the stem region suggested the influence of secondary structure in selecting the pattern of base substitutions. This differential pattern of ti/tv values between stem and loop regions was not observed among the Delta and Omicron variants that dominated the later stage of the pandemic. It is noteworthy that the ti/tv values in the stem and loop regions were similar among the later dominant Delta and Omicron variant strains which is to be investigated to understand the rapid evolution and global adaptation of SARS-CoV-2. Conclusion Our findings implicate the lower frequency of transversions than the transitions in the stem regions of UTRs of SARS-CoV-2. The RNA secondary structures are associated with replication, translation, and packaging, further investigations are needed to understand these base substitutions across different variants of SARS-CoV-2.
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Affiliation(s)
- Madhusmita Dash
- Department of Electronics and Communication Engineering, National Institute of Technology Arunachal Pradesh, Jote, Arunachal Pradesh, India
| | - Preetisudha Meher
- Department of Electronics and Communication Engineering, National Institute of Technology Arunachal Pradesh, Jote, Arunachal Pradesh, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | | | - Nima D. Namsa
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
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Ababio GK, Ekem I, Acquaye J, Oppong SY, Amoah AGB, Brandful J, Quaye IK. Detection of Transversions and Transitions in HBG2 Cis-Elements Associated with Sickle Cell Allele in Ghanaians. Biochem Genet 2024; 62:666-674. [PMID: 37395849 DOI: 10.1007/s10528-023-10438-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/20/2023] [Indexed: 07/04/2023]
Abstract
Short tandem repeats located 5' prime to the β-globin gene, have been observed to be in linkage disequilibrium with the HbS allele, and thought to affect the severity of sickle cell disease. Here, we report on new mutants within the HBG2 region that may impact sickle cell disease. To determine the cis-acting elements microsatellites, indels and single nucleotide polymorphisms (SNPs), within the HBG2 region by sequencing, in subjects with sickle cell disease. The case-control study was located at the Center for Clinical Genetics, Sickle cell unit, Korle-Bu Teaching Hospital. A questionnaire was used for demographic data and clinical information. Hematological profile (red blood cell, white blood cell, platelet, hemoglobin and mean corpuscular volume) were assessed in 83 subjects. A set of 45 samples comprising amplified DNA on the HBG2 gene from HbSS (22), HbSC (17) and 6 controls (HbAA) were sequenced. Differences in the microsatellite region between sickle cell disease (SCD) (HbSS and HbSC) genotypes and control subjects were identified by counting and assessed by Chi-square analysis. Red blood cells, hematocrit, platelets, white blood cells and hemoglobin indices differed in genotypic groups. HbSS subjects were affirmed to have severer hemolytic anemia than HbSC subjects. Two indels (T1824 and C905) were seen in both SS and SC genotypes. Two peculiar SNPs: G:T1860 (transition) and A:G1872 transversions were found within the HBG2 gene that were significantly associated with the HbSS genotype (Fisher's exact test, p = 0.006) and HbS allele respectively (Fisher's exact test, p = 0.006). Cis-acting elements in HbSS and HbSC were different and may contribute to the phenotype seen in the disease state.
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Affiliation(s)
- G K Ababio
- Department of Medical Biochemistry, University of Ghana Medical School, Accra, Ghana.
| | - I Ekem
- Department of Hematology, University of Cape Coast School of Medicine, Cape Coast, Ghana
| | - J Acquaye
- Department of Hematology, University of Ghana Medical School, Accra, Ghana
| | - S Y Oppong
- Department of Medical Biochemistry, University of Ghana Medical School, Accra, Ghana
- Department of Chemical Pathology, University of Ghana Medical School, Accra, Ghana
| | - A G B Amoah
- Department of Medicine, University of Ghana Medical School, Accra, Ghana
| | - J Brandful
- Department of Virology, Noguchi Memorial Institute of Medical Research, Legon, Ghana
| | - I K Quaye
- Department of Biochemistry, University of Namibia Medical School, Windhoek, Namibia.
- Regent University College of Science and Technology, Dansoman, Accra, Ghana.
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Lv T, Li J, Zhou L, Zhou T, Pritchard HW, Ren C, Chen J, Yan J, Pei J. Aging-Induced Reduction in Safflower Seed Germination via Impaired Energy Metabolism and Genetic Integrity Is Partially Restored by Sucrose and DA-6 Treatment. PLANTS (BASEL, SWITZERLAND) 2024; 13:659. [PMID: 38475505 DOI: 10.3390/plants13050659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024]
Abstract
Seed storage underpins global agriculture and the seed trade and revealing the mechanisms of seed aging is essential for enhancing seed longevity management. Safflower is a multipurpose oil crop, rich in unsaturated fatty acids that are at high risk of peroxidation as a contributory factor to seed aging. However, the molecular mechanisms responsible for safflower seed viability loss are not yet elucidated. We used controlled deterioration (CDT) conditions of 60% relative humidity and 50 °C to reduce germination in freshly harvested safflower seeds and analyzed aged seeds using biochemical and molecular techniques. While seed malondialdehyde (MDA) and fatty acid content increased significantly during CDT, catalase activity and soluble sugar content decreased. KEGG analysis of gene function and qPCR validation indicated that aging severely impaired several key functional and biosynthetic pathways including glycolysis, fatty acid metabolism, antioxidant activity, and DNA replication and repair. Furthermore, exogenous sucrose and diethyl aminoethyl hexanoate (DA-6) treatment partially promoted germination in aged seeds, further demonstrating the vital role of impaired sugar and fatty acid metabolism during the aging and recovery processes. We concluded that energy metabolism and genetic integrity are impaired during aging, which contributes to the loss of seed vigor. Such energy metabolic pathways as glycolysis, fatty acid degradation, and the tricarboxylic acid cycle (TCA) are impaired, especially fatty acids produced by the hydrolysis of triacylglycerols during aging, as they are not efficiently converted to sucrose via the glyoxylate cycle to provide energy supply for safflower seed germination and seedling growth. At the same time, the reduced capacity for nucleotide synthesis capacity and the deterioration of DNA repair ability further aggravate the damage to DNA, reducing seed vitality.
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Affiliation(s)
- Tang Lv
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Juan Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lanyu Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tao Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hugh W Pritchard
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, China
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, West Sussex, UK
| | - Chaoxiang Ren
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jiang Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jie Yan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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6
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Xu Q, del Mundo IMA, Zewail-Foote M, Luke BT, Vasquez KM, Kowalski J. MoCoLo: a testing framework for motif co-localization. Brief Bioinform 2024; 25:bbae019. [PMID: 38521050 PMCID: PMC10960634 DOI: 10.1093/bib/bbae019] [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: 10/26/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 03/25/2024] Open
Abstract
Sequence-level data offers insights into biological processes through the interaction of two or more genomic features from the same or different molecular data types. Within motifs, this interaction is often explored via the co-occurrence of feature genomic tracks using fixed-segments or analytical tests that respectively require window size determination and risk of false positives from over-simplified models. Moreover, methods for robustly examining the co-localization of genomic features, and thereby understanding their spatial interaction, have been elusive. We present a new analytical method for examining feature interaction by introducing the notion of reciprocal co-occurrence, define statistics to estimate it and hypotheses to test for it. Our approach leverages conditional motif co-occurrence events between features to infer their co-localization. Using reverse conditional probabilities and introducing a novel simulation approach that retains motif properties (e.g. length, guanine-content), our method further accounts for potential confounders in testing. As a proof-of-concept, motif co-localization (MoCoLo) confirmed the co-occurrence of histone markers in a breast cancer cell line. As a novel analysis, MoCoLo identified significant co-localization of oxidative DNA damage within non-B DNA-forming regions that significantly differed between non-B DNA structures. Altogether, these findings demonstrate the potential utility of MoCoLo for testing spatial interactions between genomic features via their co-localization.
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Affiliation(s)
- Qi Xu
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Imee M A del Mundo
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas, 78723, USA
| | - Maha Zewail-Foote
- Department of Chemistry and Biochemistry, Southwestern University, Georgetown, TX, 78626, USA
| | - Brian T Luke
- Bioinformatics and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21701, USA
| | - Karen M Vasquez
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas, 78723, USA
| | - Jeanne Kowalski
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
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7
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Gu S, Al-Hashimi HM. Direct Measurement of 8OG syn-anti Flips in Mutagenic 8OG•A and Long-Range Damage-Dependent Hoogsteen Breathing Dynamics Using 1H CEST NMR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575532. [PMID: 38293035 PMCID: PMC10827055 DOI: 10.1101/2024.01.15.575532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Elucidating how damage impacts DNA dynamics is essential for understanding the mechanisms of damage recognition and repair. Many DNA lesions alter the propensities to form lowly-populated and short-lived conformational states. However, NMR methods to measure these dynamics require isotopic enrichment, which is difficult for damaged nucleotides. Here, we demonstrate the utility of the 1H chemical exchange saturation transfer (CEST) NMR experiment in measuring the dynamics of oxidatively damaged 8-oxoguanine (8OG) in the mutagenic 8OGsyn•Aanti mismatch. Using 8OG-H7 as an NMR probe of the damaged base, we directly measured 8OG syn-anti flips to form a lowly-populated (pop. ~ 5%) and short-lived (lifetime ~ 50 ms) non-mutagenic 8OGanti•Aanti. These exchange parameters were in quantitative agreement with values from 13C off-resonance R1ρ and CEST on a labeled partner adenine. The Watson-Crick-like 8OGsyn•Aanti mismatch also rescued the kinetics of Hoogsteen motions at distance A-T base pairs, which the G•A mismatch had slowed down. The results lend further support for 8OGanti•Aanti as a minor conformational state of 8OG•A, reveal that 8OG damage can impact Hoogsteen dynamics at a distance, and demonstrate the utility of 1H CEST for measuring damage-dependent dynamics in unlabeled DNA.
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Affiliation(s)
- Stephanie Gu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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8
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Kılıç M, Diamantis P, Johnson SK, Toth O, Rothlisberger U. Redox-Based Defect Detection in Packed DNA: Insights from Hybrid Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations. J Chem Theory Comput 2023; 19:8434-8445. [PMID: 37963372 PMCID: PMC10687876 DOI: 10.1021/acs.jctc.3c01013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
The impact of an 8-oxoguanine (8oxoG) defect on the redox properties of DNA within the nucleosome core particle (NCP) was investigated employing hybrid quantum mechanical/molecular mechanics (QM/MM) molecular dynamics simulations of native and 8oxoG-containing NCP systems with an explicit representation of a biologically relevant environment. Two distinct NCP positions with varying solvent accessibility were considered for 8oxoG insertion. In both cases, it is found that the presence of 8oxoG drastically decreases the redox free energy of oxidation by roughly 1 eV, which is very similar to what was recently reported for free native and 8oxoG-containing DNA. In contrast, the effect of 8oxoG on the reorganization free energy is even smaller for packed DNA (decrease of 0.13 and 0.01 eV for defect-free and defect-containing systems, respectively) compared to the one for free DNA (0.25 eV), consistent with the increased rigidity of the NCP as compared to free DNA. Furthermore, the presence of an 8oxoG defect does not yield any significant changes in the packed DNA structure. Such a conclusion favors the idea that in the case of chromatin, defect-induced changes in DNA redox chemistry can also be exploited to detect damaged bases via DNA-mediated hole transfer.
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Affiliation(s)
| | | | - Sophia K. Johnson
- Laboratory of Computational Chemistry
and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Oliver Toth
- Laboratory of Computational Chemistry
and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry
and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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9
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Andrés CMC, de la Lastra JMP, Juan CA, Plou FJ, Pérez-Lebeña E. Chemical Insights into Oxidative and Nitrative Modifications of DNA. Int J Mol Sci 2023; 24:15240. [PMID: 37894920 PMCID: PMC10607741 DOI: 10.3390/ijms242015240] [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: 09/05/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
This review focuses on DNA damage caused by a variety of oxidizing, alkylating, and nitrating species, and it may play an important role in the pathophysiology of inflammation, cancer, and degenerative diseases. Infection and chronic inflammation have been recognized as important factors in carcinogenesis. Under inflammatory conditions, reactive oxygen species (ROS) and reactive nitrogen species (RNS) are generated from inflammatory and epithelial cells, and result in the formation of oxidative and nitrative DNA lesions, such as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-nitroguanine. Cellular DNA is continuously exposed to a very high level of genotoxic stress caused by physical, chemical, and biological agents, with an estimated 10,000 modifications occurring every hour in the genetic material of each of our cells. This review highlights recent developments in the chemical biology and toxicology of 2'-deoxyribose oxidation products in DNA.
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Affiliation(s)
| | - José Manuel Pérez de la Lastra
- Institute of Natural Products and Agrobiology, CSIC-Spanish Research Council, Avda. AstrofísicoFco. Sánchez, 3, 38206 La Laguna, Spain
| | - Celia Andrés Juan
- Cinquima Institute and Department of Organic Chemistry, Faculty of Sciences, Valladolid University, Paseo de Belén, 7, 47011 Valladolid, Spain;
| | - Francisco J. Plou
- Institute of Catalysis and Petrochemistry, CSIC-Spanish Research Council, 28049 Madrid, Spain;
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Tomoda F, Koike T, Nitta A, Kurosaki H, Sugimori H, Oh-Hara M, Kinugawa K. Urinary levels of cortisol but not catecholamines are associated with those of 8-hydroxy-2'-deoxyguanosine in uncomplicated primary hypertension. J Hypertens 2023; 41:1571-1577. [PMID: 37642591 DOI: 10.1097/hjh.0000000000003507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
OBJECTIVES The relationships between stress hormones and oxidative DNA damage have not yet been explored in human hypertension. We investigated the associations of urinary levels of cortisol or catecholamines with those of 8-hydroxy-2'-deoxyguanosine, a marker of oxidative DNA damage in primary hypertension. METHODS Untreated 156 primary hypertensives without apparent cardiovascular diseases were entered into the study. Following blood sampling after an overnight fast, 24-h blood pressure monitoring and 24-h urinary sampling were performed simultaneously to determine 24-h averaged values for blood pressure and urinary levels of cortisol, catecholamines and 8-hydroxy-2'-deoxyguanosine. RESULTS Urinary cortisol significantly correlated positively with urinary 8-hydroxy-2'-deoxyguanosine in all studied participants (r = 0.334, P < 0.001). Contrary, either urinary adrenaline or urinary noradrenaline did not significantly correlate with urinary 8-hydroxy-2'-deoxyguanosine (r = 0.050, P = 0.553 or r = 0.063, P = 0.435). Additionally, the positive association of urinary cortisol with urinary 8-hydroxy-2'-deoxyguanosine remained highly significant after the adjustments for multiple confounders of oxidative stress such as age, gender, body mass index, smoking status, 24-h blood pressure, C-reactive protein and estimated glomerular filtration rate (partial r = 0.323, P < 0.001), although only approximately 10% of the variance in urinary cortisol was attributable to differences in urinary 8-OHdG (partial r2 = 0.104). Thus, our data indicate that cortisol but not catecholamines could at least partially contribute to the occurrence of oxidative DNA damage in primary hypertensives. CONCLUSION The present study suggested the possibility that the overactivation of hypothalamic-pituitary-adrenal axis rather than sympathoadrenal system could enhance oxidative stress and attendant DNA oxidation in uncomplicated primary hypertension.
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Affiliation(s)
- Fumihiro Tomoda
- The Faculty of Health Science, Fukui Health Science University, Fukui
- The Second Department of Internal Medicine
| | | | - Atsumi Nitta
- The Department of Pharmaceutical Therapy & Neuropharmacology, University of Toyama, Toyama, Japan
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11
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Cipriano A, Viviano M, Feoli A, Milite C, Sarno G, Castellano S, Sbardella G. NADPH Oxidases: From Molecular Mechanisms to Current Inhibitors. J Med Chem 2023; 66:11632-11655. [PMID: 37650225 PMCID: PMC10510401 DOI: 10.1021/acs.jmedchem.3c00770] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Indexed: 09/01/2023]
Abstract
NADPH oxidases (NOXs) form a family of electron-transporting membrane enzymes whose main function is reactive oxygen species (ROS) generation. Strong evidence suggests that ROS produced by NOX enzymes are major contributors to oxidative damage under pathologic conditions. Therefore, blocking the undesirable actions of these enzymes is a therapeutic strategy for treating various pathological disorders, such as cardiovascular diseases, inflammation, and cancer. To date, identification of selective NOX inhibitors is quite challenging, precluding a pharmacologic demonstration of NOX as therapeutic targets in vivo. The aim of this Perspective is to furnish an updated outlook about the small-molecule NOX inhibitors described over the last two decades. Structures, activities, and in vitro/in vivo specificity are discussed, as well as the main biological assays used.
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Affiliation(s)
- Alessandra Cipriano
- Department
of Pharmacy, Epigenetic Med Chem Lab, and PhD Program in Drug Discovery and
Development, University of Salerno, via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Monica Viviano
- Department
of Pharmacy, Epigenetic Med Chem Lab, and PhD Program in Drug Discovery and
Development, University of Salerno, via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Alessandra Feoli
- Department
of Pharmacy, Epigenetic Med Chem Lab, and PhD Program in Drug Discovery and
Development, University of Salerno, via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Ciro Milite
- Department
of Pharmacy, Epigenetic Med Chem Lab, and PhD Program in Drug Discovery and
Development, University of Salerno, via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Giuliana Sarno
- Department
of Pharmacy, Epigenetic Med Chem Lab, and PhD Program in Drug Discovery and
Development, University of Salerno, via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Sabrina Castellano
- Department
of Pharmacy, Epigenetic Med Chem Lab, and PhD Program in Drug Discovery and
Development, University of Salerno, via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Gianluca Sbardella
- Department
of Pharmacy, Epigenetic Med Chem Lab, and PhD Program in Drug Discovery and
Development, University of Salerno, via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
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12
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Vetritti L, Kopyra J, Wierzbicka P, Varella MTDN. Fragmentation of the DNA Lesion 8-oxo-Guanine by Low-Energy Electrons. J Phys Chem A 2023; 127:7470-7478. [PMID: 37661383 DOI: 10.1021/acs.jpca.3c03704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
8-oxo-Guanine is a mutagenic lesion produced by reactions involving reactive oxygen species and guanine in DNA. Its production induces mispairing between the canonical nucleobases during DNA replication such that various types of cancers are associated with the DNA lesion. Since radiation therapy is used in some cases, the interaction of low-energy electrons with 8-oxo-guanine can in turn produce other reactive species, which in principle could have either a detrimental or protective effect on the organism. Motivated by these facts, we report a comparative experimental study of electron-induced fragmentation of guanine and 8-oxo-guanine, along with a theoretical study of the π* shape resonances and bound anion states, which may trigger those dissociation reactions. The electron-induced fragmentation of 8-oxo-guanine is remarkably distinct from the native form. More complex reactions were observed for the oxidized species, which may produce several anion fragments at very low energies (∼0 eV). The dehydrogenated parent anion, which is already a minor fragment in guanine, was completely suppressed in 8-oxo-guanine. The calculated thermodynamical thresholds also suggest that NH2 elimination in guanine, at sub-excitation energies, proceeds via a complex reaction involving rearrangement steps.
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Affiliation(s)
- Leonardo Vetritti
- Instituto de Física, Universidade de São Paulo, Caixa Postal 66318, 05315-970 São Paulo, São Paulo, Brazil
| | - Janina Kopyra
- Faculty of Sciences, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland
| | - Paulina Wierzbicka
- Faculty of Sciences, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland
| | - Márcio T do N Varella
- Instituto de Física, Universidade de São Paulo, Caixa Postal 66318, 05315-970 São Paulo, São Paulo, Brazil
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13
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Wang Y, Su M, Chen Y, Huang X, Ruan L, Lv Q, Li L. Research progress on the role and mechanism of DNA damage repair in germ cell development. Front Endocrinol (Lausanne) 2023; 14:1234280. [PMID: 37529603 PMCID: PMC10390305 DOI: 10.3389/fendo.2023.1234280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 06/28/2023] [Indexed: 08/03/2023] Open
Abstract
In the complex and dynamic processes of replication, transcription, and translation of DNA molecules, a large number of replication errors or damage can occur which lead to obstacles in the development process of germ cells and result in a decreased reproductive rate. DNA damage repair has attracted widespread attention due to its important role in the maintenance and regulation of germ cells. This study reports on a systematic review of the role and mechanism of DNA damage repair in germline development. First, the causes, detection methods, and repair methods of DNA damage, and the mechanism of DNA damage repair are summarized. Second, a summary of the causes of abnormal DNA damage repair in germ cells is introduced along with common examples, and the relevant effects of germ cell damage. Third, we introduce the application of drugs related to DNA damage repair in the treatment of reproductive diseases and related surgical treatment of abnormal DNA damage, and summarize various applications of DNA damage repair in germ cells. Finally, a summary and discussion is given of the current deficiencies in DNA damage repair during germ cell development and future research development. The purpose of this paper is to provide researchers engaged in relevant fields with a further systematic understanding of the relevant applications of DNA damage repair in germ cells and to gain inspiration from it to provide new research ideas for related fields.
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Affiliation(s)
- Yan Wang
- College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Mengrong Su
- College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Yujie Chen
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Xinyu Huang
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Lian Ruan
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Qizhuang Lv
- College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Li Li
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
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14
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Gu S, Szymanski ES, Rangadurai AK, Shi H, Liu B, Manghrani A, Al-Hashimi HM. Dynamic basis for dA•dGTP and dA•d8OGTP misincorporation via Hoogsteen base pairs. Nat Chem Biol 2023; 19:900-910. [PMID: 37095237 DOI: 10.1038/s41589-023-01306-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/08/2023] [Indexed: 04/26/2023]
Abstract
Replicative errors contribute to the genetic diversity needed for evolution but in high frequency can lead to genomic instability. Here, we show that DNA dynamics determine the frequency of misincorporating the A•G mismatch, and altered dynamics explain the high frequency of 8-oxoguanine (8OG) A•8OG misincorporation. NMR measurements revealed that Aanti•Ganti (population (pop.) of >91%) transiently forms sparsely populated and short-lived Aanti+•Gsyn (pop. of ~2% and kex = kforward + kreverse of ~137 s-1) and Asyn•Ganti (pop. of ~6% and kex of ~2,200 s-1) Hoogsteen conformations. 8OG redistributed the ensemble, rendering Aanti•8OGsyn the dominant state. A kinetic model in which Aanti+•Gsyn is misincorporated quantitatively predicted the dA•dGTP misincorporation kinetics by human polymerase β, the pH dependence of misincorporation and the impact of the 8OG lesion. Thus, 8OG increases replicative errors relative to G because oxidation of guanine redistributes the ensemble in favor of the mutagenic Aanti•8OGsyn Hoogsteen state, which exists transiently and in low abundance in the A•G mismatch.
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Affiliation(s)
- Stephanie Gu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Eric S Szymanski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Base4, Durham, NC, USA
| | - Atul K Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Hospital for Sick Children, Toronto, Ontario, Canada
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Akanksha Manghrani
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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15
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da Costa Xavier LA, Navoni JA, Souza do Amaral V. Oxidative genomic damage in humans exposed to high indoor radon levels in Northeast Brazil. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 889:503652. [PMID: 37491111 DOI: 10.1016/j.mrgentox.2023.503652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 06/18/2023] [Accepted: 06/22/2023] [Indexed: 07/27/2023]
Abstract
Radon gas inhalation is the main source of exposure to ionizing radiation by humans. There is still lack in knowledge concerning the chronic and indirect effects of exposure to this carcinogenic factor. Therefore, the aim of this work is to analyze the levels of oxidative genomic damage in inhabitants of a medium-high background radiation area (HBRA) (N = 82) in Northeastern Brazil and compare them with people living in a low background radiation area (LBRA) (N = 46). 8-hydroxy-2-deoxyguanosine (8-OHdG) was quantified in urine, Ser326Cys polymorphism was determined in the hOGG1 gene and indoor radon was measured. HBRA houses had 6.5 times higher indoor radon levels than those from LBRA (p-value < 0.001). The 8-OHdG mean (95% confidence interval) were significantly different, 8.42 (5.98-11.9) ng/mg creatinine and 29.91 (23.37-38.30) ng/mg creatinine for LBRA and HBRA, respectively. The variables representing lifestyle and environmental and occupational exposures did not have a significant association with oxidized guanosine concentrations. On the other hand, lower 8-OHdG values were observed in subjects that had one mutant allele (326Cys) in the hOGG1 gene than those who had both wild alleles (Ser/Ser (p-value < 0.05). It can be concluded that high radon levels have significantly influenced the genome oxidative metabolism and hOGG1 gene polymorphism would mediate the observed biological response.
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Affiliation(s)
- Luíza Araújo da Costa Xavier
- Post-graduation Program of Biochemistry and Molecular Biology, Laboratory of Toxicological Genetic, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Julio Alejandro Navoni
- Post-graduation Program of Development and Environment - DDMA, Federal University of Rio Grande do Norte (UFRN), Natal/RN, Brazil
| | - Viviane Souza do Amaral
- Post-graduation Program of Biochemistry and Molecular Biology, Laboratory of Toxicological Genetic, Federal University of Rio Grande do Norte, Natal, RN, Brazil; Post-graduation Program of Development and Environment - DDMA, Federal University of Rio Grande do Norte (UFRN), Natal/RN, Brazil..
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16
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De Silva WGM, McCarthy BY, Han J, Yang C, Holland AJA, Stern H, Dixon KM, Tang EKY, Tuckey RC, Rybchyn MS, Mason RS. The Over-Irradiation Metabolite Derivative, 24-Hydroxylumister-ol 3, Reduces UV-Induced Damage in Skin. Metabolites 2023; 13:775. [PMID: 37512482 PMCID: PMC10383208 DOI: 10.3390/metabo13070775] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
The hormonal form of vitamin D3, 1,25(OH)2D3, reduces UV-induced DNA damage. UV exposure initiates pre-vitamin D3 production in the skin, and continued UV exposure photoisomerizes pre-vitamin D3 to produce "over-irradiation products" such as lumisterol3 (L3). Cytochrome P450 side-chain cleavage enzyme (CYP11A1) in skin catalyzes the conversion of L3 to produce three main derivatives: 24-hydroxy-L3 [24(OH)L3], 22-hydroxy-L3 [22(OH)L3], and 20,22-dihydroxy-L3 [20,22(OH)L3]. The current study investigated the photoprotective properties of the major over-irradiation metabolite, 24(OH)L3, in human primary keratinocytes and human skin explants. The results indicated that treatment immediately after UV with either 24(OH)L3 or 1,25(OH)2D3 reduced UV-induced cyclobutane pyrimidine dimers and oxidative DNA damage, with similar concentration response curves in keratinocytes, although in skin explants, 1,25(OH)2D3 was more potent. The reductions in DNA damage by both compounds were, at least in part, the result of increased DNA repair through increased energy availability via increased glycolysis, as well as increased DNA damage recognition proteins in the nucleotide excision repair pathway. Reductions in UV-induced DNA photolesions by either compound occurred in the presence of lower reactive oxygen species. The results indicated that under in vitro and ex vivo conditions, 24(OH)L3 provided photoprotection against UV damage similar to that of 1,25(OH)2D3.
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Affiliation(s)
| | - Bianca Yuko McCarthy
- School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jeremy Han
- School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chen Yang
- School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Andrew J A Holland
- Douglas Cohen Department of Paediatric Surgery, The Children's Hospital at Westmead Clinical School, The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Harvey Stern
- Department of Plastic and Constructive Surgery, The Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
- Strathfield Private Hospital, Sydney, NSW 2042, Australia
| | - Katie Marie Dixon
- School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edith Kai Yan Tang
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Robert Charles Tuckey
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Mark Stephen Rybchyn
- School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Rebecca Sara Mason
- School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
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17
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Dupuy P, Ghosh S, Fay A, Adefisayo O, Gupta R, Shuman S, Glickman MS. Roles for mycobacterial DinB2 in frameshift and substitution mutagenesis. eLife 2023; 12:e83094. [PMID: 37141254 PMCID: PMC10159617 DOI: 10.7554/elife.83094] [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: 08/31/2022] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Translesion synthesis by translesion polymerases is a conserved mechanism of DNA damage tolerance. In bacteria, DinB enzymes are the widely distributed promutagenic translesion polymerases. The role of DinBs in mycobacterial mutagenesis was unclear until recent studies revealed a role for mycobacterial DinB1 in substitution and frameshift mutagenesis, overlapping with that of translesion polymerase DnaE2. Mycobacterium smegmatis encodes two additional DinBs (DinB2 and DinB3) and Mycobacterium tuberculosis encodes DinB2, but the roles of these polymerases in mycobacterial damage tolerance and mutagenesis is unknown. The biochemical properties of DinB2, including facile utilization of ribonucleotides and 8-oxo-guanine, suggest that DinB2 could be a promutagenic polymerase. Here, we examine the effects of DinB2 and DinB3 overexpression in mycobacterial cells. We demonstrate that DinB2 can drive diverse substitution mutations conferring antibiotic resistance. DinB2 induces frameshift mutations in homopolymeric sequences, both in vitro and in vivo. DinB2 switches from less to more mutagenic in the presence of manganese in vitro. This study indicates that DinB2 may contribute to mycobacterial mutagenesis and antibiotic resistance acquisition in combination with DinB1 and DnaE2.
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Affiliation(s)
- Pierre Dupuy
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Shreya Ghosh
- Molecular Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Allison Fay
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Oyindamola Adefisayo
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate SchoolNew YorkUnited States
| | - Richa Gupta
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Michael S Glickman
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate SchoolNew YorkUnited States
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18
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Basaran MM, Hazar M, Aydın M, Uzuğ G, Özdoğan İ, Pala E, Aydın Dilsiz S, Basaran N. Effects of COVID-19 Disease on DNA Damage, Oxidative Stress and Immune Responses. TOXICS 2023; 11:386. [PMID: 37112613 PMCID: PMC10145820 DOI: 10.3390/toxics11040386] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 06/19/2023]
Abstract
Coronavirus disease 2019 (COVID-19) has posed a great threat to public health and has caused concern due to its fatal consequences over the last few years. Most people with COVID-19 show mild-to-moderate symptoms and recover without the need for special treatment, while others become seriously ill and need medical attention. Additionally, some serious outcomes, such as heart attacks and even stroke, have been later reported in patients who had recovered. There are limited studies on how SARS-CoV-2 infection affects some molecular pathways, including oxidative stress and DNA damage. In this study, we aimed to evaluate DNA damage, using the alkaline comet assay, and its relationship with oxidative stress and immune response parameters in COVID-19-positive patients. Our results show that DNA damage, oxidative stress parameters and cytokine levels significantly increased in SARS-CoV-2-positive patients when compared with healthy controls. The effects of SARS-CoV-2 infection on DNA damage, oxidative stress and immune responses may be crucial in the pathophysiology of the disease. It is suggested that the illumination of these pathways will contribute to the development of clinical treatments and to reduce adverse effects in the future.
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Affiliation(s)
- M. Mert Basaran
- Department of Otolaryngology, Faculty of Medicine, Kafkas University, 36000 Kars, Türkiye
| | - Merve Hazar
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, İbrahim Cecen University, 04100 Ağrı, Türkiye;
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Hacettepe University, 06100 Ankara, Türkiye;
| | - Mehtap Aydın
- Department of Infectious Diseases and Clinical Microbiology, Health Sciences University, Ümraniye Training and Research Hospital, 34764 İstanbul, Türkiye; (M.A.); (G.U.); (İ.Ö.)
| | - Gülsüm Uzuğ
- Department of Infectious Diseases and Clinical Microbiology, Health Sciences University, Ümraniye Training and Research Hospital, 34764 İstanbul, Türkiye; (M.A.); (G.U.); (İ.Ö.)
| | - İlkima Özdoğan
- Department of Infectious Diseases and Clinical Microbiology, Health Sciences University, Ümraniye Training and Research Hospital, 34764 İstanbul, Türkiye; (M.A.); (G.U.); (İ.Ö.)
| | - Emin Pala
- Department of Family Medicine, Health Sciences University, Ümraniye Training and Research Hospital, 34764 İstanbul, Türkiye;
| | - Sevtap Aydın Dilsiz
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Hacettepe University, 06100 Ankara, Türkiye;
| | - Nursen Basaran
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Başkent University, 06490 Ankara, Türkiye
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19
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Li J, Zhang H, Wang ZH, Li YX, Zhang LQ, Cui J, Li DN, Wang ZH, Liu Q, Liu Z, Iwakuma T, Cai JP. 8-oxo-dGTP curbs tumor development via S phase arrest and AIF-mediated apoptosis. Free Radic Biol Med 2023; 196:53-64. [PMID: 36640852 DOI: 10.1016/j.freeradbiomed.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/19/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Oxidative stress can attack precursor nucleotides, resulting in nucleic acid damage in cells. It remains unclear how 8-oxo-dGTP and 8-oxoGTP, oxidized forms of dGTP and GTP, respectively, could affect DNA or RNA oxidation levels and tumor development. To address this, we intravenously administered 8-oxo-dGTP and 8-oxoGTP to wild-type and MTH1-knockout mice. 8-oxoGTP administration increased frequency of tumor incidence, which is more prominent in MTH1-knockout mice. However, 8-oxo-dGTP treatment rather reduced tumor development regardless of the mouse genotype. The tumor suppressive effects of 8-oxo-dGTP were further confirmed using xenograft and C57/6J-ApcMin/Nju mouse models. Mechanistically, 8-oxo-dGTP increased the 8-oxo-dG contents in DNA and DNA strand breakage, induced cell cycle arrest in S phase and apoptosis mediated by AIF, eventually leading to reduced tumor incidence. These results suggest distinct roles of 8-oxo-dGTP and 8-oxoGTP in tumor development.
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Affiliation(s)
- Jin Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - He Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, PR China
| | - Zhen-He Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Yun-Xuan Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Li-Qun Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Ju Cui
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Dan-Ni Li
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Zi-Hui Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, PR China
| | - Qian Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, PR China
| | - Zhen Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, PR China
| | - Tomoo Iwakuma
- Children's Mercy Research Institute, Kansas City, MO, 64108, USA
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
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20
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Aging, Physical Exercise, Telomeres, and Sarcopenia: A Narrative Review. Biomedicines 2023; 11:biomedicines11020598. [PMID: 36831134 PMCID: PMC9952920 DOI: 10.3390/biomedicines11020598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
Human aging is a gradual and adaptive process characterized by a decrease in the homeostatic response, leading to biochemical and molecular changes that are driven by hallmarks of aging, such as oxidative stress (OxS), chronic inflammation, and telomere shortening. One of the diseases associated with the hallmarks of aging, which has a great impact on functionality and quality of life, is sarcopenia. However, the relationship between telomere length, sarcopenia, and age-related mortality has not been extensively studied. Moderate physical exercise has been shown to have a positive effect on sarcopenia, decreasing OxS and inflammation, and inducing protective effects on telomeric DNA. This results in decreased DNA strand breaks, reduced OxS and IA, and activation of repair pathways. Higher levels of physical activity are associated with an apparent increase in telomere length. This review aims to present the current state of the art of knowledge on the effect of physical exercise on telomeric maintenance and activation of repair mechanisms in sarcopenia.
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21
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Gene-Environment Interactions in Repeat Expansion Diseases: Mechanisms of Environmentally Induced Repeat Instability. Biomedicines 2023; 11:biomedicines11020515. [PMID: 36831049 PMCID: PMC9953593 DOI: 10.3390/biomedicines11020515] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Short tandem repeats (STRs) are units of 1-6 base pairs that occur in tandem repetition to form a repeat tract. STRs exhibit repeat instability, which generates expansions or contractions of the repeat tract. Over 50 diseases, primarily affecting the central nervous system and muscles, are characterized by repeat instability. Longer repeat tracts are typically associated with earlier age of onset and increased disease severity. Environmental exposures are suspected to play a role in the pathogenesis of repeat expansion diseases. Here, we review the current knowledge of mechanisms of environmentally induced repeat instability in repeat expansion diseases. The current evidence demonstrates that environmental factors modulate repeat instability via DNA damage and induction of DNA repair pathways, with distinct mechanisms for repeat expansion and contraction. Of particular note, oxidative stress is a key mediator of environmentally induced repeat instability. The preliminary evidence suggests epigenetic modifications as potential mediators of environmentally induced repeat instability. Future research incorporating an array of environmental exposures, new human cohorts, and improved model systems, with a continued focus on cell-types, tissues, and critical windows, will aid in identifying mechanisms of environmentally induced repeat instability. Identifying environmental modulators of repeat instability and their mechanisms of action will inform preventions, therapies, and public health measures.
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22
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Molecular targets that sensitize cancer to radiation killing: From the bench to the bedside. Biomed Pharmacother 2023; 158:114126. [PMID: 36521246 DOI: 10.1016/j.biopha.2022.114126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Radiotherapy is a standard cytotoxic therapy against solid cancers. It uses ionizing radiation to kill tumor cells through damage to DNA, either directly or indirectly. Radioresistance is often associated with dysregulated DNA damage repair processes. Most radiosensitizers enhance radiation-mediated DNA damage and reduce the rate of DNA repair ultimately leading to accumulation of DNA damages, cell-cycle arrest, and cell death. Recently, agents targeting key signals in DNA damage response such as DNA repair pathways and cell-cycle have been developed. This new class of molecularly targeted radiosensitizing agents is being evaluated in preclinical and clinical studies to monitor their activity in potentiating radiation cytotoxicity of tumors and reducing normal tissue toxicity. The molecular pathways of DNA damage response are reviewed with a focus on the repair mechanisms, therapeutic targets under current clinical evaluation including ATM, ATR, CDK1, CDK4/6, CHK1, DNA-PKcs, PARP-1, Wee1, & MPS1/TTK and potential new targets (BUB1, and DNA LIG4) for radiation sensitization.
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23
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Gorini F, Ambrosio S, Lania L, Majello B, Amente S. The Intertwined Role of 8-oxodG and G4 in Transcription Regulation. Int J Mol Sci 2023; 24:ijms24032031. [PMID: 36768357 PMCID: PMC9916577 DOI: 10.3390/ijms24032031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
The guanine base in nucleic acids is, among the other bases, the most susceptible to being converted into 8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) when exposed to reactive oxygen species. In double-helix DNA, 8-oxodG can pair with adenine; hence, it may cause a G > T (C > A) mutation; it is frequently referred to as a form of DNA damage and promptly corrected by DNA repair mechanisms. Moreover, 8-oxodG has recently been redefined as an epigenetic factor that impacts transcriptional regulatory elements and other epigenetic modifications. It has been proposed that 8-oxodG exerts epigenetic control through interplay with the G-quadruplex (G4), a non-canonical DNA structure, in transcription regulatory regions. In this review, we focused on the epigenetic roles of 8-oxodG and the G4 and explored their interplay at the genomic level.
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Affiliation(s)
- Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Susanna Ambrosio
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Luigi Lania
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Barbara Majello
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
- Correspondence:
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24
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Di Minno A, Aveta A, Gelzo M, Tripodi L, Pandolfo SD, Crocetto F, Imbimbo C, Castaldo G. 8-Hydroxy-2-Deoxyguanosine and 8-Iso-Prostaglandin F2α: Putative Biomarkers to assess Oxidative Stress Damage Following Robot-Assisted Radical Prostatectomy (RARP). J Clin Med 2022; 11:jcm11206102. [PMID: 36294423 PMCID: PMC9605140 DOI: 10.3390/jcm11206102] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/11/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
Objective: Prostate cancer (PCa) is the most common type of cancer. Biomarkers help researchers to understand the mechanisms of disease and refine diagnostic panels. We measured urinary 8-hydroxy-2-deoxyguanosine (8-OHdG) and 8-iso-prostaglandin F2α (8-IsoF2α) to assess oxidative stress damage in PCa patients undergoing robot-assisted radical prostatectomy (RARP). Methods: Forty PCa patients were enrolled in the study. Urine was collected before (T0) and 3 months after the RARP procedure (T1). 8-OHdG and 8-IsoF2α were measured through liquid chromatography-tandem mass spectrometry. Sex- and age-matched healthy subjects served as controls (CTRL). Results: At T0, patients exhibited significantly higher levels of 8-OHdG than CTRL (p = 0.026). At T1, 23/40 patients who completed the 3-month follow-up showed levels of 8-OHdG that were significantly lower than at T0 (p = 0.042), and comparable to those of the CTRL subjects (p = 0.683). At T0, 8-Iso-PGF2α levels were significantly higher in PCa patients than in CTRL subjects (p = 0.0002). At T1, 8-Iso-PGF2α levels were significantly lower than at T0 (p < 0.001) and were comparable to those of CTRL patients (p = 0.087). Conclusions: A liquid chromatography-tandem mass spectrometry method reveals enhanced OHdG and 8-Iso-PGF2α in the urine of PCa patients. RARP normalizes such indices of oxidative stress. Large-sized sample studies and long-term follow-ups are now needed to validate these urinary biomarkers for use in the early prevention and successful treatment of PCa.
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Affiliation(s)
- Alessandro Di Minno
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy
- Correspondence:
| | - Achille Aveta
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy
- Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
| | - Monica Gelzo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
| | - Lorella Tripodi
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
| | - Savio Domenico Pandolfo
- Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
| | - Felice Crocetto
- Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
| | - Ciro Imbimbo
- Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
| | - Giuseppe Castaldo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
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25
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Liu Y, Zhu X, Wang Z, Dai X, You C. Next-Generation Sequencing-Based Analysis of the Roles of DNA Polymerases ν and θ in the Replicative Bypass of 8-Oxo-7,8-dihydroguanine in Human Cells. ACS Chem Biol 2022; 17:2315-2319. [PMID: 35815634 DOI: 10.1021/acschembio.2c00415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA polymerase (Pol) ν and Pol θ are two specialized A-family DNA polymerases that function in the translesion synthesis of certain DNA lesions. However, the biological functions of human Pols ν and θ in cellular replicative bypass of 8-oxo-7,8-dihydroguanine (8-oxoG), an important carcinogenesis-related biomarker of oxidative DNA damage, remain unclear. Herein, we showed that depletion of Pols ν and θ in human cells could cause an elevated hypersensitivity to oxidative stress induced by hydrogen peroxide. Using next-generation sequencing-based lesion bypass and mutagenesis assay, we further demonstrated that Pols ν and θ had important roles in promoting translesion synthesis of 8-oxoG in human cells. We also found that the depletion of Pol ν, but not Pol θ, caused a substantial reduction in G → T mutation frequency for 8-oxoG. These findings provided novel insights into the involvement of A-family DNA polymerases in oxidative DNA damage response.
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Affiliation(s)
- Yini Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xiaowen Zhu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Ziyu Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xiaoxia Dai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Changjun You
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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26
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Lee Y, Onishi Y, McPherson L, Kietrys AM, Hebenbrock M, Jun YW, Das I, Adimoolam S, Ji D, Mohsen MG, Ford JM, Kool ET. Enhancing Repair of Oxidative DNA Damage with Small-Molecule Activators of MTH1. ACS Chem Biol 2022; 17:2074-2087. [PMID: 35830623 PMCID: PMC11163517 DOI: 10.1021/acschembio.2c00038] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Impaired DNA repair activity has been shown to greatly increase rates of cancer clinically. It has been hypothesized that upregulating repair activity in susceptible individuals may be a useful strategy for inhibiting tumorigenesis. Here, we report that selected tyrosine kinase (TK) inhibitors including nilotinib, employed clinically in the treatment of chronic myeloid leukemia, are activators of the repair enzyme Human MutT Homolog 1 (MTH1). MTH1 cleanses the oxidatively damaged cellular nucleotide pool by hydrolyzing the oxidized nucleotide 8-oxo-2'-deoxyguanosine (8-oxo-dG)TP, which is a highly mutagenic lesion when incorporated into DNA. Structural optimization of analogues of TK inhibitors resulted in compounds such as SU0448, which induces 1000 ± 100% activation of MTH1 at 10 μM and 410 ± 60% at 5 μM. The compounds are found to increase the activity of the endogenous enzyme, and at least one (SU0448) decreases levels of 8-oxo-dG in cellular DNA. The results suggest the possibility of using MTH1 activators to decrease the frequency of mutagenic nucleotides entering DNA, which may be a promising strategy to suppress tumorigenesis in individuals with elevated cancer risks.
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Affiliation(s)
- Yujeong Lee
- Departmeut of Chemistry, Stanford University, Stanford. CA 94305, United States
| | - Yoshiyuki Onishi
- Departmeut of Chemistry, Stanford University, Stanford. CA 94305, United States
| | - Lisa McPherson
- Department of Medicine, Stanford University, Stanford, CA 94305, United States
| | - Anna M. Kietrys
- Departmeut of Chemistry, Stanford University, Stanford. CA 94305, United States
| | - Marian Hebenbrock
- Departmeut of Chemistry, Stanford University, Stanford. CA 94305, United States
| | - Yong Woong Jun
- Departmeut of Chemistry, Stanford University, Stanford. CA 94305, United States
| | - Ishani Das
- Department of Medicine, Stanford University, Stanford, CA 94305, United States
| | - Shanthi Adimoolam
- Department of Medicine, Stanford University, Stanford, CA 94305, United States
| | - Debin Ji
- Departmeut of Chemistry, Stanford University, Stanford. CA 94305, United States
| | - Michael G. Mohsen
- Departmeut of Chemistry, Stanford University, Stanford. CA 94305, United States
| | - James M. Ford
- Department of Medicine, Stanford University, Stanford, CA 94305, United States
| | - Eric T. Kool
- Departmeut of Chemistry, Stanford University, Stanford. CA 94305, United States
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27
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Mueller FS, Amport R, Notter T, Schalbetter SM, Lin HY, Garajova Z, Amini P, Weber-Stadlbauer U, Markkanen E. Deficient DNA base-excision repair in the forebrain leads to a sex-specific anxiety-like phenotype in mice. BMC Biol 2022; 20:170. [PMID: 35907861 PMCID: PMC9339204 DOI: 10.1186/s12915-022-01377-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background Neuropsychiatric disorders, such as schizophrenia (SZ) and autism spectrum disorder (ASD), are common, multi-factorial and multi-symptomatic disorders. Ample evidence implicates oxidative stress, deficient repair of oxidative DNA lesions and DNA damage in the development of these disorders. However, it remains unclear whether insufficient DNA repair and resulting DNA damage are causally connected to their aetiopathology, or if increased levels of DNA damage observed in patient tissues merely accumulate as a consequence of cellular dysfunction. To assess a potential causal role for deficient DNA repair in the development of these disorders, we behaviourally characterized a mouse model in which CaMKIIa-Cre-driven postnatal conditional knockout (KO) of the core base-excision repair (BER) protein XRCC1 leads to accumulation of unrepaired DNA damage in the forebrain. Results CaMKIIa-Cre expression caused specific deletion of XRCC1 in the dorsal dentate gyrus (DG), CA1 and CA2 and the amygdala and led to increased DNA damage therein. While motor coordination, cognition and social behaviour remained unchanged, XRCC1 KO in the forebrain caused increased anxiety-like behaviour in males, but not females, as assessed by the light–dark box and open field tests. Conversely, in females but not males, XRCC1 KO caused an increase in learned fear-related behaviour in a cued (Pavlovian) fear conditioning test and a contextual fear extinction test. The relative density of the GABA(A) receptor alpha 5 subunit (GABRA5) was reduced in the amygdala and the dorsal CA1 in XRCC1 KO females, whereas male XRCC1 KO animals exhibited a significant reduction of GABRA5 density in the CA3. Finally, assessment of fast-spiking, parvalbumin-positive (PV) GABAergic interneurons revealed a significant increase in the density of PV+ cells in the DG of male XRCC1 KO mice, while females remained unchanged. Conclusions Our results suggest that accumulation of unrepaired DNA damage in the forebrain alters the GABAergic neurotransmitter system and causes behavioural deficits in relation to innate and learned anxiety in a sex-dependent manner. Moreover, the data uncover a previously unappreciated connection between BER deficiency, unrepaired DNA damage in the hippocampus and a sex-specific anxiety-like phenotype with implications for the aetiology and therapy of neuropsychiatric disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01377-1.
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Affiliation(s)
- Flavia S Mueller
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - René Amport
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - Tina Notter
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, Faculty of Science, University of Zurich, 8057, Zurich, Switzerland
| | - Sina M Schalbetter
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - Han-Yu Lin
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - Zuzana Garajova
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - Parisa Amini
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - Ulrike Weber-Stadlbauer
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland. .,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.
| | - Enni Markkanen
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland.
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28
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Hsu CW, Conrad JW, Sowers ML, Baljinnyam T, Herring JL, Hackfeld LC, Hatch SS, Sowers LC. A combinatorial system to examine the enzymatic repair of multiply damaged DNA substrates. Nucleic Acids Res 2022; 50:7406-7419. [PMID: 35776119 PMCID: PMC9303388 DOI: 10.1093/nar/gkac530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/18/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
DNA damage drives genetic mutations that underlie the development of cancer in humans. Multiple pathways have been described in mammalian cells which can repair this damage. However, most work to date has focused upon single lesions in DNA. We present here a combinatorial system which allows assembly of duplexes containing single or multiple types of damage by ligating together six oligonucleotides containing damaged or modified bases. The combinatorial system has dual fluorescent labels allowing examination of both strands simultaneously, in order to study interactions or competition between different DNA repair pathways. Using this system, we demonstrate how repair of oxidative damage in one DNA strand can convert a mispaired T:G deamination intermediate into a T:A mutation. We also demonstrate that slow repair of a T:G mispair, relative to a U:G mispair, by the human methyl-binding domain 4 DNA glycosylase provides a competitive advantage to competing repair pathways, and could explain why CpG dinucleotides are hotspots for C to T mutations in human tumors. Data is also presented that suggests repair of closely spaced lesions in opposing strands can be repaired by a combination of short and long-patch base excision repair and simultaneous repair of multiply damage sites can potentially lead to lethal double strand breaks.
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Affiliation(s)
- Chia Wei Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,MD-PhD Combined Degree Program, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - James W Conrad
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Mark L Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,MD-PhD Combined Degree Program, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Jason L Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Linda C Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Sandra S Hatch
- Department of Radiation Oncology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lawrence C Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,Department of Internal Medicine, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
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29
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Patra A, Nag A, Chakraborty A, Bhattacharyya N. PA1 cells containing a truncated DNA polymerase β protein are more sensitive to gamma radiation. Radiat Oncol J 2022; 40:66-78. [PMID: 35368202 PMCID: PMC8984132 DOI: 10.3857/roj.2021.00689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/05/2022] [Indexed: 11/03/2022] Open
Abstract
Purpose: DNA polymerase β (Polβ) acts in the base excision repair (BER) pathway. Mutations in DNA polymerase β (Polβ) are associated with different cancers. A variant of Polβ with a 97 amino acid deletion (PolβΔ), in heterozygous conditions with wild-type Polβ, was identified in sporadic ovarian tumor samples. This study aims to evaluate the gamma radiation sensitivity of PolβΔ for possible target therapy in ovarian cancer treatment.Materials and Methods: PolβΔ cDNA was cloned in a GFP vector and transfected in PA1 cells. Stable cells (PA1PolβΔ) were treated with 60Co sourced gamma-ray (0–15 Gy) to investigate their radiation sensitivity. The affinity of PolβΔ with DNA evaluated by DNA protein in silico docking experiments.Result: The result showed a statistically significant (p < 0.05) higher sensitivity towards radiation at different doses (0–15 Gy) and time-point (48–72 hours) for PA1PolβΔ cells in comparison with normal PA1 cells. Ten Gy of gamma radiation was found to be the optimal dose. Significantly more PA1PolβΔ cells were killed at this dose than PA1 cells after 48 hours of treatment via an apoptotic pathway. The in silico docking experiments revealed that PolβΔ has more substantial binding potential towards the dsDNA than wild-type Polβ, suggesting a possible failure of BER pathway that results in cell death.Conclusion: Our study showed that the PA1PolβΔ cells were more susceptible than PA1 cells to gamma radiation. In the future, the potentiality of ionizing radiation to treat this type of cancer will be checked in animal models.
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Affiliation(s)
- Anutosh Patra
- Department of Biotechnology, Panskura Banamali College, West Bengal, India
| | - Anish Nag
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore, India
| | | | - Nandan Bhattacharyya
- Department of Biotechnology, Panskura Banamali College, West Bengal, India
- Correspondence: Nandan Bhattacharyya Department of Biotechnology, Panskura Banamali College, Panskura R.S., Purba Medinipur, West Bengal 721152, India. Tel: +91 9434453188 E-mail:
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30
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Chen LN, Jing T, Lin ZB, Song W, Du WH, Fan XY, Li C, Li S, Xie FY, Ou XH, Huang L, Ma JY. Metabolomic and transcriptomic responses of mouse testis to the dextran sulfate sodium induced colitis. Reprod Toxicol 2022; 108:35-42. [PMID: 35093514 DOI: 10.1016/j.reprotox.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/11/2022] [Accepted: 01/22/2022] [Indexed: 11/23/2022]
Abstract
Inflammatory bowel diseases (IBDs), including Crohn's disease (CD) and ulcerative colitis, are widespread in developed countries and gradually increasing in developing countries. Evidences showed that man with CD has a decrease of serum testosterone, but how IBD take effects on testicular testosterone synthesis is not well elucidated. To investigate the effects of IBD on testis, we analyzed testicular metabolome and transcriptome data of the dextran sulfate sodium (DSS) induced IBD mice. As a result, metabolomic data showed that DSS indeed induced androgen decrease in mouse testis. Correspondingly, androgen synthesis associated genes, especially Lhcgr, were down-regulated in DSS testis. From the metabolomic data, we found vitamin intake associated metabolites vitamin B2 and pyridoxamine were significantly decreased, whereas fatty acid metabolism associated molecules N-lauroylglycine and N-decanoylglycine were increased in DSS testis. In addition, we found 8-hydroxy-deoxyguanosine, a DNA oxidative damage marker, and 8-oxoguanine, a molecule responsible for DNA damage repair, were also changed in DSS testis. Simultaneously, our data also showed that DSS up-regulated the expression of meiosis initiation associated gene Stra8 and oxygen transport associated genes in testis. In summary, these results depicted the complex effects of colitis on testis. These metabolites and transcripts changed in DSS testis could be used as potential targets for IBD treatment or symptom relieve.
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Affiliation(s)
- Lei-Ning Chen
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Tao Jing
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Zi-Bin Lin
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Wei Song
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wen-Hao Du
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Xiao-Yan Fan
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Chao Li
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sen Li
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Feng-Yun Xie
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Xiang-Hong Ou
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510320, China
| | - Lin Huang
- Clinical Research Institute, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China.
| | - Jun-Yu Ma
- Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China.
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Circulating Tumor Cells in Breast Cancer Patients: A Balancing Act between Stemness, EMT Features and DNA Damage Responses. Cancers (Basel) 2022; 14:cancers14040997. [PMID: 35205744 PMCID: PMC8869884 DOI: 10.3390/cancers14040997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 02/04/2023] Open
Abstract
Circulating tumor cells (CTCs) traverse vessels to travel from the primary tumor to distant organs where they adhere, transmigrate, and seed metastases. To cope with these challenges, CTCs have reached maximal flexibility to change their differentiation status, morphology, migratory capacity, and their responses to genotoxic stress caused by metabolic changes, hormones, the inflammatory environment, or cytostatic treatment. A significant percentage of breast cancer cells are defective in homologous recombination repair and other mechanisms that protect the integrity of the replication fork. To prevent cell death caused by broken forks, alternative, mutagenic repair, and bypass pathways are engaged but these increase genomic instability. CTCs, arising from such breast tumors, are endowed with an even larger toolbox of escape mechanisms that can be switched on and off at different stages during their journey according to the stress stimulus. Accumulating evidence suggests that DNA damage responses, DNA repair, and replication are integral parts of a regulatory network orchestrating the plasticity of stemness features and transitions between epithelial and mesenchymal states in CTCs. This review summarizes the published information on these regulatory circuits of relevance for the design of biomarkers reflecting CTC functions in real-time to monitor therapeutic responses and detect evolving chemoresistance mechanisms.
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Jun YW, Albarran E, Wilson DL, Ding J, Kool ET. Fluorescence Imaging of Mitochondrial DNA Base Excision Repair Reveals Dynamics of Oxidative Stress Responses. Angew Chem Int Ed Engl 2022; 61:e202111829. [PMID: 34851014 PMCID: PMC8792287 DOI: 10.1002/anie.202111829] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/04/2021] [Indexed: 02/03/2023]
Abstract
Mitochondrial function in cells declines with aging and with neurodegeneration, due in large part to accumulated mutations in mitochondrial DNA (mtDNA) that arise from deficient DNA repair. However, measuring this repair activity is challenging. We employ a molecular approach for visualizing mitochondrial base excision repair (BER) activity in situ by use of a fluorescent probe (UBER) that reacts rapidly with AP sites resulting from BER activity. Administering the probe to cultured cells revealed signals that were localized to mitochondria, enabling selective observation of mtDNA BER intermediates. The probe showed elevated DNA repair activity under oxidative stress, and responded to suppression of glycosylase activity. Furthermore, the probe illuminated the time lag between the initiation of oxidative stress and the initial step of BER. Absence of MTH1 in cells resulted in elevated demand for BER activity upon extended oxidative stress, while the absence of OGG1 activity limited glycosylation capacity.
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Affiliation(s)
- Yong Woong Jun
- Department of Chemistry, ChEM-H Institute, and Stanford Cancer Institute, Stanford University, Stanford, California, 94305, United States
| | - Eddy Albarran
- Department of Neurosurgery, Department of Neurology and Neurological Sciences, and Wu Tsai Neuroscience institute, Stanford University School of Medicine, Stanford, California, 94305, United States
| | - David L. Wilson
- Department of Chemistry, ChEM-H Institute, and Stanford Cancer Institute, Stanford University, Stanford, California, 94305, United States
| | - Jun Ding
- Department of Neurosurgery, Department of Neurology and Neurological Sciences, and Wu Tsai Neuroscience institute, Stanford University School of Medicine, Stanford, California, 94305, United States
| | - Eric T. Kool
- Department of Chemistry, ChEM-H Institute, and Stanford Cancer Institute, Stanford University, Stanford, California, 94305, United States
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33
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Jun YW, Albarran E, Wilson DL, Ding J, Kool ET. Fluorescence Imaging of Mitochondrial DNA Base Excision Repair Reveals Dynamics of Oxidative Stress Responses. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yong Woong Jun
- Department of Chemistry, ChEM-H Institute, and Stanford Cancer Institute Stanford University Stanford CA 94305 USA
| | - Eddy Albarran
- Department of Neurosurgery Department of Neurology and Neurological Sciences, and Wu Tsai Neuroscience institute Stanford University School of Medicine Stanford CA 94305 USA
| | - David L. Wilson
- Department of Chemistry, ChEM-H Institute, and Stanford Cancer Institute Stanford University Stanford CA 94305 USA
| | - Jun Ding
- Department of Neurosurgery Department of Neurology and Neurological Sciences, and Wu Tsai Neuroscience institute Stanford University School of Medicine Stanford CA 94305 USA
| | - Eric T. Kool
- Department of Chemistry, ChEM-H Institute, and Stanford Cancer Institute Stanford University Stanford CA 94305 USA
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34
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Nonmalignant Features Associated with Inherited Colorectal Cancer Syndromes-Clues for Diagnosis. Cancers (Basel) 2022; 14:cancers14030628. [PMID: 35158896 PMCID: PMC8833640 DOI: 10.3390/cancers14030628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Familiarity with nonmalignant features and comorbidities of cancer predisposition syndromes may raise awareness and assist clinicians in the diagnosis and interpretation of molecular test results. Genetic predisposition to colorectal cancer (CRC) should be suspected mainly in young patients, in patients with significant family histories, multiple polyps, mismatch repair-deficient tumors, and in association with malignant or nonmalignant comorbidities. The aim of this review is to describe the main nonmalignant comorbidities associated with selected CRC predisposition syndromes that may serve as valuable diagnostic clues for clinicians and genetic professionals. Abstract Genetic diagnosis of affected individuals and predictive testing of their at-risk relatives, combined with intensive cancer surveillance, has an enormous cancer-preventive potential in these families. A lack of awareness may be part of the reason why the underlying germline cause remains unexplained in a large proportion of patients with CRC. Various extracolonic features, mainly dermatologic, ophthalmic, dental, endocrine, vascular, and reproductive manifestations occur in many of the cancer predisposition syndromes associated with CRC and polyposis. Some are mediated via the WNT, TGF-β, or mTOR pathways. However the pathogenesis of most features is still obscure. Here we review the extracolonic features of the main syndromes, the existing information regarding their prevalence, and the pathways involved in their pathogenesis. This knowledge could be useful for care managers from different professional disciplines, and used to raise awareness, enable diagnosis, and assist in the process of genetic testing and interpretation.
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Aerssens D, Cadoni E, Tack L, Madder A. A Photosensitized Singlet Oxygen ( 1O 2) Toolbox for Bio-Organic Applications: Tailoring 1O 2 Generation for DNA and Protein Labelling, Targeting and Biosensing. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030778. [PMID: 35164045 PMCID: PMC8838016 DOI: 10.3390/molecules27030778] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/17/2022]
Abstract
Singlet oxygen (1O2) is the excited state of ground, triplet state, molecular oxygen (O2). Photosensitized 1O2 has been extensively studied as one of the reactive oxygen species (ROS), responsible for damage of cellular components (protein, DNA, lipids). On the other hand, its generation has been exploited in organic synthesis, as well as in photodynamic therapy for the treatment of various forms of cancer. The aim of this review is to highlight the versatility of 1O2, discussing the main bioorganic applications reported over the past decades, which rely on its production. After a brief introduction on the photosensitized production of 1O2, we will describe the main aspects involving the biologically relevant damage that can accompany an uncontrolled, aspecific generation of this ROS. We then discuss in more detail a series of biological applications featuring 1O2 generation, including protein and DNA labelling, cross-linking and biosensing. Finally, we will highlight the methodologies available to tailor 1O2 generation, in order to accomplish the proposed bioorganic transformations while avoiding, at the same time, collateral damage related to an untamed production of this reactive species.
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36
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The potential role of COVID-19 in the induction of DNA damage. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108411. [PMID: 35690420 PMCID: PMC8767986 DOI: 10.1016/j.mrrev.2022.108411] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/30/2021] [Accepted: 01/17/2022] [Indexed: 01/07/2023]
Abstract
The coronavirus disease-2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is challenging global health and economic systems. In some individuals, COVID-19 can cause a wide array of symptoms, affecting several organs, such as the lungs, heart, bowels, kidneys and brain, causing multiorgan failure, sepsis and death. These effects are related in part to direct viral infection of these organs, immunological deregulation, a hypercoagulatory state and the potential for development of cytokine storm syndrome. Since the appearance of COVID-19 is recent, the long-term effects on the health of recovered patients remain unknown. In this review, we focused on current evidence of the mechanisms of DNA damage mediated by coronaviruses. Data supports that these viruses can induce DNA damage, genomic instability, and cell cycle deregulation during their replication in mammalian cells. Since the induction of DNA damage and aberrant DNA repair mechanisms are related to the development of chronic diseases such as cancer, diabetes, neurodegenerative disorders, and atherosclerosis, it will be important to address similar effects and outcomes in recovered COVID-19 patients.
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37
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Clementi E, Garajova Z, Markkanen E. Measurement of DNA Damage Using the Neutral Comet Assay in Cultured Cells. Bio Protoc 2021; 11:e4226. [PMID: 34909447 DOI: 10.21769/bioprotoc.4226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 11/02/2022] Open
Abstract
Maintenance of DNA integrity is of pivotal importance for cells to circumvent detrimental processes that can ultimately lead to the development of various diseases. In the face of a plethora of endogenous and exogenous DNA damaging agents, cells have evolved a variety of DNA repair mechanisms that are responsible for safeguarding genetic integrity. Given the relevance of DNA damage and its repair for disease pathogenesis, measuring them is of considerable interest, and the comet assay is a widely used method for this. Cells treated with DNA damaging agents are embedded into a thin layer of agarose on top of a microscope slide. Subsequent lysis removes all protein and lipid components to leave 'nucleoids' consisting of naked DNA remaining in the agarose. These nucleoids are then subjected to electrophoresis, whereby the negatively charged DNA migrates towards the anode depending on its degree of fragmentation, creating shapes resembling comets, which can be visualized and analysed by fluorescence microscopy. The comet assay can be adapted to assess a wide variety of genotoxins and repair kinetics, and both DNA single-strand and double-strand breaks. In this protocol, we describe in detail how to perform the neutral comet assay to assess double-strand breaks and their repair using cultured human cell lines. We describe the workflow for assessing the amount of DNA damage generated by ionizing radiation or present endogenously in the cells, and how to assess the repair kinetics after such an insult. The procedure described herein is easy to follow and cost-effective.
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Affiliation(s)
- Elena Clementi
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Zuzana Garajova
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Enni Markkanen
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
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38
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Nguyen L, Jager M, Lieshout R, de Ruiter PE, Locati MD, Besselink N, van der Roest B, Janssen R, Boymans S, de Jonge J, IJzermans JNM, Doukas M, Verstegen MMA, van Boxtel R, van der Laan LJW, Cuppen E, Kuijk E. Precancerous liver diseases do not cause increased mutagenesis in liver stem cells. Commun Biol 2021; 4:1301. [PMID: 34795391 PMCID: PMC8602268 DOI: 10.1038/s42003-021-02839-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/30/2021] [Indexed: 12/18/2022] Open
Abstract
Inflammatory liver disease increases the risk of developing primary liver cancer. The mechanism through which liver disease induces tumorigenesis remains unclear, but is thought to occur via increased mutagenesis. Here, we performed whole-genome sequencing on clonally expanded single liver stem cells cultured as intrahepatic cholangiocyte organoids (ICOs) from patients with alcoholic cirrhosis, non-alcoholic steatohepatitis (NASH), and primary sclerosing cholangitis (PSC). Surprisingly, we find that these precancerous liver disease conditions do not result in a detectable increased accumulation of mutations, nor altered mutation types in individual liver stem cells. This finding contrasts with the mutational load and typical mutational signatures reported for liver tumors, and argues against the hypothesis that liver disease drives tumorigenesis via a direct mechanism of induced mutagenesis. Disease conditions in the liver may thus act through indirect mechanisms to drive the transition from healthy to cancerous cells, such as changes to the microenvironment that favor the outgrowth of precancerous cells.
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Affiliation(s)
- Luan Nguyen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Myrthe Jager
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Mauro D Locati
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bastiaan van der Roest
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | | | | | | | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
- Hartwig Medical Foundation, Amsterdam, The Netherlands.
| | - Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
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39
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Tuieng RJ, Cartmell SH, Kirwan CC, Sherratt MJ. The Effects of Ionising and Non-Ionising Electromagnetic Radiation on Extracellular Matrix Proteins. Cells 2021; 10:3041. [PMID: 34831262 PMCID: PMC8616186 DOI: 10.3390/cells10113041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/28/2021] [Accepted: 10/30/2021] [Indexed: 02/07/2023] Open
Abstract
Exposure to sub-lethal doses of ionising and non-ionising electromagnetic radiation can impact human health and well-being as a consequence of, for example, the side effects of radiotherapy (therapeutic X-ray exposure) and accelerated skin ageing (chronic exposure to ultraviolet radiation: UVR). Whilst attention has focused primarily on the interaction of electromagnetic radiation with cells and cellular components, radiation-induced damage to long-lived extracellular matrix (ECM) proteins has the potential to profoundly affect tissue structure, composition and function. This review focuses on the current understanding of the biological effects of ionising and non-ionising radiation on the ECM of breast stroma and skin dermis, respectively. Although there is some experimental evidence for radiation-induced damage to ECM proteins, compared with the well-characterised impact of radiation exposure on cell biology, the structural, functional, and ultimately clinical consequences of ECM irradiation remain poorly defined.
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Affiliation(s)
- Ren Jie Tuieng
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK;
| | - Sarah H. Cartmell
- Department of Materials, School of Natural Sciences, Faculty of Science and Engineering and The Henry Royce Institute, Royce Hub Building, University of Manchester, Manchester M13 9PL, UK;
| | - Cliona C. Kirwan
- Division of Cancer Sciences and Manchester Breast Centre, Oglesby Cancer Research Building, Manchester Cancer Research Centre, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M20 4BX, UK;
| | - Michael J. Sherratt
- Division of Cell Matrix Biology & Regenerative Medicine and Manchester Breast Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
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40
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Jiang T, Monari A, Dumont E, Bignon E. Molecular Mechanisms Associated with Clustered Lesion-Induced Impairment of 8-oxoG Recognition by the Human Glycosylase OGG1. Molecules 2021; 26:molecules26216465. [PMID: 34770874 PMCID: PMC8587150 DOI: 10.3390/molecules26216465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022] Open
Abstract
The 8-oxo-7,8-dihydroguanine, referred to as 8-oxoG, is a highly mutagenic DNA lesion that can provoke the appearance of mismatches if it escapes the DNA Damage Response. The specific recognition of its structural signature by the hOGG1 glycosylase is the first step along the Base Excision Repair pathway, which ensures the integrity of the genome by preventing the emergence of mutations. 8-oxoG formation, structural features, and repair have been matters of extensive research; more recently, this active field of research expended to the more complicated case of 8-oxoG within clustered lesions. Indeed, the presence of a second lesion within 1 or 2 helix turns can dramatically impact the repair yields of 8-oxoG by glycosylases. In this work, we use μs-range molecular dynamics simulations and machine-learning-based postanalysis to explore the molecular mechanisms associated with the recognition of 8-oxoG by hOGG1 when embedded in a multiple-lesion site with a mismatch in 5′ or 3′. We delineate the stiffening of the DNA–protein interactions upon the presence of the mismatches, and rationalize the much lower repair yields reported with a 5′ mismatch by describing the perturbation of 8-oxoG structural features upon addition of an adjacent lesion.
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Affiliation(s)
- Tao Jiang
- Laboratoire de Chimie—UMR CNRS 5182, ENS de Lyon, Université de Lyon, 46 Allée d’Italie, F-69000 Lyon, France; (T.J.); (E.D.)
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques—UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, Boulevard des Aiguillettes, F-54506 Vandoeuvre-les-Nancy, France;
- Université de Paris and CNRS, ITODYS, F-75006 Paris, France
| | - Elise Dumont
- Laboratoire de Chimie—UMR CNRS 5182, ENS de Lyon, Université de Lyon, 46 Allée d’Italie, F-69000 Lyon, France; (T.J.); (E.D.)
- Institut Universitaire de France, 5 rue Descartes, F-75005 Paris, France
| | - Emmanuelle Bignon
- Laboratoire de Physique et Chimie Théoriques—UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, Boulevard des Aiguillettes, F-54506 Vandoeuvre-les-Nancy, France;
- Correspondence:
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41
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Insights into the Role of Oxidative Stress in Ovarian Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:8388258. [PMID: 34659640 PMCID: PMC8516553 DOI: 10.1155/2021/8388258] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/07/2021] [Indexed: 12/24/2022]
Abstract
Oxidative stress (OS) arises when the body is subjected to harmful endogenous or exogenous factors that overwhelm the antioxidant system. There is increasing evidence that OS is involved in a number of diseases, including ovarian cancer (OC). OC is the most lethal gynecological malignancy, and risk factors include genetic factors, age, infertility, nulliparity, microbial infections, obesity, smoking, etc. OS can promote the proliferation, metastasis, and therapy resistance of OC, while high levels of OS have cytotoxic effects and induce apoptosis in OC cells. This review focuses on the relationship between OS and the development of OC from four aspects: genetic alterations, signaling pathways, transcription factors, and the tumor microenvironment. Furthermore, strategies to target aberrant OS in OC are summarized and discussed, with a view to providing new ideas for clinical treatment.
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42
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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43
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Clementi E, Garajova Z, Markkanen E. Measuring DNA Damage Using the Alkaline Comet Assay in Cultured Cells. Bio Protoc 2021; 11:e4119. [PMID: 34541038 DOI: 10.21769/bioprotoc.4119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 01/28/2023] Open
Abstract
Maintenance of DNA integrity is of pivotal importance for cells to circumvent detrimental processes that can ultimately lead to the development of various diseases. In the face of a plethora of endogenous and exogenous DNA-damaging agents, cells have evolved a variety of DNA repair mechanisms that are responsible for safeguarding genetic integrity. Given the relevance of DNA damage and its repair in disease, measuring the amount of both aspects is of considerable interest. The comet assay is a widely used method that allows the measurement of both DNA damage and its repair in cells. For this, cells are treated with DNA-damaging agents and embedded into a thin layer of agarose on top of a microscope slide. Subsequent lysis removes all protein and lipid components to leave so-called 'nucleoids' consisting of naked DNA remaining in the agarose. These nucleoids are then subjected to electrophoresis, whereby the negatively charged DNA migrates toward the anode depending on its degree of fragmentation and creates shapes resembling comets, which can be subsequently visualized and analyzed by fluorescence microscopy. The comet assay can be adapted to assess a wide variety of genotoxins and repair kinetics, in addition to both DNA single-strand and double-strand breaks. In this protocol, we describe in detail how to perform the alkaline comet assay to assess single-strand breaks and their repair using cultured human cell lines. We describe the workflow for assessing the amount of DNA damage generated by agents such as hydrogen peroxide (H2O2) and methyl-methanesulfonate (MMS) or present endogenously in cells, and how to assess the repair kinetics after such an insult. The procedure described herein is easy to follow and allows the cost-effective assessment of single-strand breaks and their repair kinetics in cultured cells.
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Affiliation(s)
- Elena Clementi
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Zuzana Garajova
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Enni Markkanen
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
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44
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Saad AM, Abdel-Megied AES, Elbaz RA, Hassab El-Nabi SE, Elshazli RM. Genetic variants of APEX1 p.Asp148Glu and XRCC1 p.Gln399Arg with the susceptibility of hepatocellular carcinoma. J Med Virol 2021; 93:6278-6291. [PMID: 34289138 DOI: 10.1002/jmv.27217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 07/17/2021] [Indexed: 12/30/2022]
Abstract
The DNA repair genes have a crucial function in the base excision repair (BER) mechanism among different cancerous disorders, particularly hepatocellular carcinoma (HCC). The foremost objective of this study is to explore the association of genetic variants of the APEX1 p.Asp148Glu and the XRCC1 p.Gln399Arg with the susceptibility of HCC and to identify the computational bioinformatics frameworks of these missense variants. A total of 250 participants were enrolled in this study, including 150 HCC patients and 100 cancer-free controls. The genomic DNA was characterized and genotyped by applying the PCR-CTPP method. The frequency of the APEX1 (rs1130409*Glu) allele was statistically significant with increased risk of HCC (OR = 1.66, 95% CI = 1.12-2.45), while the XRCC1 (rs25487*Gln) allele conferred a protection against the progression of HCC (OR = 0.64, 95% CI = 0.42-0.96). Furthermore, HCC patients carrying the APEX1 p.Asp148Glu and the XRCC1 p.Gln399Arg variants indicated no significant difference with the clinical, and laboratory parameters (p > .05). Our findings confirmed that the APEX1 p.Asp148Glu variant was associated with increased risk of HCC, while the XRCC1 p.Gln399Arg variant revealed protection against the development of HCC.
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Affiliation(s)
- Ahmad M Saad
- Biochemistry Section, Department of Chemistry, Faculty of Science, Menoufia University, Menoufia, Egypt
| | | | - Rizk A Elbaz
- Genetic Unit, Children Hospital, Mansoura University, Mansoura, Egypt
| | | | - Rami M Elshazli
- Biochemistry and Molecular Genetics Unit, Department of Basic Sciences, Faculty of Physical Therapy, Horus University-Egypt, New Damietta, Egypt
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Demirbağ-Sarikaya S, Çakir H, Gözüaçik D, Akkoç Y. Crosstalk between autophagy and DNA repair systems. ACTA ACUST UNITED AC 2021; 45:235-252. [PMID: 34377049 PMCID: PMC8313936 DOI: 10.3906/biy-2103-51] [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: 03/19/2021] [Accepted: 06/09/2021] [Indexed: 12/15/2022]
Abstract
Autophagy and DNA repair are two essential biological mechanisms that maintain cellular homeostasis. Impairment of these mechanisms was associated with several pathologies such as premature aging, neurodegenerative diseases, and cancer. Intrinsic or extrinsic stress stimuli (e.g., reactive oxygen species or ionizing radiation) cause DNA damage. As a biological stress response, autophagy is activated following insults that threaten DNA integrity. Hence, in collaboration with DNA damage repair and response mechanisms, autophagy contributes to the maintenance of genomic stability and integrity. Yet, connections and interactions between these two systems are not fully understood. In this review article, current status of the associations and crosstalk between autophagy and DNA repair systems is documented and discussed.
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Affiliation(s)
| | - Hatice Çakir
- SUNUM Nanotechnology Research and Application Center, İstanbul Turkey
| | - Devrim Gözüaçik
- SUNUM Nanotechnology Research and Application Center, İstanbul Turkey.,Koç University School of Medicine, İstanbul Turkey.,Koç University Research Center for Translational Medicine (KUTTAM), İstanbul Turkey
| | - Yunus Akkoç
- Koç University Research Center for Translational Medicine (KUTTAM), İstanbul Turkey
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46
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DNA glycosylases for 8-oxoguanine repair in Staphylococcus aureus. DNA Repair (Amst) 2021; 105:103160. [PMID: 34192601 DOI: 10.1016/j.dnarep.2021.103160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/20/2022]
Abstract
GO system is part of base excision DNA repair and is required for the correct repair of 8-oxoguanine (8-oxoG), one of the most abundant oxidative lesions. Due to the ability of 8-oxoG to mispair with A, this base is highly mutagenic, and its repair requires two enzymes: Fpg that removes 8-oxoG from 8-oxoG:C pairs, and MutY that excises the normal A from 8-oxoG:A mispairs. Here we characterize the properties of putative GO system DNA glycosylases from Staphylococcus aureus, an important human opportunistic pathogen that causes hospital infections and presents a serious health concern due to quick spread of antibiotic-resistant strains. In addition to Fpg and MutY from the reference NCTC 8325 strain (SauFpg1 and SauMutY), we have also studied an Fpg homolog from a multidrug-resistant C0673 isolate (SauFpg2), which is different from SauFpg1 in its sequence. Both SauFpg enzymes showed the highest activity at pH 7.0-9.0 and NaCl concentrations 25-75 mM (SauFpg1) or 50-100 mM (SauFpg2), whereas SauMutY was active at a broad pH range and had a salt optimum at ∼75 mM NaCl. Both SauFpg1 and SauFpg2 bound and cleaved duplexes containing 8-oxoG, 5-hydroxyuracil, 5,6-dihydrouracil or apurinic/apyrimidinic site paired with C, T, or G, but not with A. For SauFpg1 and SauFpg2, 8-oxoG was the best substrate tested, and 5,6-dihydrouracil was the worst one. SauMutY efficiently excised adenine from duplex substrates containing A:8-oxoG or A:G pairs. SauFpg enzymes were readily trapped on DNA by NaBH4 treatment, indicating formation of a Schiff base reaction intermediate. Surprisingly, SauMutY was also trapped significantly better than its E. coli homolog. All three S. aureus GO glycosylases drastically reduced spontaneous mutagenesis when expressed in an fpg mutY E. coli double mutant. Overall, we conclude that S. aureus possesses an active GO system, which could possibly be targeted for sensitization of this pathogen to oxidative stress.
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Staphylococcus aureus isolates from hospital clinics induce ROS-mediated DNA damage, apoptosis and gene expression alterations in male mice. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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49
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Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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Staphylococcus aureus Internalization in Osteoblast Cells: Mechanisms, Interactions and Biochemical Processes. What Did We Learn from Experimental Models? Pathogens 2021; 10:pathogens10020239. [PMID: 33669789 PMCID: PMC7922271 DOI: 10.3390/pathogens10020239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
Bacterial internalization is a strategy that non-intracellular microorganisms use to escape the host immune system and survive inside the human body. Among bacterial species, Staphylococcus aureus showed the ability to interact with and infect osteoblasts, causing osteomyelitis as well as bone and joint infection, while also becoming increasingly resistant to antibiotic therapy and a reservoir of bacteria that can make the infection difficult to cure. Despite being a serious issue in orthopedic surgery, little is known about the mechanisms that allow bacteria to enter and survive inside the osteoblasts, due to the lack of consistent experimental models. In this review, we describe the current knowledge about S. aureus internalization mechanisms and various aspects of the interaction between bacteria and osteoblasts (e.g., best experimental conditions, bacteria-induced damages and immune system response), focusing on studies performed using the MG-63 osteoblastic cell line, the best traditional (2D) model for the study of this phenomenon to date. At the same time, as it has been widely demonstrated that 2D culture systems are not completely indicative of the dynamic environment in vivo, and more recent 3D models—representative of bone infection—have also been investigated.
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