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Dong Y, Huang X, Zhang W, Shao Y, Cloutier P, Zheng Y, Sanche L. Hyperthermal Reactions in DNA Triggered by 1-20 eV Electrons: Absolute Cross Sections for Crosslinks, Strand Breaks, Clustered Damages and Base Modifications. Int J Mol Sci 2025; 26:4057. [PMID: 40362296 PMCID: PMC12072190 DOI: 10.3390/ijms26094057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2025] [Revised: 04/11/2025] [Accepted: 04/17/2025] [Indexed: 05/15/2025] Open
Abstract
Absolute cross sections (ACSs) are needed to estimate cellular damage induced by high-energy radiation (HER). Low-energy electrons (LEEs), which are the most numerous secondary particles generated by HER, can trigger hyperthermal reactions in DNA. ACSs for such reactions are essential input parameters to calculate radiobiological effectiveness, particularly in targeted radiotherapy. Using a mathematical model, we generate ACSs from effective damage yields induced by LEE impact on 3197 base-pair plasmid DNA films. Direct or enzyme-revealed conformational damages, quantified by electrophoresis, provide the first complete set of ACSs for inducing crosslinks, double-strand breaks (DSBs), single-strand breaks, base-damage-related crosslinks, non-DSB clustered damages (NDCDs), and isolated base damages. These ACSs are generated across the 1-20 eV range, at one eV intervals. They exhibit a strong energy dependence with maximum values at 10 eV of 3.7 ± 0.8, 3.5 ± 0.6, 45.4 ± 4.1, 2.9 ± 1.1, 5.1 ± 1.4, and 54.0 ± 16.4 × 10-15 cm2, respectively. ACSs for DSBs, NDCDs, and crosslinks clearly indicate that lesions threatening cell function and genetic stability can be generated by a single LEE. At 5 and 10 eV, total damage ACSs are 63% and 80% larger, respectively, than those previously determined for the same plasmids bound to arginine, a constituent of histones protecting DNA.
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Affiliation(s)
- Yanfang Dong
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang 471000, China; (Y.D.); (W.Z.)
| | - Xin Huang
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry, Fuzhou University, Fuzhou 350116, China; (X.H.); (Y.S.); (Y.Z.)
| | - Wenlu Zhang
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang 471000, China; (Y.D.); (W.Z.)
| | - Yu Shao
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry, Fuzhou University, Fuzhou 350116, China; (X.H.); (Y.S.); (Y.Z.)
| | - Pierre Cloutier
- Department of Medical Imaging and Radiation Sciences, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry, Fuzhou University, Fuzhou 350116, China; (X.H.); (Y.S.); (Y.Z.)
- Department of Medical Imaging and Radiation Sciences, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
| | - Léon Sanche
- Department of Medical Imaging and Radiation Sciences, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
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Chauhan R, Damerla RR, Dhyani VS. Synthetic lethality in cancer: a protocol for scoping review of gene interactions from synthetic lethal screens and functional studies. Syst Rev 2025; 14:81. [PMID: 40200332 PMCID: PMC11978169 DOI: 10.1186/s13643-025-02814-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 03/12/2025] [Indexed: 04/10/2025] Open
Abstract
BACKGROUND Two genes are synthetically lethal if loss of function of either one of the two genes does not result in cell death, whereas loss of function of both genes together results in being detrimental to cell survival. This concept has been the basis for developing personalized, precision treatments, which can selectively damage tumor cells and minimize toxicity to normal tissues. Tumor cells often harbor mutations in genes involved in DNA repair pathways, forcing them to switch to alternative repair pathways, leading to chemotherapeutic resistance. These interactions, if targeted, could be synthetically lethal. We aimed to summarize synthetically lethal gene pairs that could be utilized to selectively target cancer cells and minimize side effects on normal tissues. The objective of this review is to study druggable synthetically lethal gene pairs for targeted cancer therapy that have been identified through various genetic screens and functional studies. METHODS A systematic literature search will be conducted to extract synthetically lethal gene pairs that can be specifically targeted to cancer cells. Owing to the relatively recent research pertaining to this field, the literature search will incorporate data from 1956. The search will be conducted on PubMed, Web of Science, Embase, and Scopus. The narrative approach will guide the analysis and synthesis of the results. DISCUSSION This review highlights scientific articles that report druggable synthetically lethal gene pairs by testing the efficacy of targeted inhibitors in clonogenic assays. These include research studies that identify synthetically lethal gene pairs detected through CRISPR screens by knocking out one or two genes within the same cell and testing the potency of inhibitors to specifically kill malignant cells. SYSTEMATIC REVIEW REGISTRATION https://doi.org/10.17605/OSF.IO/5BCW6 .
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Affiliation(s)
- Raashi Chauhan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Rama Rao Damerla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India.
| | - Vijay Shree Dhyani
- Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
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Peña-Gómez MJ, Rodríguez-Martín Y, del Rio Oliva M, Wijesekara Hanthi Y, Berrada S, Freire R, Masson JY, Reyes JC, Costanzo V, Rosado IV. HMCES corrupts replication fork stability during base excision repair in homologous recombination-deficient cells. SCIENCE ADVANCES 2025; 11:eads3227. [PMID: 40138423 PMCID: PMC11939059 DOI: 10.1126/sciadv.ads3227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 02/21/2025] [Indexed: 03/29/2025]
Abstract
Apurinic/apyrimidinic (AP) sites and single-strand breaks arising from base excision repair (BER) during the misincorporation of damaged nucleobases may hinder replication fork stability in homologous recombination-deficient (HRD) cells. At templated AP sites, cross-links between the DNA and 5-hydroxymethylcytosine binding, embryonic stem cell-specific (HMCES) regulate replication fork speed, avoiding cytotoxic double-strand breaks. While the role of HMCES at the template DNA strand is well studied, its effects on nascent DNA are not. We provide evidence that HMCES-DNA-protein cross-links (DPCs) are detrimental to the BER-mediated removal of 5-hydroxymethyl-2'-deoxycytidine (5hmdC)-derived 5-hydroxymethyl-2'-deoxyuridine from replication forks. HRD cells have heightened HMCES-DPCs, which increase further upon 5hmdC exposure, suggesting that HMCES binds both spontaneous and 5hmdC-induced AP sites. HMCES depletion substantially suppresses 5hmdC-mediated replication fork defects, chromosomal aberrations, and cell death in HRD cells. This reveals that HMCES-DPCs are a source of BER-initiated single-stranded DNA gaps, which indicates that endogenous DPCs contribute to genomic instability in HRD tumors.
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Affiliation(s)
- María José Peña-Gómez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville 41092, Spain
- Departamento de Genética, Facultad de Biologia, Universidad de Sevilla, Seville 41012, Spain
| | - Yaiza Rodríguez-Martín
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville 41092, Spain
- Departamento de Genética, Facultad de Biologia, Universidad de Sevilla, Seville 41012, Spain
| | - Marta del Rio Oliva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville 41092, Spain
- Departamento de Genética, Facultad de Biologia, Universidad de Sevilla, Seville 41012, Spain
| | - Yodhara Wijesekara Hanthi
- IFOM, The AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Sara Berrada
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Investigación Sanitaria de Canarias (IISC), La Laguna, Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Centro de Investigaciones Biomédicas de Canarias, Facultad de Medicina, Campus Ciencias de la Salud, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Jean Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - José Carlos Reyes
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville 41092, Spain
| | - Vincenzo Costanzo
- IFOM, The AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Iván V. Rosado
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville 41092, Spain
- Departamento de Genética, Facultad de Biologia, Universidad de Sevilla, Seville 41012, Spain
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Wang Y, Zhang Y, Huang C, Fu Q, Huang T. Impact of Ultra-High-Dose-Rate Irradiation on DNA: Single-Strand Breaks and Base Damage. Int J Mol Sci 2025; 26:1800. [PMID: 40076429 PMCID: PMC11899290 DOI: 10.3390/ijms26051800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2025] [Revised: 02/13/2025] [Accepted: 02/18/2025] [Indexed: 03/14/2025] Open
Abstract
Studying different types of DNA damage induced by ultra-high-dose-rate (UHDR) irradiation is essential for understanding the mechanism underlying the FLASH effect. pBR322 plasmid DNA was irradiated using an electron FLASH beam. The content of each subtype of plasmid DNA was measured via gel electrophoresis, and the extent of DNA double-strand breaks (DSBs) and single-strand breaks (SSBs) under UHDR and conventional-dose-rate irradiation (CONV) was quantitatively compared. Furthermore, by adding the endonucleases Nth and Fpg, the extent of base damage in the UHDR and CONV group was quantitatively analyzed. In addition, the effects of different plasmid concentrations on the damage degree were studied. The induction rates of SSBs (×10-3 SSB/Gy/molecule) under UHDR and CONV were 21.7 ± 0.4 and 25.8 ± 0.3, respectively. When treated with the Fpg and Nth enzymes, the base damage induction rates (×10-3 SSB/Gy/molecule) under UHDR and CONV irradiation were 43.3 ± 2.0 and 58.4 ± 4.5, respectively. Additionally, UHDR irradiation consistently reduced SSBs and base damage at both high and low plasmid concentrations, although the absolute level of DNA damage was still influenced by the plasmid concentration. UHDR has a significant effect on reducing SSBs and base damage when compared to CONV across plasmid concentrations.
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Affiliation(s)
| | | | | | - Qibin Fu
- Sino-French Institute of Nuclear Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China; (Y.W.); (Y.Z.); (C.H.)
| | - Tuchen Huang
- Sino-French Institute of Nuclear Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China; (Y.W.); (Y.Z.); (C.H.)
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Pradhan S, Bush K, Zhang N, Pandita RK, Tsai CL, Smith C, Pandlebury DF, Gaikwad S, Leonard F, Nie L, Tao A, Russell W, Yuan S, Choudhary S, Ramos KS, Elferink C, Wairkar YP, Tainer JA, Thompson LM, Pandita TK, Sarkar PS. Chromatin remodeler BRG1 recruits huntingtin to repair DNA double-strand breaks in neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.19.613927. [PMID: 39345557 PMCID: PMC11429940 DOI: 10.1101/2024.09.19.613927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Persistent DNA double-strand breaks (DSBs) are enigmatically implicated in neurodegenerative diseases including Huntington's disease (HD), the inherited late-onset disorder caused by CAG repeat elongations in Huntingtin (HTT). Here we combine biochemistry, computation and molecular cell biology to unveil a mechanism whereby HTT coordinates a Transcription-Coupled Non-Homologous End-Joining (TC-NHEJ) complex. HTT joins TC-NHEJ proteins PNKP, Ku70/80, and XRCC4 with chromatin remodeler Brahma-related Gene 1 (BRG1) to resolve transcription-associated DSBs in brain. HTT recruitment to DSBs in transcriptionally active gene- rich regions is BRG1-dependent while efficient TC-NHEJ protein recruitment is HTT-dependent. Notably, mHTT compromises TC-NHEJ interactions and repair activity, promoting DSB accumulation in HD tissues. Importantly, HTT or PNKP overexpression restores TC-NHEJ in a Drosophila HD model dramatically improving genome integrity, motor defects, and lifespan. Collective results uncover HTT stimulation of DSB repair by organizing a TC-NHEJ complex that is impaired by mHTT thereby implicating dysregulation of transcription-coupled DSB repair in mHTT pathophysiology. Highlights BRG1 recruits HTT and NHEJ components to transcriptionally active DSBs.HTT joins BRG1 and PNKP to efficiently repair transcription related DSBs in brain.Mutant HTT impairs the functional integrity of TC-NHEJ complex for DSB repair.HTT expression improves DSB repair, genome integrity and phenotypes in HD flies.
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6
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Gutierrez R, Chan AYS, Lai SWT, Itoh S, Lee DH, Sun K, Battad A, Chen S, O'Connor TR, Shuck SC. Lack of mismatch repair enhances resistance to methylating agents for cells deficient in oxidative demethylation. J Biol Chem 2024; 300:107492. [PMID: 38925328 PMCID: PMC11326903 DOI: 10.1016/j.jbc.2024.107492] [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: 12/21/2023] [Revised: 05/21/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
The human alkylation B (AlkB) homologs, ALKBH2 and ALKBH3, respond to methylation damage to maintain genomic integrity and cellular viability. Both ALKBH2 and ALKBH3 are direct reversal repair enzymes that remove 1-methyladenine (1meA) and 3-methylcytosine (3meC) lesions commonly generated by alkylating chemotherapeutic agents. Thus, the existence of deficiencies in ALKBH proteins can be exploited in synergy with chemotherapy. In this study, we investigated possible interactions between ALKBH2 and ALKBH3 with other proteins that could alter damage response and discovered an interaction with the mismatch repair (MMR) system. To test whether the lack of active MMR impacts ALKBH2 and/or ALKBH3 response to methylating agents, we generated cells deficient in ALKBH2, ALKBH3, or both in addition to Mlh homolog 1 (MLH1), another MMR protein. We found that MLH1koALKBH3ko cells showed enhanced resistance toward SN1- and SN2-type methylating agents, whereas MLH1koALKBH2ko cells were only resistant to SN1-type methylating agents. Concomitant loss of ALKBH2 and ALKBH3 (ALKBH2ko3ko) rendered cells sensitive to SN1- and SN2-agents, but the additional loss of MLH1 enhanced resistance to both types of damage. We also showed that ALKBH2ko3ko cells have an ATR-dependent arrest at the G2/M checkpoint, increased apoptotic signaling, and replication fork stress in response to methylation. However, these responses were not observed with the loss of functional MLH1 in MLH1koALKBH2ko3ko cells. Finally, in MLH1koALKBH2ko3ko cells, we observed elevated mutant frequency in untreated and temozolomide treated cells. These results suggest that obtaining a more accurate prognosis of chemotherapeutic outcome requires information on the functionality of ALKBH2, ALKBH3, and MLH1.
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Affiliation(s)
- Roberto Gutierrez
- Department of Cancer Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Annie Yin S Chan
- Department of Cancer Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Seigmund Wai Tsuen Lai
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Shunsuke Itoh
- Department of Cancer Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Dong-Hyun Lee
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, South Korea
| | - Kelani Sun
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Alana Battad
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Shiuan Chen
- Department of Cancer Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Timothy R O'Connor
- Department of Cancer Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California, USA.
| | - Sarah C Shuck
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute at the City of Hope, Duarte, California, USA.
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Odstrcil RE, Dutta P, Liu J. Enhanced Sampling for Conformational Changes and Molecular Mechanisms of Human NTHL1. J Phys Chem Lett 2024; 15:3206-3213. [PMID: 38483510 PMCID: PMC11059236 DOI: 10.1021/acs.jpclett.4c00161] [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] [Indexed: 03/22/2024]
Abstract
The functionalities of proteins rely on protein conformational changes during many processes. Identification of the protein conformations and capturing transitions among different conformations are important but extremely challenging in both experiments and simulations. In this work, we develop a machine learning based approach to identify a reaction coordinate that accelerates the exploration of protein conformational changes in molecular simulations. We implement our approach to study the conformational changes of human NTHL1 during DNA repair. Our results identified three distinct conformations: open (stable), closed (unstable), and bundle (stable). The existence of the bundle conformation can rationalize recent experimental observations. Comparison with an NTHL1 mutant demonstrates that a closely packed cluster of positively charged residues in the linker could be a factor to search when screening for genetic abnormalities. Results will lead to a better modulation of the DNA repair pathway to protect against carcinogenesis.
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Affiliation(s)
- Ryan E. Odstrcil
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, USA
| | - Prashanta Dutta
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, USA
| | - Jin Liu
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, USA
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Ghorab RA, Fouad SH, Elsaadawy Y, Hamdy M, Taha SI. Association of XRCC1 p. Arg194Trp gene polymorphism with the risk of hepatocellular carcinoma in HCV Egyptian population: A pilot case-control study. Int J Immunopathol Pharmacol 2024; 38:3946320241265263. [PMID: 38898405 PMCID: PMC11189007 DOI: 10.1177/03946320241265263] [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: 02/16/2024] [Accepted: 06/08/2024] [Indexed: 06/21/2024] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is the most common and fatal primary liver cancer. Genetic variants of DNA repair systems can reduce DNA repair capability and increase HCC risk. Objectives: This study aimed to examine, in Egyptian hepatitis C virus (HCV) patients, the relationship between the X-ray repair cross-complementing group 1 (XRCC1) rs1799782 single nucleotide polymorphism (SNP) and HCC susceptibility. Methods: We included 100 adult HCV-positive patients with HCC and 100 adult HCV-positive patients with liver cirrhosis as pathological controls. XRCC1 rs1799782 SNP genotyping was done in both groups using quantitative real-time PCR (qPCR). The distribution of genotypes in patients and controls was compared using several inheritance models. Results: We found that the CT genotype, when analyzed under both the co-dominant (OR (95 % CI): 2.147 (1.184-3.893), p = .012) and the over-dominant (OR (95 % CI): 2.055 (1.153-3.660), p = .015) models, as well as the combined CT and TT genotypes under the dominant model (OR (95 % CI) of 1.991 (1.133-3.497), p = .017), were associated with increased susceptibility to HCC. The frequency of the T allele was higher among HCC participants (32%) compared to those with cirrhosis (23.5%) and carrying the T allele increased the risk of HCC by 1.532 times, however, these associations did not reach statistical significance (p-values >0.05). Moreover, the variant T allele was associated with worse clinical manifestations and laboratory results among the HCC group, but AFP levels were not affected significantly. Conclusions: Egyptians with XRCC1 rs1799782 SNP may have a higher risk of HCV-related HCC. More extensive multi-center prospective investigations must confirm this association.
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Affiliation(s)
- Rasha Ahmed Ghorab
- Department of Clinical Pathology, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
| | - Shaimaa H. Fouad
- Department of Internal Medicine /Allergy and Clinical Immunology, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
| | - Yara Elsaadawy
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
| | - Marwa Hamdy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Sara I. Taha
- Department of Clinical Pathology, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
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9
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Wu Y, Song T, Xu Q. R-LOOPs on Short Tandem Repeat Expansion Disorders in Neurodegenerative Diseases. Mol Neurobiol 2023; 60:7185-7195. [PMID: 37540313 DOI: 10.1007/s12035-023-03531-4] [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: 05/16/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023]
Abstract
Expansions of short tandem repeats (STRs) have been found to be present in more than 50 diseases and have a close connection with neurodegenerative diseases. Transcriptional silencing and R-LOOP formation, RNA-mediated sequestration of RNA-binding proteins (RBPs), gain-of-function (GOF) proteins containing expanded repeats, and repeat-associated non-AUG (RAN) translation of toxic repeat peptides are some potential molecular mechanisms underlying STR expansion disorders. R-LOOP, a byproduct of transcription, is a three-stranded nucleic acid structure with abnormal accumulation that participates in the pathogenesis of STR expansion disorders by inducing DNA damage and genome instability. R-LOOPs can engender a series of DNA damage, such as DNA double-strand breaks (DSBs), single-strand breaks (SSBs), DNA recombination, or mutations in the DNA replication, transcription, or repair processes. In this review, we provide an in-depth discussion of recent advancements in R-LOOP and systematically elaborate on its genetic destabilizing effects in several neurodegenerative diseases. These molecular mechanisms will provide novel targets for drug design and therapeutic upgrading of these devastating diseases.
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Affiliation(s)
- Yiting Wu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Tingwei Song
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.
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Tang H, Kulkarni S, Peters C, Eddison J, Al-Ani M, Madhusudan S. The Current Status of DNA-Repair-Directed Precision Oncology Strategies in Epithelial Ovarian Cancers. Int J Mol Sci 2023; 24:7293. [PMID: 37108451 PMCID: PMC10138422 DOI: 10.3390/ijms24087293] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Survival outcomes for patients with advanced ovarian cancer remain poor despite advances in chemotherapy and surgery. Platinum-based systemic chemotherapy can result in a response rate of up to 80%, but most patients will have recurrence and die from the disease. Recently, the DNA-repair-directed precision oncology strategy has generated hope for patients. The clinical use of poly(ADP-ribose) polymerase (PARP) inhibitors in BRCA germ-line-deficient and/or platinum-sensitive epithelial ovarian cancers has improved survival. However, the emergence of resistance is an ongoing clinical challenge. Here, we review the current clinical state of PARP inhibitors and other clinically viable targeted approaches in epithelial ovarian cancers.
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Affiliation(s)
- Hiu Tang
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK
| | - Sanat Kulkarni
- Department of Medicine, Sandwell and West Birmingham Hospitals, Lyndon, West Bromwich B71 4HJ, UK
| | - Christina Peters
- Department of Oncology, Sussex Cancer Centre, University Hospitals Sussex NHS Foundation Trust, Brighton BN2 5BD, UK
| | - Jasper Eddison
- College of Medical & Dental Sciences, University of Birmingham Medical School, Birmingham B15 2TT, UK
| | - Maryam Al-Ani
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK
| | - Srinivasan Madhusudan
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham NG7 3RD, UK
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Kladova OA, Tyugashev TE, Mikushina ES, Soloviev NO, Kuznetsov NA, Novopashina DS, Kuznetsova AA. Human Polβ Natural Polymorphic Variants G118V and R149I Affects Substate Binding and Catalysis. Int J Mol Sci 2023; 24:ijms24065892. [PMID: 36982964 PMCID: PMC10051265 DOI: 10.3390/ijms24065892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
DNA polymerase β (Polβ) expression is essential for the cell's response to DNA damage that occurs during natural cellular processes. Polβ is considered the main reparative DNA polymerase, whose role is to fill the DNA gaps arising in the base excision repair pathway. Mutations in Polβ can lead to cancer, neurodegenerative diseases, or premature aging. Many single-nucleotide polymorphisms have been identified in the POLB gene, but the consequences of these polymorphisms are not always clear. It is known that some polymorphic variants in the Polβ sequence reduce the efficiency of DNA repair, thereby raising the frequency of mutations in the genome. In the current work, we studied two polymorphic variants (G118V and R149I separately) of human Polβ that affect its DNA-binding region. It was found that each amino acid substitution alters Polβ's affinity for gapped DNA. Each polymorphic variant also weakens its binding affinity for dATP. The G118V variant was found to greatly affect Polβ's ability to fill gapped DNA and slowed the catalytic rate as compared to the wild-type enzyme. Thus, these polymorphic variants seem to decrease the ability of Polβ to maintain base excision repair efficiency.
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Affiliation(s)
- Olga A Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Timofey E Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena S Mikushina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Nikita O Soloviev
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Daria S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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12
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Sible E, Attaway M, Fiorica G, Michel G, Chaudhuri J, Vuong BQ. Ataxia Telangiectasia Mutated and MSH2 Control Blunt DNA End Joining in Ig Class Switch Recombination. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:369-376. [PMID: 36603026 PMCID: PMC9915862 DOI: 10.4049/jimmunol.2200590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023]
Abstract
Class-switch recombination (CSR) produces secondary Ig isotypes and requires activation-induced cytidine deaminase (AID)-dependent DNA deamination of intronic switch regions within the IgH (Igh) gene locus. Noncanonical repair of deaminated DNA by mismatch repair (MMR) or base excision repair (BER) creates DNA breaks that permit recombination between distal switch regions. Ataxia telangiectasia mutated (ATM)-dependent phosphorylation of AID at serine 38 (pS38-AID) promotes its interaction with apurinic/apyrimidinic endonuclease 1 (APE1), a BER protein, suggesting that ATM regulates CSR through BER. However, pS38-AID may also function in MMR during CSR, although the mechanism remains unknown. To examine whether ATM modulates BER- and/or MMR-dependent CSR, Atm-/- mice were bred to mice deficient for the MMR gene mutS homolog 2 (Msh2). Surprisingly, the predicted Mendelian frequencies of Atm-/-Msh2-/- adult mice were not obtained. To generate ATM and MSH2-deficient B cells, Atm was conditionally deleted on an Msh2-/- background using a floxed ATM allele (Atmf) and B cell-specific Cre recombinase expression (CD23-cre) to produce a deleted ATM allele (AtmD). As compared with AtmD/D and Msh2-/- mice and B cells, AtmD/DMsh2-/- mice and B cells display a reduced CSR phenotype. Interestingly, Sμ-Sγ1 junctions from AtmD/DMsh2-/- B cells that were induced to switch to IgG1 in vitro showed a significant loss of blunt end joins and an increase in insertions as compared with wild-type, AtmD/D, or Msh2-/- B cells. These data indicate that the absence of both ATM and MSH2 blocks nonhomologous end joining, leading to inefficient CSR. We propose a model whereby ATM and MSH2 function cooperatively to regulate end joining during CSR through pS38-AID.
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Affiliation(s)
- Emily Sible
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY
- Department of Biology, City College of New York, The City University of New York, New York, NY; and
| | - Mary Attaway
- Department of Biology, City College of New York, The City University of New York, New York, NY; and
| | - Giuseppe Fiorica
- Department of Biology, City College of New York, The City University of New York, New York, NY; and
| | - Genesis Michel
- Department of Biology, City College of New York, The City University of New York, New York, NY; and
| | | | - Bao Q. Vuong
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY
- Department of Biology, City College of New York, The City University of New York, New York, NY; and
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13
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Mao Z, Gray ALH, Thyagarajan B, Bostick RM. Antioxidant enzyme and DNA base repair genetic risk scores' associations with systemic oxidative stress biomarker in pooled cross-sectional studies. FRONTIERS IN AGING 2023; 4:1000166. [PMID: 37152862 PMCID: PMC10161255 DOI: 10.3389/fragi.2023.1000166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/28/2023] [Indexed: 05/09/2023]
Abstract
Background: Oxidative stress is hypothesized to contribute to the pathogenesis of several chronic diseases. Numerous dietary and lifestyle factors are associated with oxidative stress; however, little is known about associations of genetic factors, individually or jointly with dietary and lifestyle factors, with oxidative stress in humans. Methods: We genotyped 22 haplotype-tagging single nucleotide polymorphisms (SNPs) in 3 antioxidant enzyme (AE) genes and 79 SNPs in 14 DNA base excision repair (BER) genes to develop oxidative stress-specific AE and BER genetic risk scores (GRS) in two pooled cross-sectional studies (n = 245) of 30-74-year-old, White, cancer- and inflammatory bowel disease-free adults. Of the genotypes, based on their associations with a systemic oxidative stress biomarker, plasma F2-isoprostanes (FiP) concentrations, we selected 4 GSTP1 SNPs for an AE GRS, and 12 SNPs of 5 genes (XRCC1, TDG, PNKP, MUTYH, and FEN1) for a BER GRS. We also calculated a previously-reported, validated, questionnaire-based, oxidative stress biomarker-weighted oxidative balance score (OBS) comprising 17 anti- and pro-oxidant dietary and lifestyle exposures, with higher scores representing a higher predominance of antioxidant exposures. We used general linear regression to assess adjusted mean FiP concentrations across GRS and OBS tertiles, separately and jointly. Results: The adjusted mean FiP concentrations among those in the highest relative to the lowest oxidative stress-specific AE and BER GRS tertiles were, proportionately, 11.8% (p = 0.12) and 21.2% (p = 0.002) higher, respectively. In the joint AE/BER GRS analysis, the highest estimated mean FiP concentration was among those with jointly high AE/BER GRS. Mean FiP concentrations across OBS tertiles were similar across AE and BER GRS strata. Conclusion: Our pilot study findings suggest that DNA BER, and possibly AE, genotypes collectively may be associated with systemic oxidative stress in humans, and support further research in larger, general populations.
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Affiliation(s)
- Ziling Mao
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Abigail L. H. Gray
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States
| | - Roberd M. Bostick
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
- *Correspondence: Roberd M. Bostick,
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14
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Paudel L, Ghimire N, Han SR, Park H, Jung SH, Oh TJ. Complete genome of Nakamurella sp. PAMC28650: genomic insights into its environmental adaptation and biotechnological potential. Funct Integr Genomics 2022; 23:18. [PMID: 36564681 PMCID: PMC9789016 DOI: 10.1007/s10142-022-00937-6] [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: 08/03/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022]
Abstract
The mechanisms underlying the survival of bacteria in low temperature and high radiation are not yet fully understood. Nakamurella sp. PAMC28650 was isolated from a glacier of Rwenzori Mountain, Uganda, which species belonged to Nakamurella genus based on 16S rRNA phylogeny, ANI (average nucleotide identity), and BLAST Ring Image Generator (BRIG) analysis among Frankineae suborder. We conducted the whole genome sequencing and comparative genomics of Nakamurella sp. PAMC28650, to understand the genomic features pertaining to survival in cold environment, along with high UV (ultraviolet) radiation. This study highlights the role of polysaccharide in cold adaptation, mining of the UV protection-related secondary metabolites and other related to cold adaptation mechanism through different bioinformatics tools, and providing a brief overview of the genes present in DNA repair systems. Nakamurella sp. PAMC28650 contained glycogen and cellulose metabolism pathways, mycosporine-like amino acids and isorenieratene-synthesizing gene cluster, and a number of DNA repair systems. Also, the genome analysis showed osmoregulation-related genes and cold shock proteins. We infer these genomic features are linked to bacterial survival in cold and UV radiation.
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Affiliation(s)
- Lakshan Paudel
- Department of Life Science and Biochemical Engineering, Graduate School, Sun-Moon University, Asan, 31460, Korea
| | - Nisha Ghimire
- Department of Life Science and Biochemical Engineering, Graduate School, Sun-Moon University, Asan, 31460, Korea
| | - So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, Sun-Moon University, Asan, 31460, Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Sang-Hee Jung
- Department of Dental Hygiene, Gangneung Yeongdong University, Gangneung, 25521, Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, Sun-Moon University, Asan, 31460, Korea. .,Genome-Based Bio-IT Convergence Institute, Asan, 31460, Korea. .,Department of Pharmaceutical Engineering and Biotechnology, Sun-Moon University, Asan, 31460, Korea.
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15
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Evolving DNA repair synthetic lethality targets in cancer. Biosci Rep 2022; 42:232162. [PMID: 36420962 PMCID: PMC9760629 DOI: 10.1042/bsr20221713] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 11/25/2022] Open
Abstract
DNA damage signaling response and repair (DDR) is a critical defense mechanism against genomic instability. Impaired DNA repair capacity is an important risk factor for cancer development. On the other hand, up-regulation of DDR mechanisms is a feature of cancer chemotherapy and radiotherapy resistance. Advances in our understanding of DDR and its complex role in cancer has led to several translational DNA repair-targeted investigations culminating in clinically viable precision oncology strategy using poly(ADP-ribose) polymerase (PARP) inhibitors in breast, ovarian, pancreatic, and prostate cancers. While PARP directed synthetic lethality has improved outcomes for many patients, the lack of sustained clinical response and the development of resistance pose significant clinical challenges. Therefore, the search for additional DDR-directed drug targets and novel synthetic lethality approaches is highly desirable and is an area of intense preclinical and clinical investigation. Here, we provide an overview of the mammalian DNA repair pathways and then focus on current state of PARP inhibitors (PARPi) and other emerging DNA repair inhibitors for synthetic lethality in cancer.
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16
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Kwok ACM, Li C, Lam WT, Wong JTY. Responses of dinoflagellate cells to ultraviolet-C irradiation. Environ Microbiol 2022; 24:5936-5950. [PMID: 35837869 DOI: 10.1111/1462-2920.16135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 01/12/2023]
Abstract
Dinoflagellates are important aquatic microbes and major harmful algal bloom (HAB) agents that form invasive species through ship ballast transfer. UV-C installations are recommended for ballast treatments and HAB controls, but there is a lack of knowledge in dinoflagellate responses to UV-C. We report here dose-dependent cell cycle delay and viability loss of dinoflagellate cells irradiated with UV-C, with significant proliferative reduction at 800 Jm-2 doses or higher, but immediate LD50 was in the range of 2400-3200 Jm-2 . At higher dosages, some dinoflagellate cells surprisingly survived after days of recovery incubation, and continued viability loss, with samples exhibiting DNA fragmentations per proliferative resumption. Sequential cell cycle postponements, suggesting DNA damages were repaired over one cell cycle, were revealed with flow cytometric analysis and transcriptomic analysis. Over a sustained level of other DNA damage repair pathways, transcript elevation was observed only for several components of base pair repair and mismatch repair. Cumulatively, our findings demonstrated special DNA damage responses in dinoflagellate cells, which we discussed in relation to their unique chromo-genomic characters, as well as indicating resilience of dinoflagellate cells to UV-C.
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Affiliation(s)
- Alvin Chun Man Kwok
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Chongping Li
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Wing Tai Lam
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Joseph Tin Yum Wong
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
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17
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Soni A, Lin X, Mladenov E, Mladenova V, Stuschke M, Iliakis G. BMN673 Is a PARP Inhibitor with Unique Radiosensitizing Properties: Mechanisms and Potential in Radiation Therapy. Cancers (Basel) 2022; 14:cancers14225619. [PMID: 36428712 PMCID: PMC9688666 DOI: 10.3390/cancers14225619] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 11/17/2022] Open
Abstract
BMN673 is a relatively new PARP inhibitor (PARPi) that exhibits superior efficacy in vitro compared to olaparib and other clinically relevant PARPi. BMN673, similar to most clinical PARPi, inhibits the catalytic activities of PARP-1 and PARP-2 and shows impressive anticancer potential as monotherapy in several pre-clinical and clinical studies. Tumor resistance to PARPi poses a significant challenge in the clinic. Thus, combining PARPi with other treatment modalities, such as radiotherapy (RT), is being actively pursued to overcome such resistance. However, the modest to intermediate radiosensitization exerted by olaparib, rucaparib, and veliparib, limits the rationale and the scope of such combinations. The recently reported strong radiosensitizing potential of BMN673 forecasts a paradigm shift on this front. Evidence accumulates that BMN673 may radiosensitize via unique mechanisms causing profound shifts in the balance among DNA double-strand break (DSB) repair pathways. According to one of the emerging models, BMN673 strongly inhibits classical non-homologous end-joining (c-NHEJ) and increases reciprocally and profoundly DSB end-resection, enhancing error-prone DSB processing that robustly potentiates cell killing. In this review, we outline and summarize the work that helped to formulate this model of BMN673 action on DSB repair, analyze the causes of radiosensitization and discuss its potential as a radiosensitizer in the clinic. Finally, we highlight strategies for combining BMN673 with other inhibitors of DNA damage response for further improvements.
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Affiliation(s)
- Aashish Soni
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Xixi Lin
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Emil Mladenov
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Veronika Mladenova
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Martin Stuschke
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, German Cancer Research Center (DKFZ), 45147 Essen, Germany
| | - George Iliakis
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Correspondence: ; Tel.: +49-201-723-4152
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18
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Polβ modulates the expression of type I interferon via STING pathway. Biochem Biophys Res Commun 2022; 621:137-143. [DOI: 10.1016/j.bbrc.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 06/28/2022] [Accepted: 07/02/2022] [Indexed: 11/18/2022]
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19
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Wen H, Feng Z, Ma Y, Liu R, Ou Q, Guo Q, Shen Y, Wu X, Shao Y, Bao H, Wu X. Homologous recombination deficiency in diverse cancer types and its correlation with platinum chemotherapy efficiency in ovarian cancer. BMC Cancer 2022; 22:550. [PMID: 35578198 PMCID: PMC9109318 DOI: 10.1186/s12885-022-09602-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Homologous recombination deficiency (HRD) is a molecular biomarker for administrating PARP inhibitor (PARPi) or platinum-based (Pt) chemotherapy. The most well-studied mechanism of causing HRD is pathogenic BRCA1/2 mutations, while HRD phenotype is also present in patients without BRCA1/2 alterations, suggesting other unknown factors. METHODS The targeted next-generation sequencing (GeneseeqPrime® HRD) was used to evaluate the HRD scores of 199 patients (Cohort I). In Cohort II, a total of 85 Pt-chemotherapy-treated high-grade serous ovarian cancer (HGSOC) patients were included for investigating the role of HRD score in predicting treatment efficacy. The concurrent genomic features analyzed along HRD score evaluation were studied in a third cohort with 416 solid tumor patients (Cohort III). RESULTS An HRD score ≥ 38 was predefined as HRD-positive by analyzing Cohort I (range: 0-107). Over 95% of the BRCA1/2-deficient cases of Cohort I were HRD-positive under this threshold. In Cohort II, Pt-sensitive patients have significantly higher HRD scores than Pt-resistant patients (median: 54 vs. 34, p = 0.031) and a significantly longer PFS was observed in HRD-positive patients (median: 548 vs. 343 days, p = 0.003). Furthermore, TP53, NCOR1, and PTK2 alterations were enriched in HRD-positive patients. In Cohort III, impaired homologous recombination repair pathway was more frequently observed in HRD-positive patients without BRCA1/2 pathogenic mutations. The alteration enrichment of TP53, NCOR1, and PTK2 observed in Cohort II was also validated by the ovarian subgroup in Cohort III. CONCLUSIONS Using an in-house HRD evaluation method, our findings show that overall HRR gene mutations account for a significant part of HRD in the absence of BRCA1/2 aberrations, and suggest that HRD positive status might be a predictive biomarker of Pt-chemotherapy.
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Affiliation(s)
- Hao Wen
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, 130 Dongan Road, Shanghai, 200032, China
| | - Zheng Feng
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, 130 Dongan Road, Shanghai, 200032, China
| | - Yutong Ma
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, No. 128 Huakang Road, Pukou District, Nanjing, Jiangsu, 210000, China
| | - Rui Liu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, No. 128 Huakang Road, Pukou District, Nanjing, Jiangsu, 210000, China
| | - Qiuxiang Ou
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, No. 128 Huakang Road, Pukou District, Nanjing, Jiangsu, 210000, China
| | - Qinhao Guo
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, 130 Dongan Road, Shanghai, 200032, China
| | - Yi Shen
- R&D, Nanjing Geneseeq Technology Inc, No. 128 Huakang Road, Pukou District, Nanjing, Jiangsu, 210000, China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, No. 128 Huakang Road, Pukou District, Nanjing, Jiangsu, 210000, China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, No. 128 Huakang Road, Pukou District, Nanjing, Jiangsu, 210000, China.,School of Public Health, Nanjing Medical University, Jiangning District, 101 Longmian Avenue, Nanjing, Jiangsu, 211166, China
| | - Hua Bao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, No. 128 Huakang Road, Pukou District, Nanjing, Jiangsu, 210000, China.
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, 130 Dongan Road, Shanghai, 200032, China.
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20
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Mao Z, Gray ALH, Gross MD, Thyagarajan B, Bostick RM. Associations of DNA Base Excision Repair and Antioxidant Enzyme Genetic Risk Scores with Biomarker of Systemic Inflammation. FRONTIERS IN AGING 2022; 3:897907. [PMID: 36338835 PMCID: PMC9632613 DOI: 10.3389/fragi.2022.897907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/14/2022] [Indexed: 06/16/2023]
Abstract
Background: Inflammation is implicated in the etiology of various aging-related diseases. Numerous dietary and lifestyle factors contribute to chronic systemic inflammation; genetic variation may too. However, despite biological plausibility, little is known about associations of antioxidant enzyme (AE) and DNA base excision repair (BER) genotypes with human systemic inflammation. Methods: We genotyped 22 single nucleotide polymorphisms (SNPs) in 3 AE genes, and 79 SNPs in 14 BER genes to develop inflammation-specific AE and BER genetic risk scores (GRS) in two pooled cross-sectional studies (n = 333) of 30-74-year-old White adults without inflammatory bowel disease, familial adenomatous polyposis, or a history of cancer or colorectal adenoma. Of the genotypes, based on their associations with a biomarker of systemic inflammation, circulating high sensitivity C-reactive protein (hsCRP) concentrations, we selected 2 SNPs of 2 genes (CAT and MnSoD) for an AE GRS, and 7 SNPs of 5 genes (MUTYH, SMUG1, TDG, UNG, and XRCC1) for a BER GRS. A higher GRS indicates a higher balance of variant alleles directly associated with hsCRP relative to variant alleles inversely associated with hsCRP. We also calculated previously-reported, validated, questionnaire-based dietary (DIS) and lifestyle (LIS) inflammation scores. We used multivariable general linear regression to compare mean hsCRP concentrations across AE and BER GRS categories, individually and jointly with the DIS and LIS. Results: The mean hsCRP concentrations among those in the highest relative to the lowest AE and BER GRS categories were, proportionately, 13.9% (p = 0.30) and 57.4% (p = 0.009) higher. Neither GRS clearly appeared to modify the associations of the DIS or LIS with hsCRP. Conclusion: Our findings suggest that genotypes of DNA BER genes collectively may be associated with systemic inflammation in humans.
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Affiliation(s)
- Ziling Mao
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Abigail L. H. Gray
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Myron D. Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota, MN, United States
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota, MN, United States
| | - Roberd M. Bostick
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
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21
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Pradhan S, Gao R, Bush K, Zhang N, Wairkar YP, Sarkar PS. Polyglutamine Expansion in Huntingtin and Mechanism of DNA Damage Repair Defects in Huntington’s Disease. Front Cell Neurosci 2022; 16:837576. [PMID: 35444517 PMCID: PMC9013776 DOI: 10.3389/fncel.2022.837576] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/07/2022] [Indexed: 12/27/2022] Open
Abstract
Emerging evidence suggests that DNA repair deficiency and genome instability may be the impending signs of many neurological diseases. Genome-wide association (GWAS) studies have established a strong correlation between genes that play a role in DNA damage repair and many neurodegenerative diseases, including Huntington’s disease (HD), and several other trinucleotides repeat expansion-related hereditary ataxias. Recently, many reports have documented a significant role played by the DNA repair processes in aging and in modifying many neurodegenerative diseases, early during their progression. Studies from our lab and others have now begun to understand the mechanisms that cause defective DNA repair in HD and surprisingly, many proteins that have a strong link to known neurodegenerative diseases seem to be important players in these cellular pathways. Mutations in huntingtin (HTT) gene that lead to polyglutamine repeat expansion at the N-terminal of HTT protein has been shown to disrupt transcription-coupled DNA repair process, a specialized DNA repair process associated with transcription. Due to the recent progress made in understanding the mechanisms of DNA repair in relation to HD, in this review, we will mainly focus on the mechanisms by which the wild-type huntingtin (HTT) protein helps in DNA repair during transcription, and the how polyglutamine expansions in HTT impedes this process in HD. Further studies that identify new players in DNA repair will help in our understanding of this process in neurons. Furthermore, it should help us understand how various DNA repair mechanism(s) coordinate to maintain the normal physiology of neurons, and provide insights for the development of novel drugs at prodromal stages of these neurodegenerative diseases.
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Affiliation(s)
- Subrata Pradhan
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, United States
| | - Rui Gao
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, United States
| | - Keegan Bush
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX, United States
| | - Nan Zhang
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, United States
| | - Yogesh P. Wairkar
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, United States
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX, United States
| | - Partha S. Sarkar
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, United States
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX, United States
- *Correspondence: Partha S. Sarkar,
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Vincent MS, Uphoff S. Cellular heterogeneity in DNA alkylation repair increases population genetic plasticity. Nucleic Acids Res 2021; 49:12320-12331. [PMID: 34850170 PMCID: PMC8643705 DOI: 10.1093/nar/gkab1143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022] Open
Abstract
DNA repair mechanisms fulfil a dual role, as they are essential for cell survival and genome maintenance. Here, we studied how cells regulate the interplay between DNA repair and mutation. We focused on the adaptive response that increases the resistance of Escherichia coli cells to DNA alkylation damage. Combination of single-molecule imaging and microfluidic-based single-cell microscopy showed that noise in the gene activation timing of the master regulator Ada is accurately propagated to generate a distinct subpopulation of cells in which all proteins of the adaptive response are essentially absent. Whereas genetic deletion of these proteins causes extreme sensitivity to alkylation stress, a temporary lack of expression is tolerated and increases genetic plasticity of the whole population. We demonstrated this by monitoring the dynamics of nascent DNA mismatches during alkylation stress as well as the frequency of fixed mutations that are generated by the distinct subpopulations of the adaptive response. We propose that stochastic modulation of DNA repair capacity by the adaptive response creates a viable hypermutable subpopulation of cells that acts as a source of genetic diversity in a clonal population.
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Affiliation(s)
- Maxence S Vincent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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[Efficient screening for 8-oxoguanine DNA glycosylase binding aptamers via capillary electrophoresis]. Se Pu 2021; 39:721-729. [PMID: 34227370 PMCID: PMC9404054 DOI: 10.3724/sp.j.1123.2020.12017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
8-氧代鸟嘌呤DNA糖基化酶(OGG1)是人体中重要的功能蛋白,在修复DNA氧化性损伤过程中起关键作用。氧化应激等引起的氧化损伤易导致炎症反应的发生,对OGG1的抑制可以一定程度上起到缓解作用;对癌细胞OGG1的抑制有望作为癌症治疗的新方法。目前的研究多集中于小分子对OGG1功能的影响和调控,而OGG1的适配体筛选尚未见报道。作为功能配体,适配体具有合成简单、高亲和力及高特异性等优点。该文筛选了OGG1的核酸适配体,结合毛细管电泳高效快速的优点建立了两种基于毛细管电泳-指数富集进化(CE-SELEX)技术的筛选方法:同步竞争法和多轮筛选法。同步竞争法利用单链结合蛋白(SSB)与核酸库中单链核酸的强结合能力,与目标蛋白OGG1组成竞争体系,并通过增加SSB浓度来增加竞争筛选压力,以去除与OGG1弱结合的核酸序列,一步筛选即可获得与OGG1强结合的核酸序列。多轮筛选法在相同孵育条件和电泳条件下,经3轮筛选获得OGG1的核酸适配体。比较两种筛选方法的筛选结果,筛选结果中频次最高的3条候选核酸适配体序列一致,其解离常数(KD)值在1.71~2.64 μmol/L之间。分子对接分析结果表明候选适配体1(Apt 1)可能与OGG1中具有修复氧化性损伤功能的活性口袋结合。通过对两种筛选方法的对比,证明同步竞争法更加快速高效,对其他蛋白核酸适配体筛选方法的选择具有一定的指导意义。得到的适配体有望用于OGG1功能调控,以抑制其修复功能。
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24
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Pidugu LS, Bright H, Lin WJ, Majumdar C, Van Ostrand RP, David SS, Pozharski E, Drohat AC. Structural Insights into the Mechanism of Base Excision by MBD4. J Mol Biol 2021; 433:167097. [PMID: 34107280 PMCID: PMC8286355 DOI: 10.1016/j.jmb.2021.167097] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/24/2021] [Accepted: 06/01/2021] [Indexed: 11/28/2022]
Abstract
DNA glycosylases remove damaged or modified nucleobases by cleaving the N-glycosyl bond and the correct nucleotide is restored through subsequent base excision repair. In addition to excising threatening lesions, DNA glycosylases contribute to epigenetic regulation by mediating DNA demethylation and perform other important functions. However, the catalytic mechanism remains poorly defined for many glycosylases, including MBD4 (methyl-CpG binding domain IV), a member of the helix-hairpin-helix (HhH) superfamily. MBD4 excises thymine from G·T mispairs, suppressing mutations caused by deamination of 5-methylcytosine, and it removes uracil and modified uracils (e.g., 5-hydroxymethyluracil) mispaired with guanine. To investigate the mechanism of MBD4 we solved high-resolution structures of enzyme-DNA complexes at three stages of catalysis. Using a non-cleavable substrate analog, 2'-deoxy-pseudouridine, we determined the first structure of an enzyme-substrate complex for wild-type MBD4, which confirms interactions that mediate lesion recognition and suggests that a catalytic Asp, highly conserved in HhH enzymes, binds the putative nucleophilic water molecule and stabilizes the transition state. Observation that mutating the Asp (to Gly) reduces activity by 2700-fold indicates an important role in catalysis, but probably not one as the nucleophile in a double-displacement reaction, as previously suggested. Consistent with direct-displacement hydrolysis, a structure of the enzyme-product complex indicates a reaction leading to inversion of configuration. A structure with DNA containing 1-azadeoxyribose models a potential oxacarbenium-ion intermediate and suggests the Asp could facilitate migration of the electrophile towards the nucleophilic water. Finally, the structures provide detailed snapshots of the HhH motif, informing how these ubiquitous metal-binding elements mediate DNA binding.
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Affiliation(s)
- Lakshmi S Pidugu
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hilary Bright
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Wen-Jen Lin
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA
| | - Chandrima Majumdar
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA
| | | | - Sheila S David
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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Apurinic/Apyrimidinic Endonuclease 2 (APE2): An ancillary enzyme for contextual base excision repair mechanisms to preserve genome stability. Biochimie 2021; 190:70-90. [PMID: 34302888 DOI: 10.1016/j.biochi.2021.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/29/2021] [Accepted: 07/19/2021] [Indexed: 01/03/2023]
Abstract
The genome of living organisms frequently undergoes various types of modifications which are recognized and repaired by the relevant repair mechanisms. These repair pathways are increasingly being deciphered to understand the mechanisms. Base excision repair (BER) is indispensable to maintain genome stability. One of the enigmatic repair proteins of BER, Apurinic/Apyrimidinic Endonuclease 2 (APE2), like APE1, is truly multifunctional and demonstrates the independent and non-redundant function in maintaining the genome integrity. APE2 is involved in ATR-Chk1 mediated DNA damage response. It also resolves topoisomerase1 mediated cleavage complex intermediate which is formed while repairing misincorporated ribonucleotides in the absence of functional RNase H2 mediated excision repair pathway. BER participates in the demethylation pathway and the role of Arabidopsis thaliana APE2 is demonstrated in this process. Moreover, APE2 is synthetically lethal to BRCA1, BRCA2, and RNase H2, and its homolog, APE1 fails to complement the function. Hence, the role of APE2 is not just an alternate to the repair mechanisms but has implications in diverse functional pathways related to the maintenance of genome integrity. This review analyses genomic features of APE2 and delineates its enzyme function as error-prone as well as efficient and accurate repair protein based on the studies on mammalian or its homolog proteins from model systems such as Arabidopsis thaliana, Schizosaccharomyces pombe, Trypanosoma curzi, Xenopus laevis, Danio rerio, Mus musculus, and Homo sapiens.
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26
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RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. Biomolecules 2021; 11:biom11010076. [PMID: 33430019 PMCID: PMC7826747 DOI: 10.3390/biom11010076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
RNA modifications are essential for proper RNA processing, quality control, and maturation steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveillance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essential for the correct assembly of small nucleolar ribonucleoproteins (snRNPs) and ribosomal RNA (rRNA) processing. Here, we review rRNA modifications and RNA quality control mechanisms in general and discuss the specific function of SMUG1 in rRNA metabolism. Cells lacking SMUG1 have elevated levels of immature rRNA molecules and accumulation of 5-hydroxymethyluridine (5hmU) in mature rRNA. SMUG1 may be required for post-transcriptional regulation and quality control of rRNAs, partly by regulating rRNA and stability.
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27
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Jia Q, Zeng H, Tu J, Sun L, Cao W, Xie W. Structural insights into an MsmUdgX mutant capable of both crosslinking and uracil excision capability. DNA Repair (Amst) 2020; 97:103008. [PMID: 33248387 DOI: 10.1016/j.dnarep.2020.103008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 11/30/2022]
Abstract
UdgX from Mycobacterium smegmatis (MsmUdgX) is a prototypical enzyme representing a new class of uracil-DNA glycosylases (UDG) closely related to the family 4 enzymes. It possesses a unique R-loop rich in positive residues and forms a covalent bond with single-stranded uracil-containing DNAs (ssDNA-Us) that is resistant to denaturants after the removal of the target uracil. We previously identified the H109E mutant of MsmUdgX that forms a weak covalent complex with ssDNA-U and yet possesses moderate uracil excision activity, but the mechanism of its action is not fully understood. To further study the catalytic process of MsmUdgX, we solved the high-resolution crystal structures of H109E in the free and DNA-bound forms, respectively. We found that the key residue Glu109 adopts a similar conformation to that of WT to form the covalent bond, suggesting that it still employs the same "excision-inhibition" mechanism to that of the WT enzyme. The enzyme remains nearly intact before and after the crosslinking reaction, but the first half of the R-loop exhibits large structural differences while the rest of the loop barely moves, owing to the salt-bridge interaction formed via Arg107. Additionally, Arg107, along with Gln53 was found to play important roles in the biochemical properties of MsmUdgX. Our studies provide new insights into the MsmUdgX catalysis and improve our understanding on this unique enzyme.
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Affiliation(s)
- Qian Jia
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, 510006, China
| | - Hui Zeng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, 510006, China
| | - Jie Tu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, 510006, China
| | - Litao Sun
- School of Public Health (Shenzhen), The Sun Yat-sen University, Guangdong, 518107, China
| | - Weiguo Cao
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, 510006, China.
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28
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Valdiglesias V, Sánchez-Flores M, Fernández-Bertólez N, Au W, Pásaro E, Laffon B. Expanded usage of the Challenge-Comet assay as a DNA repair biomarker in human populations: protocols for fresh and cryopreserved blood samples, and for different challenge agents. Arch Toxicol 2020; 94:4219-4228. [DOI: 10.1007/s00204-020-02881-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/12/2020] [Indexed: 12/19/2022]
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29
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A Multi-Endpoint Approach to Base Excision Repair Incision Activity Augmented by PARylation and DNA Damage Levels in Mice: Impact of Sex and Age. Int J Mol Sci 2020; 21:ijms21186600. [PMID: 32917005 PMCID: PMC7555950 DOI: 10.3390/ijms21186600] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023] Open
Abstract
Investigation of processes that contribute to the maintenance of genomic stability is one crucial factor in the attempt to understand mechanisms that facilitate ageing. The DNA damage response (DDR) and DNA repair mechanisms are crucial to safeguard the integrity of DNA and to prevent accumulation of persistent DNA damage. Among them, base excision repair (BER) plays a decisive role. BER is the major repair pathway for small oxidative base modifications and apurinic/apyrimidinic (AP) sites. We established a highly sensitive non-radioactive assay to measure BER incision activity in murine liver samples. Incision activity can be assessed towards the three DNA lesions 8-oxo-2’-deoxyguanosine (8-oxodG), 5-hydroxy-2’-deoxyuracil (5-OHdU), and an AP site analogue. We applied the established assay to murine livers of adult and old mice of both sexes. Furthermore, poly(ADP-ribosyl)ation (PARylation) was assessed, which is an important determinant in DDR and BER. Additionally, DNA damage levels were measured to examine the overall damage levels. No impact of ageing on the investigated endpoints in liver tissue were found. However, animal sex seems to be a significant impact factor, as evident by sex-dependent alterations in all endpoints investigated. Moreover, our results revealed interrelationships between the investigated endpoints indicative for the synergetic mode of action of the cellular DNA integrity maintaining machinery.
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30
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Zhang L, Li Y, Shi H, Zhang D, Yang Z, Oger P, Zheng J. Biochemical characterization and mutational studies of the 8-oxoguanine DNA glycosylase from the hyperthermophilic and radioresistant archaeon Thermococcus gammatolerans. Appl Microbiol Biotechnol 2019; 103:8021-8033. [PMID: 31372707 DOI: 10.1007/s00253-019-10031-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/08/2019] [Accepted: 07/13/2019] [Indexed: 12/22/2022]
Abstract
8-oxoguanine (GO) is a major lesion found in DNA that arises from guanine oxidation. The hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans encodes an archaeal GO DNA glycosylase (Tg-AGOG). Here, we characterized biochemically Tg-AGOG and probed its GO removal mechanism by mutational studies. Tg-AGOG can remove GO from DNA at high temperature through a β-elimination reaction. The enzyme displays an optimal temperature, ca.85-95 °C, and an optimal pH, ca.7.0-8.5. In addition, Tg-AGOG activity is independent on a divalent metal ion. However, both Co2+ and Cu2+ inhibit its activity. The enzyme activity is also inhibited by NaCl. Furthermore, Tg-AGOG specifically cleaves GO-containing dsDNA in the order: GO:C, GO:T, GO:A, and GO:G. Moreover, the temperature dependence of cleavage rates of the enzyme was determined, and from this, the activation energy for GO removal from DNA was first estimated to be 16.9 ± 0.9 kcal/mol. In comparison with the wild-type Tg-AGOG, the R197A mutant has a reduced cleavage activity for GO-containing DNA, whereas both the P193A and F167A mutants exhibit similar cleavage activities for GO-containing DNA. While the mutations of P193 and F167 to Ala lead to increased binding, the mutation of R197 to Ala had no significant effect on binding. These observations suggest that residue R197 is involved in catalysis, and residues P193 and F167 are flexible for conformational change.
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Affiliation(s)
- Likui Zhang
- Department of Environmental Science and Engineering Marine Science & Technology Institute, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Yuting Li
- Department of Environmental Science and Engineering Marine Science & Technology Institute, Yangzhou University, Yangzhou, Jiangsu, China
| | - Haoqiang Shi
- Department of Environmental Science and Engineering Marine Science & Technology Institute, Yangzhou University, Yangzhou, Jiangsu, China
| | - Dai Zhang
- College of Plant Protection, Agricultural University of Hebei, Baoding City, 071001, Hebei Province, China
| | - Zhihui Yang
- College of Plant Protection, Agricultural University of Hebei, Baoding City, 071001, Hebei Province, China.
| | - Philippe Oger
- Univ Lyon, INSA de Lyon, CNRS UMR 5240, Villeurbanne, France.
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Alfiky A. Effects of ultraviolet irradiation on the in vitro antagonistic potential of Trichoderma spp. against soil-borne fungal pathogens. Heliyon 2019; 5:e02111. [PMID: 31372559 PMCID: PMC6656997 DOI: 10.1016/j.heliyon.2019.e02111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/23/2019] [Accepted: 07/15/2019] [Indexed: 11/28/2022] Open
Abstract
Development of new effective biocontrol agents is largely based on the antagonistic capacity of candidate agents against targeted pathogens in vitro. Different mechanisms contribute to such capacity, including the activity of cell wall-degrading enzymes, secretion of antimicrobial secondary metabolites, growth vigour and resistance to exogenous and endogenous toxins. In this study, a series of laboratory experiments were designed to improve the antagonistic activities of Trichoderma spp. against two plant fungal pathogens, Sclerotium rolfsii and Rhizoctonia solani. A simple but efficient mutagenesis programme was carried out using ultraviolet light to induce modifications in the genetic structure of two Trichoderma biocontrol agents, T. virens and T. asperellum. The obtained mutants were subjected to a) initial screening for media-permeable antifungal metabolites using the cellophane membrane-based method, and b) selected mutants were subjected to a series of antagonistic tests. Results revealed that the antagonistic potential of selected mutants was significantly improved against the two plant pathogens. Genetic stability test results indicated that the UV-derived mutant Tv3, maintained its elevated performance after 12 rounds of sub-culture. Gene expression analysis for five antagonism-associated genes were examined using real-Time PCR. Results revealed that the gene expression of two genes, chitinase 33, a cell wall degrading enzyme and, polyketide synthase, which is responsible for polyketide biosynthesis, a class of secondary metabolites with antimicrobial roles, were significantly upregulated in one of the mutated T. virens strains. Results of our in vitro antagonistic studies along with our molecular analysis indicate that the UV mutagenesis could be an effective strategy to improve Trichoderma antagonistic potential.
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Affiliation(s)
- Alsayed Alfiky
- Genetics Department, Faculty of Agriculture, Tanta University, Egypt
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32
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Gao S, Zhang X, Song Q, Liu J, Ji X, Wang P. POLD1 deficiency is involved in cognitive function impairment in AD patients and SAMP8 mice. Biomed Pharmacother 2019; 114:108833. [PMID: 30978525 DOI: 10.1016/j.biopha.2019.108833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 02/03/2023] Open
Abstract
Age-related changes such as increased oxidative stress and DNA damage are important risk factors for Alzheimer's disease (AD). This study aimed to clarify the role of POLD1, the catalytic subunit of DNA polymerase δ, in neurodegeneration symptoms of AD. POLD1 expression levels were evaluated in patients with different neurodegenerative diseases by ELISA, RT-PCR and Western blot analysis. The impairment of cognitive ability in AD patients and senescence-accelerated mouse prone 8 (SAMP8) mice were evaluated by MMSE/MoCA score and Morris water maze (MWM) test. We found that serum concentration and expression levels of POLD1 in lymphocytes were reduced in AD patients. The cognitive impairment in AD patients and SAMP8 mice was associated with reduced POLD1 expression. In addition, POLD1 knockdown led to premature senescence and increased DNA damage in primary neuronal cells of SAMP8 mice. In conclusion, this is the first study suggesting that the deficiency of POLD1 may aggravate AD progression, and POLD1 is a potential diagnostic marker and therapeutic target for AD.
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Affiliation(s)
- Shichao Gao
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, PR China
| | - Xiaomin Zhang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, PR China
| | - Qiao Song
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, PR China
| | - Jing Liu
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, PR China
| | - Xunming Ji
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing, 100053, PR China
| | - Peichang Wang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, PR China; Beijing Institute of Brain Disorders, Capital Medical University, Beijing, 100053, PR China.
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33
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Steenwyk JL, Opulente DA, Kominek J, Shen XX, Zhou X, Labella AL, Bradley NP, Eichman BF, Čadež N, Libkind D, DeVirgilio J, Hulfachor AB, Kurtzman CP, Hittinger CT, Rokas A. Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLoS Biol 2019; 17:e3000255. [PMID: 31112549 PMCID: PMC6528967 DOI: 10.1371/journal.pbio.3000255] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
Cell-cycle checkpoints and DNA repair processes protect organisms from potentially lethal mutational damage. Compared to other budding yeasts in the subphylum Saccharomycotina, we noticed that a lineage in the genus Hanseniaspora exhibited very high evolutionary rates, low Guanine-Cytosine (GC) content, small genome sizes, and lower gene numbers. To better understand Hanseniaspora evolution, we analyzed 25 genomes, including 11 newly sequenced, representing 18/21 known species in the genus. Our phylogenomic analyses identify two Hanseniaspora lineages, a faster-evolving lineage (FEL), which began diversifying approximately 87 million years ago (mya), and a slower-evolving lineage (SEL), which began diversifying approximately 54 mya. Remarkably, both lineages lost genes associated with the cell cycle and genome integrity, but these losses were greater in the FEL. E.g., all species lost the cell-cycle regulator WHIskey 5 (WHI5), and the FEL lost components of the spindle checkpoint pathway (e.g., Mitotic Arrest-Deficient 1 [MAD1], Mitotic Arrest-Deficient 2 [MAD2]) and DNA-damage-checkpoint pathway (e.g., Mitosis Entry Checkpoint 3 [MEC3], RADiation sensitive 9 [RAD9]). Similarly, both lineages lost genes involved in DNA repair pathways, including the DNA glycosylase gene 3-MethylAdenine DNA Glycosylase 1 (MAG1), which is part of the base-excision repair pathway, and the DNA photolyase gene PHotoreactivation Repair deficient 1 (PHR1), which is involved in pyrimidine dimer repair. Strikingly, the FEL lost 33 additional genes, including polymerases (i.e., POLymerase 4 [POL4] and POL32) and telomere-associated genes (e.g., Repressor/activator site binding protein-Interacting Factor 1 [RIF1], Replication Factor A 3 [RFA3], Cell Division Cycle 13 [CDC13], Pbp1p Binding Protein [PBP2]). Echoing these losses, molecular evolutionary analyses reveal that, compared to the SEL, the FEL stem lineage underwent a burst of accelerated evolution, which resulted in greater mutational loads, homopolymer instabilities, and higher fractions of mutations associated with the common endogenously damaged base, 8-oxoguanine. We conclude that Hanseniaspora is an ancient lineage that has diversified and thrived, despite lacking many otherwise highly conserved cell-cycle and genome integrity genes and pathways, and may represent a novel, to our knowledge, system for studying cellular life without them.
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Affiliation(s)
- Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Dana A Opulente
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin, United States of America
| | - Jacek Kominek
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin, United States of America
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Abigail L Labella
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Noah P Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Neža Čadež
- University of Ljubljana Biotechnical Faculty, Department of Food Science and Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, Universidad Nacional del Comahue-CONICET, San Carlos de Bariloche, Río Negro, Argentina
| | - Jeremy DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, Illinois, United States of America
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cletus P Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, Illinois, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin, United States of America
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
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AP endonuclease 1 (Apex1) influences brain development linking oxidative stress and DNA repair. Cell Death Dis 2019; 10:348. [PMID: 31024003 PMCID: PMC6484078 DOI: 10.1038/s41419-019-1578-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/27/2019] [Accepted: 04/04/2019] [Indexed: 12/13/2022]
Abstract
Brain and neurons are particularly sensitive to reactive oxygen species (ROS). Oxidative damage from ROS results in increased 8-oxoguanine in DNA followed by repair through the base excision repair (BER) pathway. We reported earlier that AP endonuclease 1 (Apex1) not only participates directly in BER but also regulates transcription factor Creb1. Here, we investigated how Apex1 affects brain to respond effectively to oxidative damage during zebrafish development. Loss of Apex1 resulted in increased ROS, 8-oxoguanine, and abasic sites as well as loss of Ogg1, which recognizes 8-oxoguanine and is required for its repair. Moreover, knock-down of Apex1 not only resulted in reduction of expression of several major proteins in the BER pathway (Polb and Ogg1), and it also resulted in maldistribution and loss of four key brain transcription factors (fezf2, otx2, egr2a, and pax2a), leading to abnormal brain development. These results were independent of p53 protein level. In contrast, exposure to exogenous H2O2 resulted in increased transcription and protein of Apex1 along with other BER components, as well as Creb1. Taken together, these results indicate that oxidative stress increased when the level of Apex1 was reduced, revealing a novel pathway of how Apex1 manages oxidative stress in developing brain.
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35
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Desler C, Lillenes MS, Tønjum T, Rasmussen LJ. The Role of Mitochondrial Dysfunction in the Progression of Alzheimer's Disease. Curr Med Chem 2019; 25:5578-5587. [PMID: 28618998 PMCID: PMC6446443 DOI: 10.2174/0929867324666170616110111] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 01/02/2017] [Accepted: 01/02/2017] [Indexed: 11/22/2022]
Abstract
The current molecular understanding of Alzheimer's disease (AD) has still not resulted in successful interventions. Mitochondrial dysfunction of the AD brain is currently emerging as a hallmark of this disease. One mitochondrial function often affected in AD is oxidative phosphorylation responsible for ATP production, but also for production of reactive oxygen species (ROS) and for the de novo synthesis of pyrimidines. This paper reviews the role of mitochondrial produced ROS and pyrimidines in the aetiology of AD and their proposed role in oxidative degeneration of macromolecules, synthesis of essential phospholipids and maintenance of mitochondrial viability in the AD brain.
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Affiliation(s)
- Claus Desler
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Meryl S Lillenes
- Healthy Brain Aging Centre (HBAC), Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tone Tønjum
- Healthy Brain Aging Centre (HBAC), Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
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36
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Pichel N, Vivar M, Fuentes M. The problem of drinking water access: A review of disinfection technologies with an emphasis on solar treatment methods. CHEMOSPHERE 2019; 218:1014-1030. [PMID: 30609481 DOI: 10.1016/j.chemosphere.2018.11.205] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/19/2018] [Accepted: 11/29/2018] [Indexed: 05/17/2023]
Abstract
The lack of access to safe drinking water is one of the biggest challenges facing humanity in the 21st century. Despite the collective global effort that has been made, the drinking water sources of at least 2 billion people are faecally contaminated, resulting in more than half a million diarrhoeal deaths each year, with the majority occurring in developing countries. Technologies for the inactivation of pathogenic microorganisms in water are therefore of great significance for human health and well-being. However, conventional technologies to provide drinking water, although effective, present limitations that impede their global application. These treatment methods often have high energy and chemical demands, which limits their application for the prevention of waterborne diseases in the most vulnerable regions. These shortcomings have led to rapid research and development of advanced alternative technologies. One of these alternative methods is solar disinfection, which is recognised by the World Health Organization as one of the most appropriate methods for producing drinkable water in developing countries. This study reviews conventional technologies that are being applied at medium to large scales to purify water and emerging technologies currently in development. In addition, this paper describes the merits, demerits, and limitations of these technologies. Finally, the review focuses on solar disinfection, including a novel technology recently developed in this field.
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Affiliation(s)
- N Pichel
- IMDEA Water Institute, Alcalá de Henares, 28805, Spain.
| | - M Vivar
- Grupo IDEA, EPS Linares, Universidad de Jaén, Linares 23700, Spain
| | - M Fuentes
- IMDEA Water Institute, Alcalá de Henares, 28805, Spain; Grupo IDEA, EPS Linares, Universidad de Jaén, Linares 23700, Spain
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Barman P, Reddy D, Bhaumik SR. Mechanisms of Antisense Transcription Initiation with Implications in Gene Expression, Genomic Integrity and Disease Pathogenesis. Noncoding RNA 2019; 5:ncrna5010011. [PMID: 30669611 PMCID: PMC6468509 DOI: 10.3390/ncrna5010011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/01/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Non-coding antisense transcripts arise from the strand opposite the sense strand. Over 70% of the human genome generates non-coding antisense transcripts while less than 2% of the genome codes for proteins. Antisense transcripts and/or the act of antisense transcription regulate gene expression and genome integrity by interfering with sense transcription and modulating histone modifications or DNA methylation. Hence, they have significant pathological and physiological relevance. Indeed, antisense transcripts were found to be associated with various diseases including cancer, diabetes, cardiac and neurodegenerative disorders, and, thus, have promising potentials for prognostic and diagnostic markers and therapeutic development. However, it is not clearly understood how antisense transcription is initiated and epigenetically regulated. Such knowledge would provide new insights into the regulation of antisense transcription, and hence disease pathogenesis with therapeutic development. The recent studies on antisense transcription initiation and its epigenetic regulation, which are limited, are discussed here. Furthermore, we concisely describe how antisense transcription/transcripts regulate gene expression and genome integrity with implications in disease pathogenesis and therapeutic development.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
| | - Divya Reddy
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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38
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Oleson BJ, Corbett JA. Dual Role of Nitric Oxide in Regulating the Response of β Cells to DNA Damage. Antioxid Redox Signal 2018; 29:1432-1445. [PMID: 28978225 PMCID: PMC6166691 DOI: 10.1089/ars.2017.7351] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 09/09/2017] [Indexed: 01/09/2023]
Abstract
SIGNIFICANCE Cytokines released in and around pancreatic islets during islet inflammation are believed to contribute to impaired β cell function and β cell death during the development of diabetes. Nitric oxide, produced by β cells in response to cytokine exposure, controls many of the responses of β cells during islet inflammation. Recent Advances: Although nitric oxide has been shown to inhibit insulin secretion and oxidative metabolism and induce DNA damage in β cells, it also activates protective pathways that promote recovery of insulin secretion and oxidative metabolism and repair of damaged DNA. Recent studies have identified a novel role for nitric oxide in selectively regulating the DNA damage response in β cells. CRITICAL ISSUES Does nitric oxide mediate cytokine-induced β cell damage, or is nitric oxide produced by β cells in response to cytokines to protect β cells from damage? FUTURE DIRECTIONS β cells appear to be the only islet endocrine cell type capable of responding to proinflammatory cytokines with the production of nitric oxide, and these terminally differentiated cells have a limited capacity to regenerate. It is likely that there is a physiological purpose for this response, and understanding this could open new areas of study regarding the loss of functional β cell mass during diabetes development.
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Affiliation(s)
- Bryndon J. Oleson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - John A. Corbett
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
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Zhao H, Di Mauro G, Lungu-Mitea S, Negrini P, Guarino AM, Frigato E, Braunbeck T, Ma H, Lamparter T, Vallone D, Bertolucci C, Foulkes NS. Modulation of DNA Repair Systems in Blind Cavefish during Evolution in Constant Darkness. Curr Biol 2018; 28:3229-3243.e4. [PMID: 30318355 DOI: 10.1016/j.cub.2018.08.039] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/19/2018] [Accepted: 08/16/2018] [Indexed: 11/18/2022]
Abstract
How the environment shapes the function and evolution of DNA repair systems is poorly understood. In a comparative study using zebrafish and the Somalian blind cavefish, Phreatichthys andruzzii, we reveal that during evolution for millions of years in continuous darkness, photoreactivation DNA repair function has been lost in P. andruzzii. We demonstrate that this loss results in part from loss-of-function mutations in pivotal DNA-repair genes. Specifically, C-terminal truncations in P. andruzzii DASH and 6-4 photolyase render these proteins predominantly cytoplasmic, with consequent loss in their functionality. In addition, we reveal a general absence of light-, UV-, and ROS-induced expression of P. andruzzii DNA-repair genes. This results from a loss of function of the D-box enhancer element, which coordinates and enhances DNA repair in response to sunlight. Our results point to P. andruzzii being the only species described, apart from placental mammals, that lacks the highly evolutionary conserved photoreactivation function. We predict that in the DNA repair systems of P. andruzzii, we may be witnessing the first stages in a process that previously occurred in the ancestors of placental mammals during the Mesozoic era.
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Affiliation(s)
- Haiyu Zhao
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Giuseppe Di Mauro
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Sebastian Lungu-Mitea
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Aquatic Ecology and Toxicology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld, 69120 Heidelberg, Germany; Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Pietro Negrini
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Andrea Maria Guarino
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Biology, University of Naples "Federico II," 80126 Naples, Italy
| | - Elena Frigato
- Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Thomas Braunbeck
- Aquatic Ecology and Toxicology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Hongju Ma
- Botanical Institute, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Daniela Vallone
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Cristiano Bertolucci
- Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Nicholas S Foulkes
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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40
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Stringer JM, Winship A, Liew SH, Hutt K. The capacity of oocytes for DNA repair. Cell Mol Life Sci 2018; 75:2777-2792. [PMID: 29748894 PMCID: PMC11105623 DOI: 10.1007/s00018-018-2833-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/27/2018] [Accepted: 05/02/2018] [Indexed: 12/18/2022]
Abstract
Female fertility and offspring health are critically dependent on the maintenance of an adequate supply of high-quality oocytes. Like somatic cells, oocytes are subject to a variety of different types of DNA damage arising from endogenous cellular processes and exposure to exogenous genotoxic stressors. While the repair of intentionally induced DNA double strand breaks in gametes during meiotic recombination is well characterised, less is known about the ability of oocytes to repair pathological DNA damage and the relative contribution of DNA repair to oocyte quality is not well defined. This review will discuss emerging data suggesting that oocytes are in fact capable of efficient DNA repair and that DNA repair may be an important mechanism for ensuring female fertility, as well as the transmission of high-quality genetic material to subsequent generations.
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Affiliation(s)
- Jessica M Stringer
- Ovarian Biology Laboratory, Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Amy Winship
- Ovarian Biology Laboratory, Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Seng H Liew
- Ovarian Biology Laboratory, Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Karla Hutt
- Ovarian Biology Laboratory, Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
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41
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Jensen HLB, Lillenes MS, Rabano A, Günther CC, Riaz T, Kalayou ST, Ulstein ID, Bøhmer T, Tønjum T. Expression of nucleotide excision repair in Alzheimer's disease is higher in brain tissue than in blood. Neurosci Lett 2018; 672:53-58. [PMID: 29474873 DOI: 10.1016/j.neulet.2018.02.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/08/2018] [Accepted: 02/19/2018] [Indexed: 11/16/2022]
Abstract
Age-related changes are increased in patients with Alzheimer's disease (AD), including oxidative stress and DNA damage. We propose that genotoxic stress and DNA repair responses influence neurodegeneration in the pathogenesis of AD. Here, we focus on nucleotide excision repair (NER). Real-time qPCR and mass spectrometry were employed to determine the expression levels of selected NER components. The mRNA levels of the genes encoding the NER proteins RAD23B, RPA1, ERCC1, PCNA and LIG3 as well as the NER-interacting base excision repair protein MPG in blood and brain tissue from four brain regions in patients with AD or mild cognitive impairment and healthy controls (HC), were assessed. NER mRNA levels were significantly higher in brain tissue than in blood. Further, LIG3 mRNA levels in the frontal cortex was higher in AD versus HC, while mRNA levels of MPG and LIG3 in entorhinal cortex and RPA1 in the cerebellum were lower in AD versus HC. In blood, RPA1 and ERCC1 mRNA levels were lower in AD patients than in HC. Alterations in gene expression of NER components between brain regions were associated with AD, connecting DNA repair to AD pathogenesis and suggesting a distinct role for NER in the brain.
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Affiliation(s)
| | - Meryl S Lillenes
- Department of Microbiology, University of Oslo, Oslo, Norway; Department of Microbiology, Oslo University Hospital, Oslo, Norway.
| | - Alberto Rabano
- Centro Investigación Enfermedades Neurológicas (CIEN), Spain.
| | | | - Tahira Riaz
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.
| | - Shewit T Kalayou
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.
| | - Ingun D Ulstein
- The Memory Clinic, Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway.
| | - Thomas Bøhmer
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, Oslo, Norway; Department of Microbiology, Oslo University Hospital, Oslo, Norway.
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42
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Coelho FJRC, Cleary DFR, Gomes NCM, Pólonia ARM, Huang YM, Liu LL, de Voogd NJ. Sponge Prokaryote Communities in Taiwanese Coral Reef and Shallow Hydrothermal Vent Ecosystems. MICROBIAL ECOLOGY 2018; 75:239-254. [PMID: 28699015 DOI: 10.1007/s00248-017-1023-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
Previously, it was believed that the prokaryote communities of typical 'low-microbial abundance' (LMA) or 'non-symbiont harboring' sponges were merely subsets of the prokaryote plankton community. Recent research has, however, shown that these sponges are dominated by particular clades of Proteobacteria or Cyanobacteria. Here, we expand on this research and assess the composition and putative functional profiles of prokaryotic communities from LMA sponges collected in two ecosystems (coral reef and hydrothermal vent) from vicinal islands of Taiwan with distinct physicochemical conditions. Six sponge species identified as Acanthella cavernosa (Bubarida), Echinodictyum asperum, Ptilocaulis spiculifer (Axinellida), Jaspis splendens (Tetractinellida), Stylissa carteri (Scopalinida) and Suberites sp. (Suberitida) were sampled in coral reefs in the Penghu archipelago. One sponge species provisionally identified as Hymeniacidon novo spec. (Suberitida) was sampled in hydrothermal vent habitat. Each sponge was dominated by a limited set of operational taxonomic units which were similar to sequences from organisms previously obtained from other LMA sponges. There was a distinct bacterial community between sponges collected in coral reef and in hydrothermal vents. The putative functional profile revealed that the prokaryote community from sponges collected in hydrothermal vents was significantly enriched for pathways related to DNA replication and repair.
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Affiliation(s)
- F J R C Coelho
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - N C M Gomes
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A R M Pólonia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Y M Huang
- Department of Marine Recreation, National Penghu University of Science and Technology, Penghu, Taiwan
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | - L-L Liu
- Department of Oceanography, National Sun Yet-Sen University, Kaohsiung, Taiwan
| | - N J de Voogd
- Naturalis Biodiversity Center, Leiden, the Netherlands.
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43
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Sayed AEDH. UVA-Induced DNA Damage and Apoptosis in Red Blood Cells of the African Catfish Clarias gariepinus. Photochem Photobiol 2018; 94:158-164. [PMID: 28767143 DOI: 10.1111/php.12818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/21/2017] [Indexed: 02/05/2023]
Abstract
Ultraviolet-A light (UVA)-induced DNA damage and repair in red blood cells to investigate the sensitivity of African catfish to UVA exposure is reported. Fishes were irradiated with various doses of UVA light (15, 30, and 60 min day-1 for 3 days). Morphological and nuclear abnormalities in red blood cells were observed in the fish exposed to UVA compared with controls. Morphological alterations such as acanthocytes, crenated cells, swollen cells, teardrop-like cells, hemolyzed cells, and sickle cells were observed. Those alterations were increased after 24 h exposure to UVA light and decreased at 14 days after exposure. The percentage of apoptosis was higher in red blood cells exposed to higher doses of UVA light. No micronuclei were detected, but small nuclear abnormalities such as deformed and eccentric nuclei were observed in some groups. We concluded that exposure to UVA light induced DNA damage, apoptosis, and morphological alterations in red blood cells in catfish; however, catfish were found to be less sensitive to UVA light than wild-type medaka.
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44
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Knight JC, Koustoulidou S, Cornelissen B. Imaging the DNA damage response with PET and SPECT. Eur J Nucl Med Mol Imaging 2017; 44:1065-1078. [PMID: 28058462 PMCID: PMC5397662 DOI: 10.1007/s00259-016-3604-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/16/2016] [Indexed: 01/05/2023]
Abstract
DNA integrity is constantly challenged by endogenous and exogenous factors that can alter the DNA sequence, leading to mutagenesis, aberrant transcriptional activity, and cytotoxicity. Left unrepaired, damaged DNA can ultimately lead to the development of cancer. To overcome this threat, a series of complex mechanisms collectively known as the DNA damage response (DDR) are able to detect the various types of DNA damage that can occur and stimulate the appropriate repair process. Each DNA damage repair pathway leads to the recruitment, upregulation, or activation of specific proteins within the nucleus, which, in some cases, can represent attractive targets for molecular imaging. Given the well-established involvement of DDR during tumorigenesis and cancer therapy, the ability to monitor these repair processes non-invasively using nuclear imaging techniques may facilitate the earlier detection of cancer and may also assist in monitoring response to DNA damaging treatment. This review article aims to provide an overview of recent efforts to develop PET and SPECT radiotracers for imaging of DNA damage repair proteins.
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Affiliation(s)
- James C Knight
- CR-UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ, UK
| | - Sofia Koustoulidou
- CR-UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ, UK
| | - Bart Cornelissen
- CR-UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ, UK.
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Incorvaia L, Passiglia F, Rizzo S, Galvano A, Listȶ A, Barraco N, Maragliano R, Calò V, Natoli C, Ciaccio M, Bazan V, Russo A. "Back to a false normality": new intriguing mechanisms of resistance to PARP inhibitors. Oncotarget 2017; 8:23891-23904. [PMID: 28055979 PMCID: PMC5410353 DOI: 10.18632/oncotarget.14409] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/23/2016] [Indexed: 01/07/2023] Open
Abstract
Several evidences have shown that BRCA mutations increased tumor-cells sensitivity to PARP inhibitors by synthetic lethality leading to an accelerated development of several compounds targeting the PARP enzymes system as anticancer agents for clinical setting. Most of such compounds have been investigated in ovarian and breast cancer, showing promising efficacy in BRCA-mutated patients. Recently clinical studies of PARP-inhibitors have been extended across different tumor types harboring BRCA-mutations, including also "BRCA-like" sporadic tumors with homologous recombination deficiency (HRD). This review summarizes the biological background underlying PARP-inhibition, reporting the results of the most relevant clinical trials carried out in patients treated with PARP inhibitors alone or in combination with chemotherapy. Molecular mechanisms responsible for the occurrence of both primary and acquired resistance have been elucidated, in order to support the development of new treatment strategies.
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Affiliation(s)
- Lorena Incorvaia
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Francesc Passiglia
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Sergio Rizzo
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Antonio Galvano
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Angela Listȶ
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Nadia Barraco
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Rossella Maragliano
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valentina Calò
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Clara Natoli
- Department of Medical, Oral and Biotechnological Sciences, Centre of Ageing Sciences and Translational Medicine - CESI-MeT University “G. D'Annunzio”, Chieti, Italy
| | - Marcello Ciaccio
- Section of Clinical Biochemistry and Clinical Molecular Medicine, Department of Biopathology and Medical Biotechnology, University of Palermo - U.O.C. Laboratory Medicine - CoreLab, Policlinico University Hospital, Palermo, Italy
| | - Viviana Bazan
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
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46
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Mitochondrial transcription factor A (TFAM) rs1937 and AP endonuclease 1 (APE1) rs1130409 alleles are associated with reduced cognitive performance. Neurosci Lett 2017; 645:46-52. [DOI: 10.1016/j.neulet.2017.02.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/15/2017] [Accepted: 02/22/2017] [Indexed: 12/13/2022]
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Zhou T, Pan F, Cao Y, Han Y, Zhao J, Sun H, Zhou X, Wu X, He L, Hu Z, Chen H, Shen B, Guo Z. R152C DNA Pol β mutation impairs base excision repair and induces cellular transformation. Oncotarget 2017; 7:6902-15. [PMID: 26760506 PMCID: PMC4872757 DOI: 10.18632/oncotarget.6849] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 01/03/2016] [Indexed: 12/20/2022] Open
Abstract
DNA polymerase β (Pol β) is a key enzyme in DNA base excision repair (BER), a pathway that maintains genome integrity and stability. Pol β mutations have been detected in various types of cancers, suggesting a possible linkage between Pol β mutations and cancer. However, it is not clear whether and how Pol β mutations cause cancer onset and progression. In the current work, we show that a substitution mutation, R152C, impairs Pol β polymerase activity and BER efficiency. Cells harboring Pol β R152C are sensitive to the DNA damaging agents methyl methanesulfonate (MMS) and H2O2. Moreover, the mutant cells display a high frequency of chromatid breakages and aneuploidy and also form foci. Taken together, our data indicate that Pol β R152C can drive cellular transformation.
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Affiliation(s)
- Ting Zhou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China 210023
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China 210023
| | - Yan Cao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China 210023
| | - Ying Han
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China 210023
| | - Jing Zhao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China 210023
| | - Hongfang Sun
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China 210023
| | - Xiaolong Zhou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China 210023
| | - Xuping Wu
- The Second Hospital of Nanjing, The Second Affiliated Hospital of Southeast University, Nanjing, China 210003
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China 210023
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China 210023
| | - Haoyan Chen
- Division of Gastroenterology and Hepatology, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China 200001
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA 91010
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China 210023
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Aydin AF, Aydıngöz İE, Doğru-Abbasoğlu S, Vural P, Uysal M. Association of Leukotrichia in Vitiligo and Asp148Glu Polymorphism of Apurinic/Apyrimidinic Endonuclease 1. Int J Trichology 2017; 9:171-176. [PMID: 29118522 PMCID: PMC5655626 DOI: 10.4103/ijt.ijt_4_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background: Oxidative stress and increased DNA damage have been implicated in the etiopathogenesis of vitiligo. Oxidative DNA damage is mainly repaired by the base excision repair (BER) pathway. Aim: We sought to determine whether polymorphisms in DNA repair genes may have a role in the pathogenesis of vitiligo. Materials and Methods: We conducted a study including 100 patients with vitiligo and age- and sex-matched 193 control subjects to examine the role of single-nucleotide polymorphisms of BER genes, human 8-oxoG DNA N-glycosylase 1 (codon 326), apurinic/apyrimidinic endonuclease 1 (APE1) (codon 148), and X-ray repair cross-complementing group 1 (codon 399) as risk factors for vitiligo. These polymorphisms were determined by quantitative real-time polymerase chain reaction and melting curve analysis. Results: No significant association was observed between the variant alleles of studied genes and vitiligo. Conclusion: However, we showed that the presence of APE1 148Glu variant allele is associated with leukotrichia. This preliminary study suggests that APE1 (codon 148) polymorphism may play a role in vitiligo pathogenesis.
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Affiliation(s)
- A Fatih Aydin
- Department of Biochemistry, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - İkbal Esen Aydıngöz
- Department of Dermatology, School of Medicine, Acıbadem University, Istanbul, Turkey
| | - Semra Doğru-Abbasoğlu
- Department of Biochemistry, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Pervin Vural
- Department of Biochemistry, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Müjdat Uysal
- Department of Biochemistry, Faculty of Medicine, Istanbul University, Istanbul, Turkey
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Kwiatkowski D, Czarny P, Toma M, Korycinska A, Sowinska K, Galecki P, Bachurska A, Bielecka-Kowalska A, Szemraj J, Maes M, Sliwinski T. Association between Single-Nucleotide Polymorphisms of the hOGG1,NEIL1,APEX1, FEN1,LIG1, and LIG3 Genes and Alzheimer's Disease Risk. Neuropsychobiology 2016; 73:98-107. [PMID: 27010693 DOI: 10.1159/000444643] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 02/11/2016] [Indexed: 11/19/2022]
Abstract
BACKGROUND One of the factors that contribute to Alzheimer's disease (AD) is the DNA damage caused by oxidative stress and inflammation that occurs in nerve cells. It has been suggested that the risk of AD may be associated with an age-dependent reduction of the DNA repair efficiency. Base excision repair (BER) is, among other things, a main repair system of oxidative DNA damage. One of the reasons for the reduced efficiency of this system may be single-nucleotide polymorphisms (SNP) of the genes encoding its proteins. METHODS DNA for genotyping was obtained from the peripheral blood of 281 patients and 150 controls. In the present study, we evaluated the impact of 8 polymorphisms of 6 BER genes on the AD risk. We analyzed the following SNP: c.-468T>G and c.444T>G of APEX1, c.*50C>T and c.*83A>C of LIG3, c.977C>G of OGG1, c.*283C>G of NEIL1, c.-441G>A of FEN1, and c.-7C>T of LIG1. RESULTS We showed that the LIG1 c.-7C>T A/A and LIG3 c.*83A>C A/C variants increased, while the APEX1 c.444T>G G/T, LIG1 c.-7C>T G/, LIG3 c.*83A>C C/C variants reduced, the AD risk. We also evaluated the relation between gene-gene interactions and the AD risk. We showed that combinations of certain BER gene variants such as c.977C>G×c.*50C>T CC/CT, c.444T>G×c.*50C>T GG/CT, c.-468T>G×c.*50C>T GG/CT, c.-441G>Ac.*50C>T×c.*50C>T GG/CT, c.*83A>C× c.*50C>T CT/AC, and c.-7C>T×c.*50C>T CT/GG can substantially positively modulate the risk of AD. CONCLUSIONS In conclusion, we revealed that polymorphisms of BER genes may have a significant effect on the AD risk, and the presence of polymorphic variants may be an important marker for AD.
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Natarajan V. Regulation of DNA repair by non-coding miRNAs. Noncoding RNA Res 2016; 1:64-68. [PMID: 30159412 PMCID: PMC6096415 DOI: 10.1016/j.ncrna.2016.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 10/25/2016] [Accepted: 10/25/2016] [Indexed: 12/19/2022] Open
Abstract
DNA repair is an important signaling mechanism that is necessary to maintain genomic stability. Various types of DNA repair proteins are involved in the repair of different types of DNA damage. However, most of the DNA repair proteins are modified post-translation in order to activate their repair function, such as, ubiquitination, phosphorylation, acetylation, etc. Similarly, DNA repair proteins are also regulated by posttranscriptional modifications. Non-coding microRNAs (miRNAs) induced posttranscriptional regulation of mRNAs has gained attention in recent years. MiRNA-induced regulation of DNA repair proteins is of great interest, owing to its potential role in cancer therapy. In this review, we have summarized the role of different miRNAs in the regulation of various types of DNA repair proteins, which are essential for the maintenance of genomic stability.
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Key Words
- ATM, ataxia-telangiectasia mutated
- ATR, ataxia-telangiectasia mutated related
- BER, base excision repair
- DNA damage
- DNA repair
- DSB repair
- DSB, double strand break
- FA, Fanconi anemia
- Genomic instability
- HR, homologous recombination
- MIS, micro-instability syndrome
- NER
- NER, nucleotide excision repair
- NHEJ, non-homologous end joining
- TLS, translesion synthesis
- miRNAs
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Affiliation(s)
- Venkateswaran Natarajan
- Diagnostic Molecular Oncology Centre, Department of Pathology, National University Hospital, Singapore
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