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Oswalt LE, Eichman BF. NEIL3: A unique DNA glycosylase involved in interstrand DNA crosslink repair. DNA Repair (Amst) 2024; 139:103680. [PMID: 38663144 PMCID: PMC11162926 DOI: 10.1016/j.dnarep.2024.103680] [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: 01/16/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/09/2024]
Abstract
Endonuclease VIII-like 3 (NEIL3) is a versatile DNA glycosylase that repairs a diverse array of chemical modifications to DNA. Unlike other glycosylases, NEIL3 has a preference for lesions within single-strand DNA and at single/double-strand DNA junctions. Beyond its canonical role in base excision repair of oxidized DNA, NEIL3 initiates replication-dependent interstrand DNA crosslink repair as an alternative to the Fanconi Anemia pathway. This review outlines our current understanding of NEIL3's biological functions, role in disease, and three-dimensional structure as it pertains to substrate specificity and catalytic mechanism.
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Affiliation(s)
- Leah E Oswalt
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.
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2
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Norris JL, Rogers LO, Pytko KG, Dannenberg RL, Perreault S, Kaushik V, Kuppa S, Antony E, Hedglin M. Replication protein A dynamically re-organizes on primer/template junctions to permit DNA polymerase δ holoenzyme assembly and initiation of DNA synthesis. Nucleic Acids Res 2024:gkae475. [PMID: 38842913 DOI: 10.1093/nar/gkae475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 05/03/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024] Open
Abstract
DNA polymerase δ (pol δ) holoenzymes, comprised of pol δ and the processivity sliding clamp, PCNA, carry out DNA synthesis during lagging strand replication, initiation of leading strand replication, and the major DNA damage repair and tolerance pathways. Pol δ holoenzymes are assembled at primer/template (P/T) junctions and initiate DNA synthesis in a stepwise process involving the major single strand DNA (ssDNA)-binding protein complex, RPA, the processivity sliding clamp loader, RFC, PCNA and pol δ. During this process, the interactions of RPA, RFC and pol δ with a P/T junction all significantly overlap. A burning issue that has yet to be resolved is how these overlapping interactions are accommodated during this process. To address this, we design and utilize novel, ensemble FRET assays that continuously monitor the interactions of RPA, RFC, PCNA and pol δ with DNA as pol δ holoenzymes are assembled and initiate DNA synthesis. Results from the present study reveal that RPA remains engaged with P/T junctions throughout this process and the RPA•DNA complexes dynamically re-organize to allow successive binding of RFC and pol δ. These results have broad implications as they highlight and distinguish the functional consequences of dynamic RPA•DNA interactions in RPA-dependent DNA metabolic processes.
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Affiliation(s)
- Jessica L Norris
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lindsey O Rogers
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kara G Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Samuel Perreault
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Vikas Kaushik
- The Saint Louis University School of Medicine, Department of Biochemistry and Molecular Biology, St. Louis, MO 63104, USA
| | - Sahiti Kuppa
- The Saint Louis University School of Medicine, Department of Biochemistry and Molecular Biology, St. Louis, MO 63104, USA
| | - Edwin Antony
- The Saint Louis University School of Medicine, Department of Biochemistry and Molecular Biology, St. Louis, MO 63104, USA
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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3
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Shpilman Z, Kidane D. Dysregulation of base excision repair factors associated with low tumor immunogenicity in head and neck cancer: implication for immunotherapy. Ther Adv Med Oncol 2024; 16:17588359241248330. [PMID: 38680291 PMCID: PMC11047243 DOI: 10.1177/17588359241248330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
Background Head and neck squamous carcinoma (HNSCC) is caused by different exogenous risk factors including smoking cigarettes, alcohol consumption, and HPV infection. Base excision repair (BER) is the frontline to repair oxidative DNA damage, which is initiated by the DNA N-glycosylase proteins (OGG1) and other BER factors including DNA polymerase β (POLB). Objective Explore whether BER genes' (OGG1, POLB) overexpression in HNSCC alters genomic integrity, immunogenicity, and its role in prognostic value. Design RNA sequencing (RNA-Seq) and clinical information (age, gender, histological grade, survival status, and stage) of 530 patients of HNSCC were retrieved from the Cancer Genome Atlas. Patients' data are categorized HPV positive or negative to analyze the tumor data including the tumor stage, POLB, and OGG1 gene expression. Methods RNA-Seq of HNSCC data retrieved and mutation count and aneuploidy score were compared using an unpaired t-test. The TIMER algorithm was used to calculate the tumor abundance of six infiltrating immune cells (CD4+ T cells, CD8+ T cells, B cells, neutrophils, macrophages, and dendritic cells) based on RNA-Seq expression profile data. The correlation between the POLB, OGG1, and immune cells was calculated by Spearman correlation analysis using TIMER 2.0. Results Our data analysis reveals that BER genes frequently overexpressed in HNSCC tumors and increase mutation count. In addition, OGG1 and POLB overexpression are associated with low infiltration of immune cells, low immune checkpoint gene expression (PD-1, cytotoxic T-lymphocyte antigen 4, program death ligand 1, and program death ligand 2), and innate immune signaling genes. Furthermore, dysregulated BER factors in Human papillomavirus (HPV) positive tumors had better overall survival. Conclusion Our analysis suggests that dysregulation of the BER genes panel might be a potential prognosis marker and/or an attractive target for an immune checkpoint blockade in HNSCC cancers. However, our observation still requires further experimental-based scientific validation studies.
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Affiliation(s)
- Zackary Shpilman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
- Department of Physiology and Biophysics, College of Medicine, Howard University, Washington, DC, USA
| | - Dawit Kidane
- Department of Physiology and Biophysics, College of Medicine, Howard University, 520 W Street, Northwestern Washington, DC 20059, USA
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Cao H, Zhang Y, Song T, Xia L, Cai Y, Kapranov P. Common occurrence of hotspots of single strand DNA breaks at transcriptional start sites. BMC Genomics 2024; 25:368. [PMID: 38622509 PMCID: PMC11017599 DOI: 10.1186/s12864-024-10284-4] [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: 12/28/2023] [Accepted: 04/03/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND We recently developed two high-resolution methods for genome-wide mapping of two prominent types of DNA damage, single-strand DNA breaks (SSBs) and abasic (AP) sites and found highly complex and non-random patterns of these lesions in mammalian genomes. One salient feature of SSB and AP sites was the existence of single-nucleotide hotspots for both lesions. RESULTS In this work, we show that SSB hotspots are enriched in the immediate vicinity of transcriptional start sites (TSSs) in multiple normal mammalian tissues, however the magnitude of enrichment varies significantly with tissue type and appears to be limited to a subset of genes. SSB hotspots around TSSs are enriched on the template strand and associate with higher expression of the corresponding genes. Interestingly, SSB hotspots appear to be at least in part generated by the base-excision repair (BER) pathway from the AP sites. CONCLUSIONS Our results highlight complex relationship between DNA damage and regulation of gene expression and suggest an exciting possibility that SSBs at TSSs might function as sensors of DNA damage to activate genes important for DNA damage response.
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Affiliation(s)
- Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Yufei Zhang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Tianrong Song
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Lu Xia
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, 361000, Xiamen, China
| | - Ye Cai
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Philipp Kapranov
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, 361102, Xiamen, China.
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Berfelde J, Hildebrand LS, Kuhlmann L, Fietkau R, Distel LV. FEN1 Inhibition as a Potential Novel Targeted Therapy against Breast Cancer and the Prognostic Relevance of FEN1. Int J Mol Sci 2024; 25:2110. [PMID: 38396787 PMCID: PMC10889347 DOI: 10.3390/ijms25042110] [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: 01/23/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
To improve breast cancer treatment and to enable new strategies for therapeutic resistance, therapeutic targets are constantly being studied. Potential targets are proteins of DNA repair and replication and genomic integrity, such as Flap Endonuclease 1 (FEN1). This study investigated the effects of FEN1 inhibitor FEN1-IN-4 in combination with ionizing radiation on cell death, clonogenic survival, the cell cycle, senescence, doubling time, DNA double-strand breaks and micronuclei in breast cancer cells, breast cells and healthy skin fibroblasts. Furthermore, the variation in the baseline FEN1 level and its influence on treatment prognosis was investigated. The cell lines show specific response patterns in the aspects studied and have heterogeneous baseline FEN1 levels. FEN1-IN-4 has cytotoxic, cytostatic and radiosensitizing effects, expressed through increasing cell death by apoptosis and necrosis, G2M share, senescence, double-strand breaks and a reduced survival fraction. Nevertheless, some cells are less affected by the cytotoxicity and fibroblasts show a rather limited response. In vivo, high FEN1 mRNA expression worsens the prognosis of breast cancer patients. Due to the increased expression in breast cancer tissue, FEN1 could represent a new tumor and prognosis marker and FEN1-IN-4 may serve as a new potent agent in personalized medicine and targeted breast cancer therapy.
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Affiliation(s)
- Johanna Berfelde
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Laura S. Hildebrand
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Lukas Kuhlmann
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Rainer Fietkau
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Luitpold V. Distel
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
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Zheng Y, Liu C, Chen J, Tang J, Luo J, Zou D, Tang Z, He J, Bai J. Integrated transcriptomic and biochemical characterization of the mechanisms governing stress responses in soil-dwelling invertebrate (Folsomia candida) upon exposure to dibutyl phthalate. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132644. [PMID: 37820532 DOI: 10.1016/j.jhazmat.2023.132644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Dibutyl phthalate (DBP) is one of the most commonly utilized plasticizers and a frequently detected phthalic acid ester (PAE) compound in soil samples. However, the toxicological effects of DBP on soil-dwelling organisms remain poorly understood. This study employed a multi-biomarker approach to investigate the impact of DBP exposure on Folsomia candida's survival, reproduction, enzyme activity levels, and transcriptional profiles. Analyses of antioxidant biomarkers, including catalase (CAT) and glutathione S-transferase (GST), as well as detoxifying enzymes such as acetylcholinesterase (AChE), Cytochrome P450 (CYP450), and lipid peroxidation (LPO), revealed significant increases in CAT activity, GST levels, and CYP450 expression following treatment with various doses of DBP for 2, 4, 7, or 14 days. Additionally, LPO induction was observed along with significant AChE inhibition. In total, 3175 differentially expressed genes (DEGs) were identified following DBP treatment that were enriched in six Gene Ontology (GO) terms and 144 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including 85 upregulated and 59 downregulated primarily associated with lipid metabolism, signal transduction, DNA repair, and cell growth and death. Overall these results provide foundational insights for further research into the molecular mechanisms underlying responses of soil invertebrates to DBP exposure.
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Affiliation(s)
- Yu Zheng
- Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China; Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China.
| | - Can Liu
- Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China
| | - Jiayi Chen
- Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China
| | - Jianquan Tang
- Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China
| | - Jiali Luo
- Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China
| | - Di Zou
- Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China
| | - Zhen Tang
- Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China
| | - Jiali He
- Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China
| | - Jing Bai
- Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China.
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Reyes-Ábalos AL, Álvarez-Zabaleta M, Olivera-Bravo S, Di Tomaso MV. Astrocyte DNA damage and response upon acute exposure to ethanol and corticosterone. FRONTIERS IN TOXICOLOGY 2024; 5:1277047. [PMID: 38259729 PMCID: PMC10800529 DOI: 10.3389/ftox.2023.1277047] [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: 08/13/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Astrocytes are the glial cells responsible for brain homeostasis, but if injured, they could damage neural cells even deadly. Genetic damage, DNA damage response (DDR), and its downstream cascades are dramatic events poorly studied in astrocytes. Hypothesis and methods: We propose that 1 h of 400 mmol/L ethanol and/or 1 μmol/L corticosterone exposure of cultured hippocampal astrocytes damages DNA, activating the DDR and eliciting functional changes. Immunolabeling against γH2AX (chromatin DNA damage sites), cyclin D1 (cell cycle control), nuclear (base excision repair, BER), and cytoplasmic (anti-inflammatory functions) APE1, ribosomal nucleolus proteins together with GFAP and S100β plus scanning electron microscopy studies of the astrocyte surface were carried out. Results: Data obtained indicate significant DNA damage, immediate cell cycle arrest, and BER activation. Changes in the cytoplasmic signals of cyclin D1 and APE1, nucleolus number, and membrane-attached vesicles strongly suggest a reactivity like astrocyte response without significant morphological changes. Discussion: Obtained results uncover astrocyte genome immediate vulnerability and DDR activation, plus a functional response that might in part, be signaled through extracellular vesicles, evidencing the complex influence that astrocytes may have on the CNS even upon short-term aggressions.
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Affiliation(s)
- Ana Laura Reyes-Ábalos
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Magdalena Álvarez-Zabaleta
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | | | - María Vittoria Di Tomaso
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
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Zhang X, Zhao Q, Wang T, Long Q, Sun Y, Jiao L, Gullerova M. DNA damage response, a double-edged sword for vascular aging. Ageing Res Rev 2023; 92:102137. [PMID: 38007046 DOI: 10.1016/j.arr.2023.102137] [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: 04/14/2023] [Revised: 10/03/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Vascular aging is a major risk factor for age-related cardiovascular diseases, which have high rates of morbidity and mortality. It is characterized by changes in the blood vessels, such as macroscopically increased vascular diameter and intima-medial thickness, chronic inflammation, vascular calcification, arterial stiffening, and atherosclerosis. DNA damage and the subsequent various DNA damage response (DDR) pathways are important causative factors of vascular aging. Deficient DDR, which may result in the accumulation of unrepaired damaged DNA or mutations, can lead to vascular aging. On the other hand, over-activation of some DDR proteins, such as poly (ADP ribose) polymerase (PARP) and ataxia telangiectasia mutated (ATM), also can enhance the process of vascular aging, suggesting that DDR can have both positive and negative effects on vascular aging. Despite the evidence reviewed in this paper, the role of DDR in vascular aging and potential therapeutic targets remain poorly understood and require further investigation.
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Affiliation(s)
- Xiao Zhang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China
| | - Qing Zhao
- M.D. Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Tao Wang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China
| | - Qilin Long
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Yixin Sun
- First Hospital, Peking University, Beijing, China
| | - Liqun Jiao
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China; Department of Interventional Neuroradiology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
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Senavirathne G, London J, Gardner A, Fishel R, Yoder KE. DNA strand breaks and gaps target retroviral intasome binding and integration. Nat Commun 2023; 14:7072. [PMID: 37923737 PMCID: PMC10624929 DOI: 10.1038/s41467-023-42641-4] [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: 03/17/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023] Open
Abstract
Retrovirus integration into a host genome is essential for productive infections. The integration strand transfer reaction is catalyzed by a nucleoprotein complex (Intasome) containing the viral integrase (IN) and the reverse transcribed (RT) copy DNA (cDNA). Previous studies suggested that DNA target-site recognition limits intasome integration. Using single molecule Förster resonance energy transfer (smFRET), we show prototype foamy virus (PFV) intasomes specifically bind to DNA strand breaks and gaps. These break and gap DNA discontinuities mimic oxidative base excision repair (BER) lesion-processing intermediates that have been shown to affect retrovirus integration in vivo. The increased DNA binding events targeted strand transfer to the break/gap site without inducing substantial intasome conformational changes. The major oxidative BER substrate 8-oxo-guanine as well as a G/T mismatch or +T nucleotide insertion that typically introduce a bend or localized flexibility into the DNA, did not increase intasome binding or targeted integration. These results identify DNA breaks or gaps as modulators of dynamic intasome-target DNA interactions that encourage site-directed integration.
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Affiliation(s)
- Gayan Senavirathne
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - James London
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Anne Gardner
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA.
- Molecular Carcinogenesis and Chemoprevention Program, The James Comprehensive Cancer Center and Ohio State University, Columbus, OH, 43210, USA.
| | - Kristine E Yoder
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA.
- Molecular Carcinogenesis and Chemoprevention Program, The James Comprehensive Cancer Center and Ohio State University, Columbus, OH, 43210, USA.
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA.
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Gohil D, Sarker AH, Roy R. Base Excision Repair: Mechanisms and Impact in Biology, Disease, and Medicine. Int J Mol Sci 2023; 24:14186. [PMID: 37762489 PMCID: PMC10531636 DOI: 10.3390/ijms241814186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Base excision repair (BER) corrects forms of oxidative, deamination, alkylation, and abasic single-base damage that appear to have minimal effects on the helix. Since its discovery in 1974, the field has grown in several facets: mechanisms, biology and physiology, understanding deficiencies and human disease, and using BER genes as potential inhibitory targets to develop therapeutics. Within its segregation of short nucleotide (SN-) and long patch (LP-), there are currently six known global mechanisms, with emerging work in transcription- and replication-associated BER. Knockouts (KOs) of BER genes in mouse models showed that single glycosylase knockout had minimal phenotypic impact, but the effects were clearly seen in double knockouts. However, KOs of downstream enzymes showed critical impact on the health and survival of mice. BER gene deficiency contributes to cancer, inflammation, aging, and neurodegenerative disorders. Medicinal targets are being developed for single or combinatorial therapies, but only PARP and APE1 have yet to reach the clinical stage.
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Affiliation(s)
- Dhara Gohil
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
| | - Altaf H. Sarker
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
| | - Rabindra Roy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
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Pinto C, Guerra J, Pinheiro M, Escudeiro C, Santos C, Pinto P, Porto M, Bartosch C, Silva J, Peixoto A, Teixeira MR. Combined germline and tumor mutation signature testing identifies new families with NTHL1 tumor syndrome. Front Genet 2023; 14:1254908. [PMID: 37727376 PMCID: PMC10505957 DOI: 10.3389/fgene.2023.1254908] [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: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 09/21/2023] Open
Abstract
NTHL1 tumor syndrome is an autosomal recessive rare disease caused by biallelic inactivating variants in the NTHL1 gene and which presents a broad tumor spectrum. To contribute to the characterization of the phenotype of this syndrome, we studied 467 index patients by KASP assay or next-generation sequencing, including 228 patients with colorectal polyposis and 239 patients with familial/personal history of multiple tumors (excluding multiple breast/ovarian/polyposis). Three NTHL1 tumor syndrome families were identified in the group of patients with polyposis and none in patients with familial/personal history of multiple tumors. Altogether, we identified nine affected patients with polyposis (two of them diagnosed after initiating colorectal cancer surveillance) with biallelic pathogenic or likely pathogenic NTHL1 variants, as well as two index patients with one pathogenic or likely pathogenic NTHL1 variant in concomitance with a missense variant of uncertain significance. Here we identified a novel inframe deletion classified as likely pathogenic using the ACMG criteria, supported also by tumor mutational signature analysis. Our findings indicate that the NTHL1 tumor syndrome is a multi-tumor syndrome strongly associated with polyposis and not with multiple tumors without polyposis.
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Affiliation(s)
- Carla Pinto
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Pathological, Cytological and Thanatological Anatomy, School of Health, Polytechnic Institute of Porto, Porto, Portugal
| | - Joana Guerra
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Doctoral Programme in Biomedical Sciences, School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Manuela Pinheiro
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Carla Escudeiro
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Catarina Santos
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Pedro Pinto
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Miguel Porto
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - João Silva
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Medical Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Ana Peixoto
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Manuel R. Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
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12
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Li J, Ding H, Zhao Y, Lin M, Song L, Wang W, Dong H, Ma X, Liu W, Han L, Zheng F. DNA Repair-Responsive Engineered Whole Cell Microbial Sensors for Sensitive and High-Throughput Screening of Genotoxic Impurities. Anal Chem 2023; 95:12893-12902. [PMID: 37589895 DOI: 10.1021/acs.analchem.3c02245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Genotoxic impurities (GTIs) occurred in drugs, and food and environment pose a threat to human health. Accurate and sensitive evaluation of GTIs is of significance. Ames assay is the existing gold standard method. However, the pathogenic bacteria model lacks metabolic enzymes and requires mass GTIs, leading to insufficient safety, accuracy, and sensitivity. Whole-cell microbial sensors (WCMSs) can use normal strains to simulate the metabolic environment, achieving safe, sensitive, and high-throughput detection and evaluation for GTIs. Here, based on whether GTIs causing DNA alkylation required metabolic enzymes or not, two DNA repair-responsive engineered WCMS systems were constructed including Escherichia coli-WCMS and yeast-WCMS. A DNA repair-responsive promoter as a sensing element was coupled with an enhanced green fluorescent protein as a reporter to construct plasmids for introduction into WCMS. The ada promoter was screened out in the E. coli-WCMS, while the MAG1 promoter was selected for the yeast-WCMS. Different E. coli and yeast strains were modified by gene knockout and mutation to eliminate the interference and enhance the GTI retention in cells and further improved the sensitivity. Finally, GTI consumption of WCMS for the evaluation of methyl methanesulfonate (MMS) and nitrosamines was decreased to 0.46-8.53 μg and 0.068 ng-2.65 μg, respectively, decreasing 2-3 orders of magnitude compared to traditional methods. This study provided a novel approach to measure GTIs with different DNA damage pathways at a molecular level and facilitated the high-throughput screening and sensitive evaluation of GTIs.
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Affiliation(s)
- Jie Li
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Haotian Ding
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Yuning Zhao
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Mingbin Lin
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Linqi Song
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Wei Wang
- Chongqing Fuling Institute for Food and Drug Control, Chongqing 408102, China
| | - Haijuan Dong
- The Public Laboratory Platform, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao Ma
- Gansu Institute for Drug Control, Lanzhou 730000, China
| | - Wenyuan Liu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
- Zhejiang Center for Safety Study of Drug Substances (Industrial Technology Innovation Platform), Hangzhou 310018, China
| | - Lingfei Han
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Feng Zheng
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
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13
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Tong H, Wang X, Liu Y, Liu N, Li Y, Luo J, Ma Q, Wu D, Li J, Xu C, Yang H. Programmable A-to-Y base editing by fusing an adenine base editor with an N-methylpurine DNA glycosylase. Nat Biotechnol 2023; 41:1080-1084. [PMID: 36624150 DOI: 10.1038/s41587-022-01595-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/01/2022] [Indexed: 01/11/2023]
Abstract
Here we developed an adenine transversion base editor, AYBE, for A-to-C and A-to-T transversion editing in mammalian cells by fusing an adenine base editor (ABE) with hypoxanthine excision protein N-methylpurine DNA glycosylase (MPG). We also engineered AYBE variants enabling targeted editing at genomic loci with higher transversion editing activity (up to 72% for A-to-C or A-to-T editing).
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Affiliation(s)
- Huawei Tong
- HuiGene Therapeutics Co., Ltd., Shanghai, China.
| | - Xuchen Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanhua Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Nana Liu
- HuiGene Therapeutics Co., Ltd., Shanghai, China
| | - Yun Li
- HuiGene Therapeutics Co., Ltd., Shanghai, China
| | - Jiamin Luo
- HuiGene Therapeutics Co., Ltd., Shanghai, China
| | - Qian Ma
- HuiGene Therapeutics Co., Ltd., Shanghai, China
| | - Danni Wu
- HuiGene Therapeutics Co., Ltd., Shanghai, China
| | - Jiyong Li
- HuiGene Therapeutics Co., Ltd., Shanghai, China
| | | | - Hui Yang
- HuiGene Therapeutics Co., Ltd., Shanghai, China.
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, China.
- HuiEdit Therapeutics Co., Ltd., Shanghai, China.
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14
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Tong H, Liu N, Wei Y, Zhou Y, Li Y, Wu D, Jin M, Cui S, Li H, Li G, Zhou J, Yuan Y, Zhang H, Shi L, Yao X, Yang H. Programmable deaminase-free base editors for G-to-Y conversion by engineered glycosylase. Natl Sci Rev 2023; 10:nwad143. [PMID: 37404457 PMCID: PMC10317176 DOI: 10.1093/nsr/nwad143] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/13/2023] [Accepted: 05/13/2023] [Indexed: 07/06/2023] Open
Abstract
Current DNA base editors contain nuclease and DNA deaminase that enables deamination of cytosine (C) or adenine (A), but no method for guanine (G) or thymine (T) editing is available at present. Here we developed a deaminase-free glycosylase-based guanine base editor (gGBE) with G editing ability, by fusing Cas9 nickase with engineered N-methylpurine DNA glycosylase protein (MPG). By several rounds of MPG mutagenesis via unbiased and rational screening using an intron-split EGFP reporter, we demonstrated that gGBE with engineered MPG could increase G editing efficiency by more than 1500 fold. Furthermore, this gGBE exhibited high base editing efficiency (up to 81.2%) and high G-to-T or G-to-C (i.e. G-to-Y) conversion ratio (up to 0.95) in both cultured human cells and mouse embryos. Thus, we have provided a proof-of-concept of a new base editing approach by endowing the engineered DNA glycosylase the capability to selectively excise a new type of substrate.
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Affiliation(s)
| | | | | | | | | | | | - Ming Jin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Shuna Cui
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Hengbin Li
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Guoling Li
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Jingxing Zhou
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Yuan Yuan
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Hainan Zhang
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Linyu Shi
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Xuan Yao
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
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15
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Lirussi L, Nilsen HL. DNA Glycosylases Define the Outcome of Endogenous Base Modifications. Int J Mol Sci 2023; 24:10307. [PMID: 37373453 DOI: 10.3390/ijms241210307] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Chemically modified nucleic acid bases are sources of genomic instability and mutations but may also regulate gene expression as epigenetic or epitranscriptomic modifications. Depending on the cellular context, they can have vastly diverse impacts on cells, from mutagenesis or cytotoxicity to changing cell fate by regulating chromatin organisation and gene expression. Identical chemical modifications exerting different functions pose a challenge for the cell's DNA repair machinery, as it needs to accurately distinguish between epigenetic marks and DNA damage to ensure proper repair and maintenance of (epi)genomic integrity. The specificity and selectivity of the recognition of these modified bases relies on DNA glycosylases, which acts as DNA damage, or more correctly, as modified bases sensors for the base excision repair (BER) pathway. Here, we will illustrate this duality by summarizing the role of uracil-DNA glycosylases, with particular attention to SMUG1, in the regulation of the epigenetic landscape as active regulators of gene expression and chromatin remodelling. We will also describe how epigenetic marks, with a special focus on 5-hydroxymethyluracil, can affect the damage susceptibility of nucleic acids and conversely how DNA damage can induce changes in the epigenetic landscape by altering the pattern of DNA methylation and chromatin structure.
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Affiliation(s)
- Lisa Lirussi
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Hilde Loge Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
- Unit for Precision Medicine, Akershus University Hospital, 1478 Lørenskog, Norway
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16
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Nischwitz E, Schoonenberg VA, Fradera-Sola A, Dejung M, Vydzhak O, Levin M, Luke B, Butter F, Scheibe M. DNA damage repair proteins across the Tree of Life. iScience 2023; 26:106778. [PMID: 37250769 PMCID: PMC10220248 DOI: 10.1016/j.isci.2023.106778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/27/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Genome maintenance is orchestrated by a highly regulated DNA damage response with specific DNA repair pathways. Here, we investigate the phylogenetic diversity in the recognition and repair of three well-established DNA lesions, primarily repaired by base excision repair (BER) and ribonucleotide excision repair (RER): (1) 8-oxoguanine, (2) abasic site, and (3) incorporated ribonucleotide in DNA in 11 species: Escherichia coli, Bacillus subtilis, Halobacterium salinarum, Trypanosoma brucei, Tetrahymena thermophila, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, and Zea mays. Using quantitative mass spectrometry, we identified 337 binding proteins across these species. Of these proteins, 99 were previously characterized to be involved in DNA repair. Through orthology, network, and domain analysis, we linked 44 previously unconnected proteins to DNA repair. Our study presents a resource for future study of the crosstalk and evolutionary conservation of DNA damage repair across all domains of life.
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Affiliation(s)
| | | | | | - Mario Dejung
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Olga Vydzhak
- Institute of Developmental Biology and Neurobiology (IDN), Johannes-Gutenberg-University, 55128 Mainz, Germany
| | - Michal Levin
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes-Gutenberg-University, 55128 Mainz, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Marion Scheibe
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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17
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Wuri L, Burghardt RC, Arosh JA, Long CR, Banu SK. Hexavalent Chromium Disrupts Oocyte Development in Rats by Elevating Oxidative Stress, DNA Double-Strand Breaks, Microtubule Disruption, and Aberrant Segregation of Chromosomes. Int J Mol Sci 2023; 24:10003. [PMID: 37373153 DOI: 10.3390/ijms241210003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Environmental and occupational exposure to hexavalent chromium, Cr(VI), causes female reproductive failures and infertility. Cr(VI) is used in more than 50 industries and is a group A carcinogen, mutagenic and teratogenic, and a male and female reproductive toxicant. Our previous findings indicate that Cr(VI) causes follicular atresia, trophoblast cell apoptosis, and mitochondrial dysfunction in metaphase II (MII) oocytes. However, the integrated molecular mechanism of Cr(VI)-induced oocyte defects is not understood. The current study investigates the mechanism of Cr(VI) in causing meiotic disruption of MII oocytes, leading to oocyte incompetence in superovulated rats. Postnatal day (PND) 22 rats were treated with potassium dichromate (1 and 5 ppm) in drinking water from PND 22-29 and superovulated. MII oocytes were analyzed by immunofluorescence, and images were captured by confocal microscopy and quantified by Image-Pro Plus software, Version 10.0.5. Our data showed that Cr(VI) increased microtubule misalignment (~9 fold), led to missegregation of chromosomes and bulged and folded actin caps, increased oxidative DNA (~3 fold) and protein (~9-12 fold) damage, and increased DNA double-strand breaks (~5-10 fold) and DNA repair protein RAD51 (~3-6 fold). Cr(VI) also induced incomplete cytokinesis and delayed polar body extrusion. Our study indicates that exposure to environmentally relevant doses of Cr(VI) caused severe DNA damage, distorted oocyte cytoskeletal proteins, and caused oxidative DNA and protein damage, resulting in developmental arrest in MII oocytes.
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Affiliation(s)
- Liga Wuri
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Robert C Burghardt
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Joe A Arosh
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Charles R Long
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Sakhila K Banu
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
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18
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Norris JL, Rogers LO, Pytko KG, Dannenberg RL, Perreault S, Kaushik V, Kuppa S, Antony E, Hedglin M. Interplay of macromolecular interactions during assembly of human DNA polymerase δ holoenzymes and initiation of DNA synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539896. [PMID: 37215012 PMCID: PMC10197535 DOI: 10.1101/2023.05.09.539896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In humans, DNA polymerase δ (Pol δ) holoenzymes, comprised of Pol δ and the processivity sliding clamp, proliferating cell nuclear antigen (PCNA), carry out DNA synthesis during lagging strand DNA replication, initiation of leading strand DNA replication, and the major DNA damage repair and tolerance pathways. Pol δ holoenzymes are assembled at primer/template (P/T) junctions and initiate DNA synthesis in a coordinated process involving the major single strand DNA-binding protein complex, replication protein A (RPA), the processivity sliding clamp loader, replication factor C (RFC), PCNA, and Pol δ. Each of these factors interact uniquely with a P/T junction and most directly engage one another. Currently, the interplay between these macromolecular interactions is largely unknown. In the present study, novel Förster Resonance Energy Transfer (FRET) assays reveal that dynamic interactions of RPA with a P/T junction during assembly of a Pol δ holoenzyme and initiation of DNA synthesis maintain RPA at a P/T junction and accommodate RFC, PCNA, and Pol δ, maximizing the efficiency of each process. Collectively, these studies significantly advance our understanding of human DNA replication and DNA repair.
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Affiliation(s)
- Jessica L. Norris
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Lindsey O. Rogers
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Kara G. Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Rachel L. Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Samuel Perreault
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Vikas Kaushik
- The Saint Louis University School of Medicine, Department of Biochemistry and Molecular Biology, St. Louis MO, 63104
| | - Sahiti Kuppa
- The Saint Louis University School of Medicine, Department of Biochemistry and Molecular Biology, St. Louis MO, 63104
| | - Edwin Antony
- The Saint Louis University School of Medicine, Department of Biochemistry and Molecular Biology, St. Louis MO, 63104
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
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19
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Kladova OA, Tyugashev TE, Mikushina ES, Kuznetsov NA, Novopashina DS, Kuznetsova AA. The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain. Cells 2023; 12:cells12091300. [PMID: 37174699 PMCID: PMC10177036 DOI: 10.3390/cells12091300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
To maintain the integrity of the genome, there is a set of enzymatic systems, one of which is base excision repair (BER), which includes sequential action of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases. Normally, BER works efficiently, but the enzymes themselves (whose primary function is the recognition and removal of damaged bases) are subject to amino acid substitutions owing to natural single-nucleotide polymorphisms (SNPs). One of the enzymes in BER is DNA polymerase β (Polβ), whose function is to fill gaps in DNA with complementary dNMPs. It is known that many SNPs can cause an amino acid substitution in this enzyme and a significant decrease in the enzymatic activity. In this study, the activity of four natural variants of Polβ, containing substitution E154A, G189D, M236T, or R254I in the transferase domain, was analyzed using molecular dynamics simulations and pre-steady-state kinetic analyses. It was shown that all tested substitutions lead to a significant reduction in the ability to form a complex with DNA and with incoming dNTP. The G189D substitution also diminished Polβ catalytic activity. Thus, a decrease in the activity of studied mutant forms may be associated with an increased risk of damage to the genome.
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Affiliation(s)
- Olga A Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Timofey E Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena S Mikushina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Daria S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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20
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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:ijms24087293. [PMID: 37108451 PMCID: PMC10138422 DOI: 10.3390/ijms24087293] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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21
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Krishnamoorthy K, Sherman LS, Romagano MP, El Far M, Etchegaray JP, Williams SF, Rameshwar P. Low dose acetyl salicylic acid (LDA) mediates epigenetic changes in preeclampsia placental mesenchymal stem cells similar to cells from healthy pregnancy. Placenta 2023; 137:49-58. [PMID: 37071955 DOI: 10.1016/j.placenta.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 04/20/2023]
Abstract
INTRODUCTION Preeclampsia (PE) affects 2-8% of all pregnancies, and is the leading cause of maternal and fetal morbidity and mortality. We reported on pathophysiological changes in placenta mesenchymal stem cells (P-MSCs) in PE. P-MSCs can be isolated from different layers of the placenta at the interface between the fetus and mother. The ability of MSCs from other sources to be immune licensed as immune suppressor cells indicated that P-MSCs could mitigate fetal rejection. Acetylsalicylic acid (aspirin) is indicated for treating PE. Indeed, low-dose aspirin is recommended to prevent PE in high risk patients. METHODS We conducted robust computational analyses to study changes in gene expression in P-MSCs from PE and healthy term pregnancies as compared with PE-MSCs treated with low dose acetyl salicylic acid (LDA). Confocal microscopy studied phospho-H2AX levels in P-MSCs. RESULTS We identified changes in >400 genes with LDA, similar to levels of healthy pregnancy. The top canonical pathways that incorporate these genes were linked to DNA repair damage - Basic excision repair (BER), Nucleotide excision repair (NER) and DNA replication. A role for the sumoylation (SUMO) pathway, which could regulate gene expression and protein stabilization was significant although reduced as compared to BER and NER pathways. Labeling for phopho-H2AX indicated no evidence of double strand break in PE P-MSCs. DISCUSSION The overlapping of key genes within each pathway suggested a major role for LDA in the epigenetic landscape of PE P-MSCs. Overall, this study showed a new insight into how LDA reset the P-MSCs in PE subjects around the DNA.
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Affiliation(s)
- Kaila Krishnamoorthy
- Dept of Obstetrics, Gynecology and Reproductive Health, D - Maternal Fetal Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Lauren S Sherman
- Dept of Medicine - Hematology/Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA; Rutgers School of Graduate Studies at New Jersey Medical School, Newark, NJ, USA
| | - Matthew P Romagano
- Dept of Obstetrics, Gynecology and Reproductive Health, D - Maternal Fetal Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Markos El Far
- Dept of Medicine - Hematology/Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | | | - Shauna F Williams
- Dept of Obstetrics, Gynecology and Reproductive Health, D - Maternal Fetal Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
| | - Pranela Rameshwar
- Dept of Medicine - Hematology/Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA.
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22
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A Metabolomic and Transcriptomic Study Revealed the Mechanisms of Lumefantrine Inhibition of Toxoplasma gondii. Int J Mol Sci 2023; 24:ijms24054902. [PMID: 36902335 PMCID: PMC10003460 DOI: 10.3390/ijms24054902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/21/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
Toxoplasma gondii is an obligate protozoon that can infect all warm-blooded animals including humans. T. gondii afflicts one-third of the human population and is a detriment to the health of livestock and wildlife. Thus far, traditional drugs such as pyrimethamine and sulfadiazine used to treat T. gondii infection are inadequate as therapeutics due to relapse, long treatment period, and low efficacy in parasite clearance. Novel, efficacious drugs have not been available. Lumefantrine, as an antimalarial, is effective in killing T. gondii but has no known mechanism of action. We combined metabolomics with transcriptomics to investigate how lumefantrine inhibits T. gondii growth. We identified significant alternations in transcripts and metabolites and their associated functional pathways that are attributed to lumefantrine treatment. RH tachyzoites were used to infect Vero cells for three hours and subsequently treated with 900 ng/mL lumefantrine. Twenty-four hours post-drug treatment, we observed significant changes in transcripts associated with five DNA replication and repair pathways. Metabolomic data acquired through liquid chromatography-tandem mass spectrometry (LC-MS) showed that lumefantrine mainly affected sugar and amino acid metabolism, especially galactose and arginine. To investigate whether lumefantrine damages T. gondii DNA, we conducted a terminal transferase assay (TUNEL). TUNEL results showed that lumefantrine significantly induced apoptosis in a dose-dependent manner. Taken together, lumefantrine effectively inhibited T. gondii growth by damaging DNA, interfering with DNA replication and repair, and altering energy and amino acid metabolisms.
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Tarpley M, Chen Y, Bhakat KK. Genome-Wide Binding Analysis of DNA Repair Protein APE1 in Tumor Cells by ChIP-Seq. Methods Mol Biol 2023; 2701:243-252. [PMID: 37574487 DOI: 10.1007/978-1-0716-3373-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The base excision repair (BER) is the primary damage repair pathway for repairing most of the endogenous DNA damage including oxidative base lesions, apurinic/apyrimidinic (AP) sites, and single-strand breaks (SSBs) in the genome. Repair of these damages in cells relies on sequential recruitment and coordinated actions of multiple DNA repair enzymes, which include DNA glycosylases (such as OGG1), AP-endonucleases (APE1), DNA polymerases, and DNA ligases. APE1 plays a key role in the BER pathway by repairing the AP sites and SSBs in the genome. Several methods have been developed to generate a map of endogenous AP sites or SSBs in the genome and the binding of DNA repair proteins. In this chapter, we describe detailed approaches to map genome-wide occupancy or enrichment of APE1 in human cells using chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). Further, we discuss standard bioinformatics approaches for analyzing ChIP-seq data to identify APE1 enrichment or binding peaks in the genome.
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Affiliation(s)
- Mason Tarpley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yingling Chen
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
- Fred and Pamela Buffett Cancer Center, Omaha, NE, USA.
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Roy R. Simultaneous Short- and Long-Patch Base Excision Repair (BER) Assay in Live Mammalian Cells. Methods Mol Biol 2023; 2701:3-19. [PMID: 37574472 DOI: 10.1007/978-1-0716-3373-1_1] [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] [Indexed: 08/15/2023]
Abstract
The base excision repair (BER) pathway repairs small, non-bulky DNA lesions, including oxidized, alkylated, and deaminated bases, and is responsible for the removal of at least 20,000 DNA lesions per cell per day. BER is initiated by DNA damage-specific DNA glycosylases that excise the damaged base and generates an abasic (AP) site or single-strand breaks, which are subsequently repaired in mammalian cells either by single-nucleotide (SN) or multiple-nucleotide incorporation via the SN-BER or long-patch BER (LP-BER) pathway, respectively. This chapter describes a plaque-based host cell reactivation (PL-HCR) assay system for measuring BER mechanisms in live mammalian cells using a plasmid-based assay. After transfection of a phagemid (M13mp18) containing a single modified base (representative BER DNA substrates) within a restriction site into human cells, restriction digestions detect the presence or absence (complete repair) of the adduct by the transformation of the digestion products into E. coli and counting the transformants as plaques. To monitor the patch size, different plasmids are constructed containing C:A mismatches within different restriction sites (inhibiting digestion) at various distances on both sides (5' or 3') of the modified base-containing restriction sites. Using this assay, the percentage of repair events that occur via 5' and 3' patch formation can be quantified.
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Affiliation(s)
- Rabindra Roy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
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25
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Zhang Z, Huang Q, Zhao D, Lian F, Li X, Qi W. The impact of oxidative stress-induced mitochondrial dysfunction on diabetic microvascular complications. Front Endocrinol (Lausanne) 2023; 14:1112363. [PMID: 36824356 PMCID: PMC9941188 DOI: 10.3389/fendo.2023.1112363] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
Diabetes mellitus (DM) is a metabolic disease characterized by chronic hyperglycaemia, with absolute insulin deficiency or insulin resistance as the main cause, and causes damage to various target organs including the heart, kidney and neurovascular. In terms of the pathological and physiological mechanisms of DM, oxidative stress is one of the main mechanisms leading to DM and is an important link between DM and its complications. Oxidative stress is a pathological phenomenon resulting from an imbalance between the production of free radicals and the scavenging of antioxidant systems. The main site of reactive oxygen species (ROS) production is the mitochondria, which are also the main organelles damaged. In a chronic high glucose environment, impaired electron transport chain within the mitochondria leads to the production of ROS, prompts increased proton leakage and altered mitochondrial membrane potential (MMP), which in turn releases cytochrome c (cyt-c), leading to apoptosis. This subsequently leads to a vicious cycle of impaired clearance by the body's antioxidant system, impaired transcription and protein synthesis of mitochondrial DNA (mtDNA), which is responsible for encoding mitochondrial proteins, and impaired DNA repair systems, contributing to mitochondrial dysfunction. This paper reviews the dysfunction of mitochondria in the environment of high glucose induced oxidative stress in the DM model, and looks forward to providing a new treatment plan for oxidative stress based on mitochondrial dysfunction.
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Affiliation(s)
- Ziwei Zhang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Qingxia Huang
- Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Jilin Provincial Key Laboratory of Biomacromolecules of Chinese Medicine, Ministry of Education, Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
- Research Center of Traditional Chinese Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Daqing Zhao
- Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Jilin Provincial Key Laboratory of Biomacromolecules of Chinese Medicine, Ministry of Education, Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Fengmei Lian
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
- Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Fengmei Lian, ; Xiangyan Li, ; Wenxiu Qi,
| | - Xiangyan Li
- Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Jilin Provincial Key Laboratory of Biomacromolecules of Chinese Medicine, Ministry of Education, Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
- *Correspondence: Fengmei Lian, ; Xiangyan Li, ; Wenxiu Qi,
| | - Wenxiu Qi
- Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Jilin Provincial Key Laboratory of Biomacromolecules of Chinese Medicine, Ministry of Education, Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
- *Correspondence: Fengmei Lian, ; Xiangyan Li, ; Wenxiu Qi,
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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: 0] [Impact Index Per Article: 0] [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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Zhang H, Gong Z, Zhu JK. Active DNA demethylation in plants: 20 years of discovery and beyond. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2217-2239. [PMID: 36478523 DOI: 10.1111/jipb.13423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Maintaining proper DNA methylation levels in the genome requires active demethylation of DNA. However, removing the methyl group from a modified cytosine is chemically difficult and therefore, the underlying mechanism of demethylation had remained unclear for many years. The discovery of the first eukaryotic DNA demethylase, Arabidopsis thaliana REPRESSOR OF SILENCING 1 (ROS1), led to elucidation of the 5-methylcytosine base excision repair mechanism of active DNA demethylation. In the 20 years since ROS1 was discovered, our understanding of this active DNA demethylation pathway, as well as its regulation and biological functions in plants, has greatly expanded. These exciting developments have laid the groundwork for further dissecting the regulatory mechanisms of active DNA demethylation, with potential applications in epigenome editing to facilitate crop breeding and gene therapy.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory of Molecular Plant Genetics, Shanghai Centre for Plant Stress Biology, Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Jian-Kang Zhu
- School of Life Sciences, Institute of Advanced Biotechnology, Southern University of Science and Technology, Shenzhen, 518055, China
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Novel Curcumin Monocarbonyl Analogue-Dithiocarbamate hybrid molecules target human DNA ligase I and show improved activity against colon cancer. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02983-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ulhusna A, Murata A, Nakatani K. Inhibitory Effects of Mismatch Binding Molecules on the Repair Reaction of Uracil-Containing DNA. Biochemistry 2022; 61:2522-2530. [PMID: 36250600 DOI: 10.1021/acs.biochem.2c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stable R-loop formed during transcription induces enzyme-mediated deamination of cytosine, and the uracil in the DNA produced activates the base excision repair (BER) pathway. DNA cleavage involved in the BER pathway is thought to be one of the possible causes of trinucleotide repeat instability. Here, we performed an in vitro assay to investigate the effect of a DNA-binding small molecule, naphthyridine carbamate dimer (NCD), on BER enzyme reactions. The gel electrophoretic mobility shift assay (EMSA) and thermal melting analysis revealed the binding of NCD to a 5'-XGG-3'/5'-XGG-3' triad (X = C or U or apurinic/apyrimidinic site), which is a mimic of a BER enzyme substrate. Polyacrylamide gel electrophoresis (PAGE) of the reaction products of these substrates with hSMUG1 and APE1 enzymes in the presence of NCD showed that NCD interfered with the repair reaction in the 5'-XGG-3'/5'-XGG-3' triad. These findings would broaden the potential of small molecules in modulating trinucleotide repeat instability.
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Affiliation(s)
- Anisa Ulhusna
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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30
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Diao W, Yan S, Farrell JD, Wang B, Ye F, Wang Z. Preorganized Internal Electric Field Powers Catalysis in the Active Site of Uracil-DNA Glycosylase. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wenwen Diao
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - James D. Farrell
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fangfu Ye
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325001, China
| | - Zhanfeng Wang
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
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31
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Mitochondrial DNA Repair in Neurodegenerative Diseases and Ageing. Int J Mol Sci 2022; 23:ijms231911391. [PMID: 36232693 PMCID: PMC9569545 DOI: 10.3390/ijms231911391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the only organelles, along with the nucleus, that have their own DNA. Mitochondrial DNA (mtDNA) is a double-stranded circular molecule of ~16.5 kbp that can exist in multiple copies within the organelle. Both strands are translated and encode for 22 tRNAs, 2 rRNAs, and 13 proteins. mtDNA molecules are anchored to the inner mitochondrial membrane and, in association with proteins, form a structure called nucleoid, which exerts a structural and protective function. Indeed, mitochondria have evolved mechanisms necessary to protect their DNA from chemical and physical lesions such as DNA repair pathways similar to those present in the nucleus. However, there are mitochondria-specific mechanisms such as rapid mtDNA turnover, fission, fusion, and mitophagy. Nevertheless, mtDNA mutations may be abundant in somatic tissue due mainly to the proximity of the mtDNA to the oxidative phosphorylation (OXPHOS) system and, consequently, to the reactive oxygen species (ROS) formed during ATP production. In this review, we summarise the most common types of mtDNA lesions and mitochondria repair mechanisms. The second part of the review focuses on the physiological role of mtDNA damage in ageing and the effect of mtDNA mutations in neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease. Considering the central role of mitochondria in maintaining cellular homeostasis, the analysis of mitochondrial function is a central point for developing personalised medicine.
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Wang J, Xia B. Effects of chromium (VI) on the toxicity of benzo[z]pyrene in 16HBE cells. Toxicol Ind Health 2022; 38:733-744. [DOI: 10.1177/07482337221127095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Contamination of human habitats with complex mixtures of heavy metals and polycyclic aromatic hydrocarbons (PAHs) is an important environmental and industrial health problem. Hexavalent chromium (Cr(VI)) and benzo(a)pyrene (B[a] P) are typical of the two, respectively. In recent decades, a great deal of research has focused on their carcinogenicity and mechanisms of action. However, few studies have been conducted to evaluate their combined effects on humans and cells, which has important implications for overall understanding of their toxicity and interaction. In the current study, the combined toxic effects of B[a] P and Cr(VI) were studied in human bronchial epithelial cells (16 HBE). We measured the genotoxic activity and epigenetic changes of these two toxicants alone and in combination on these cells and analyzed the difference between their single and combined toxicity. The results showed that B[a]P caused DNA damage in 16HBE cells in a concentration-dependent manner, while the presence of Cr(VI) showed a sharp decrease in DNA damage, and it inhibited the expression of genes related to base excision repair induced by B[a]P. In addition, Cr(VI) also reduced B[a]P-triggered epigenetic changes in 16HBE cells. In conclusion, the combined effect of B[a]P and Cr(VI) on 16HBE cells was less toxic than single B[a]P exposure, indicating that the combined toxicity of the two toxicants is partially antagonistic. Further research is required to explore the mechanism of this antagonism.
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Affiliation(s)
- Jialin Wang
- College of Food Science and Technology, Hunan Agricultural University, Changsha, China
| | - Bo Xia
- College of Food Science and Technology, Hunan Agricultural University, Changsha, China
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Feng M, Luo J, Wan Y, Zhang J, Lu C, Wang M, Dai L, Cao X, Yang X, Wang Y. Polystyrene Nanoplastic Exposure Induces Developmental Toxicity by Activating the Oxidative Stress Response and Base Excision Repair Pathway in Zebrafish ( Danio rerio). ACS OMEGA 2022; 7:32153-32163. [PMID: 36119974 PMCID: PMC9476205 DOI: 10.1021/acsomega.2c03378] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/22/2022] [Indexed: 02/05/2023]
Abstract
The widespread accumulation of nanoplastics is a growing concern for the environmental and human health. However, studies on the mechanisms of nanoplastic-induced developmental toxicity are still limited. Here, we systematically investigated the potential biological roles of nanoplastic exposure in zebrafish during the early developmental stage. The zebrafish embryos were subjected to exposure to 100 nm polystyrene nanoplastics with different concentrations (0, 100, 200, and 400 mg/L). The results indicated that nanoplastic exposure could decrease the hatching and survival rates of zebrafish embryos. In addition, the developmental toxicity test indicated that nanoplastic exposure exhibits developmental toxicity via the inhibition of the heart rate and body length in zebrafish embryos. Besides, behavioral activity was also significantly suppressed after 96 h of nanoplastic exposure in zebrafish larvae. Further biochemical assays revealed that nanoplastic-induced activation of the oxidative stress responses, including reactive oxygen species accumulation and enhanced superoxide dismutase and catalase activities, might affect developmental toxicity in zebrafish embryos. Furthermore, a quantitative polymerase chain reaction assay demonstrated that the mRNA levels of the base excision repair (BER) pathway-related genes, including lig1, lig3, polb, parp1, pold, fen1, nthl1, apex, xrcc1, and ogg1, were altered in zebrafish embryos for 24 h after nanoplastic exposure, indicating that the activation of the BER pathway would be stimulated after nanoplastic exposure in zebrafish embryos. Therefore, our findings illustrated that nanoplastics could induce developmental toxicity through activation of the oxidative stress response and BER pathways in zebrafish.
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Affiliation(s)
- Meilan Feng
- Key
Laboratory of Bio-resources and Eco-environment of Ministry of Education,
College of Life Science, Sichuan University, Chengdu 610065, China
| | - Juanjuan Luo
- Key
Laboratory of Bio-resources and Eco-environment of Ministry of Education,
College of Life Science, Sichuan University, Chengdu 610065, China
| | - Yiping Wan
- Key
Laboratory of Bio-resources and Eco-environment of Ministry of Education,
College of Life Science, Sichuan University, Chengdu 610065, China
| | - Jiannan Zhang
- Key
Laboratory of Bio-resources and Eco-environment of Ministry of Education,
College of Life Science, Sichuan University, Chengdu 610065, China
| | - Chunjiao Lu
- Guangdong
Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
| | - Maya Wang
- Key
Laboratory of Bio-resources and Eco-environment of Ministry of Education,
College of Life Science, Sichuan University, Chengdu 610065, China
| | - Lu Dai
- Key
Laboratory of Bio-resources and Eco-environment of Ministry of Education,
College of Life Science, Sichuan University, Chengdu 610065, China
| | - Xiaoqian Cao
- Key
Laboratory of Bio-resources and Eco-environment of Ministry of Education,
College of Life Science, Sichuan University, Chengdu 610065, China
| | - Xiaojun Yang
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou 515041,China
| | - Yajun Wang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
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Small molecule-mediated allosteric activation of the base excision repair enzyme 8-oxoguanine DNA glycosylase and its impact on mitochondrial function. Sci Rep 2022; 12:14685. [PMID: 36038587 PMCID: PMC9424235 DOI: 10.1038/s41598-022-18878-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/22/2022] [Indexed: 02/07/2023] Open
Abstract
8-Oxoguanine DNA glycosylase (OGG1) initiates base excision repair of the oxidative DNA damage product 8-oxoguanine. OGG1 is bifunctional; catalyzing glycosyl bond cleavage, followed by phosphodiester backbone incision via a β-elimination apurinic lyase reaction. The product from the glycosylase reaction, 8-oxoguanine, and its analogues, 8-bromoguanine and 8-aminoguanine, trigger the rate-limiting AP lyase reaction. The precise activation mechanism remains unclear. The product-assisted catalysis hypothesis suggests that 8-oxoguanine and analogues bind at the product recognition (PR) pocket to enhance strand cleavage as catalytic bases. Alternatively, they may allosterically activate OGG1 by binding outside of the PR pocket to induce an active-site conformational change to accelerate apurinic lyase. Herein, steady-state kinetic analyses demonstrated random binding of substrate and activator. 9-Deazaguanine, which can't function as a substrate-competent base, activated OGG1, albeit with a lower Emax value than 8-bromoguanine and 8-aminoguanine. Random compound screening identified small molecules with Emax values similar to 8-bromoguanine. Paraquat-induced mitochondrial dysfunction was attenuated by several small molecule OGG1 activators; benefits included enhanced mitochondrial membrane and DNA integrity, less cytochrome c translocation, ATP preservation, and mitochondrial membrane dynamics. Our results support an allosteric mechanism of OGG1 and not product-assisted catalysis. OGG1 small molecule activators may improve mitochondrial function in oxidative stress-related diseases.
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35
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Small-Molecule Inhibitors Targeting FEN1 for Cancer Therapy. Biomolecules 2022; 12:biom12071007. [PMID: 35883563 PMCID: PMC9312813 DOI: 10.3390/biom12071007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
DNA damage repair plays a key role in maintaining genomic stability and integrity. Flap endonuclease 1 (FEN1) is a core protein in the base excision repair (BER) pathway and participates in Okazaki fragment maturation during DNA replication. Several studies have implicated FEN1 in the regulation of other DNA repair pathways, including homologous recombination repair (HRR) and non-homologous end joining (NHEJ). Abnormal expression or mutation of FEN1 in cells can cause a series of pathological responses, leading to various diseases, including cancers. Moreover, overexpression of FEN1 contributes to drug resistance in several types of cancers. All this supports the hypothesis that FEN1 could be a therapeutic target for cancer treatment. Targeting FEN1 has been verified as an effective strategy in mono or combined treatment of cancer. Small-molecule compounds targeting FEN1 have also been developed and detected in cancer regression. In this review, we summarize the recent development of small-molecule inhibitors targeting FEN1 in recent years, thereby expanding their therapeutic potential and application.
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Ahmad HI, Iqbal A, Ijaz N, Ullah MI, Asif AR, Rahman A, Mehmood T, Haider G, Ahmed S, Mahmoud SF, Alghamdi FO, Al Amari HA, Simirgiotis MJ, Chen J. Molecular Evolution of the Activating Transcription Factors Shapes the Adaptive Cellular Responses to Oxidative Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2153996. [PMID: 35873797 PMCID: PMC9300285 DOI: 10.1155/2022/2153996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022]
Abstract
Reactive oxygen species (ROS) play an essential part in physiology of individual cell. ROS can cause damage to various biomolecules, including DNA. The systems that have developed to harness the impacts of ROS are antique evolutionary adaptations that are intricately linked to almost every aspect of cellular function. This research reveals the idea that during evolution, rather than being largely conserved, the molecular pathways reacting to oxidative stress have intrinsic flexibility. The coding sequences of the ATF2, ATF3, ATF4, and ATF6 genes were aligned to examine selection pressure on the genes, which were shown to be very highly conserved among vertebrate species. A total of 33 branches were explicitly evaluated for their capacity to diversify selection. After accounting for multiple testing, significance was determined using the likelihood ratio test with a threshold of p ≤ 0.05. Positive selection signs in these genes were detected across vertebrate lineages. In the selected test branches of our phylogeny, the synonymous rate variation revealed evidence (LRT, p value = 0.011 ≤ 0.05) of gene-wide episodic diversifying selection. As a result, there is evidence that diversifying selection occurred at least once on at least one test branch. These findings indicate that the activities of ROS-responsive systems are also theoretically flexible and may be altered by environmental selection pressure. By determining where the genes encoding these processes are "targeted" during evolution, we may better understand the mechanism of adaptation to oxidative stress during evolution.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Asia Iqbal
- Department of Wild Life and Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Nabeel Ijaz
- Department of Clinical Science, Faculty of Veterinary Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Irfan Ullah
- Department of Pathobiology, Faculty of Veterinary Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Akhtar Rasool Asif
- Department of Animal Sciences, University of Veterinary and Animal Sciences, Jhang, Pakistan
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, China
| | - Abdur Rahman
- Department of Animal Sciences, University of Veterinary and Animal Sciences, Jhang, Pakistan
- Department of Animal Nutrition, Afyon Kocatepe University, Turkey
| | - Tahir Mehmood
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore 53700, Punjab, Pakistan
| | - Ghulam Haider
- Department of Biological Sciences, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki, Pakistan
| | - Shakeel Ahmed
- Instituto de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, 5090000 Valdivia, Chile
| | - Samy F. Mahmoud
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Fatimah Othman Alghamdi
- National Center for Biotechnology King Abdulaziz City for Science and Technology Riyadh, Saudi Arabia
| | - Hala Abdulrahman Al Amari
- National Center for Biotechnology King Abdulaziz City for Science and Technology Riyadh, Saudi Arabia
| | - Mario Juan Simirgiotis
- Instituto de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, 5090000 Valdivia, Chile
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong, Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
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Zhao Y, Qing B, Xu C, Zhao J, Liao Y, Cui P, Wang G, Cai S, Song Y, Cao L, Duan J. DNA Damage Response Gene-Based Subtypes Associated With Clinical Outcomes in Early-Stage Lung Adenocarcinoma. Front Mol Biosci 2022; 9:901829. [PMID: 35813819 PMCID: PMC9257065 DOI: 10.3389/fmolb.2022.901829] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/11/2022] [Indexed: 12/04/2022] Open
Abstract
DNA damage response (DDR) pathways play a crucial role in lung cancer. In this retrospective analysis, we aimed to develop a prognostic model and molecular subtype based on the expression profiles of DDR-related genes in early-stage lung adenocarcinoma (LUAD). A total of 1,785 lung adenocarcinoma samples from one RNA-seq dataset of The Cancer Genome Atlas (TCGA) and six microarray datasets of Gene Expression Omnibus (GEO) were included in the analysis. In the TCGA dataset, a DNA damage response gene (DRG)–based signature consisting of 16 genes was constructed to predict the clinical outcomes of LUAD patients. Patients in the low-DRG score group had better outcomes and lower genomic instability. Then, the same 16 genes were used to develop DRG-based molecular subtypes in the TCGA dataset to stratify early-stage LUAD into two subtypes (DRG1 and DRG2) which had significant differences in clinical outcomes. The Kappa test showed good consistency between molecular subtype and DRG (K = 0.61, p < 0.001). The DRG subtypes were significantly associated with prognosis in the six GEO datasets (pooled estimates of hazard ratio, OS: 0.48 (0.41–0.57), p < 0.01; DFS: 0.50 (0.41–0.62), p < 0.01). Furthermore, patients in the DRG2 group benefited more from adjuvant therapy than standard-of-care, which was not observed in the DRG1 group. In summary, we constructed a DRG-based molecular subtype that had the potential to predict the prognosis of early-stage LUAD and guide the selection of adjuvant therapy for early-stage LUAD patients.
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Affiliation(s)
- Yang Zhao
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Bei Qing
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Chunwei Xu
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- *Correspondence: Liming Cao, ; Jianchun Duan,
| | - Jing Zhao
- Burning Rock Biotech, Guangzhou, China
| | | | - Peng Cui
- Burning Rock Biotech, Guangzhou, China
| | | | | | - Yong Song
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Liming Cao
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Liming Cao, ; Jianchun Duan,
| | - Jianchun Duan
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing, China
- *Correspondence: Liming Cao, ; Jianchun Duan,
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Tan T, Li Y, Tang B, Chen Y, Chen X, Xie Q, Hu Z, Chen G. Knockout of SlALKBH2 weakens the DNA damage repair ability of tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111266. [PMID: 35487670 DOI: 10.1016/j.plantsci.2022.111266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/01/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
During the growth and evolution of plants, genomic DNA is subject to constant assault from endogenous and environmental DNA damage compounds, which will result in mutagenic or genotoxic covalent adducts. Whether for prokaryotes, eukaryotes or even viruses, maintaining genome integrity is critical for the continuation of life. Escherichia coli and mammals have evolved the AlkB family of Fe(II)/alpha-ketoglutarate-dependent dioxygenases that repair DNA alkylation damage. We identified a functional homologue with EsAlkB and HsALKBH2 in tomatoes, and named it SlALKBH2. In our study, the SlALKBH2 knockout mutant showed hypersensitivity to the DNA mutagen MMS and displayed more severe growth abnormalities than wild-type plants under mutagen treatment, such as slow growth, leaf deformation and early senescence. Additionally, genes with high transcriptional activity, such as rDNA, have increased methylation under MMS treatment. In conclusion, this study shows that the tomato SlALKBH2 gene may play an important role in ensuring the integrity of the genome.
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Affiliation(s)
- Tingting Tan
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Yangyang Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Boyan Tang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Yating Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Xinru Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
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Roy A, Kandettu A, Ray S, Chakrabarty S. Mitochondrial DNA replication and repair defects: Clinical phenotypes and therapeutic interventions. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148554. [PMID: 35341749 DOI: 10.1016/j.bbabio.2022.148554] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/06/2022] [Accepted: 03/16/2022] [Indexed: 12/15/2022]
Abstract
Mitochondria is a unique cellular organelle involved in multiple cellular processes and is critical for maintaining cellular homeostasis. This semi-autonomous organelle contains its circular genome - mtDNA (mitochondrial DNA), that undergoes continuous cycles of replication and repair to maintain the mitochondrial genome integrity. The majority of the mitochondrial genes, including mitochondrial replisome and repair genes, are nuclear-encoded. Although the repair machinery of mitochondria is quite efficient, the mitochondrial genome is highly susceptible to oxidative damage and other types of exogenous and endogenous agent-induced DNA damage, due to the absence of protective histones and their proximity to the main ROS production sites. Mutations in replication and repair genes of mitochondria can result in mtDNA depletion and deletions subsequently leading to mitochondrial genome instability. The combined action of mutations and deletions can result in compromised mitochondrial genome maintenance and lead to various mitochondrial disorders. Here, we review the mechanism of mitochondrial DNA replication and repair process, key proteins involved, and their altered function in mitochondrial disorders. The focus of this review will be on the key genes of mitochondrial DNA replication and repair machinery and the clinical phenotypes associated with mutations in these genes.
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Affiliation(s)
- Abhipsa Roy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Amoolya Kandettu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Swagat Ray
- Department of Life Sciences, School of Life and Environmental Sciences, University of Lincoln, Lincoln LN6 7TS, United Kingdom
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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40
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Genome Integrity and Neurological Disease. Int J Mol Sci 2022; 23:ijms23084142. [PMID: 35456958 PMCID: PMC9025063 DOI: 10.3390/ijms23084142] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 02/06/2023] Open
Abstract
Neurological complications directly impact the lives of hundreds of millions of people worldwide. While the precise molecular mechanisms that underlie neuronal cell loss remain under debate, evidence indicates that the accumulation of genomic DNA damage and consequent cellular responses can promote apoptosis and neurodegenerative disease. This idea is supported by the fact that individuals who harbor pathogenic mutations in DNA damage response genes experience profound neuropathological manifestations. The review article here provides a general overview of the nervous system, the threats to DNA stability, and the mechanisms that protect genomic integrity while highlighting the connections of DNA repair defects to neurological disease. The information presented should serve as a prelude to the Special Issue “Genome Stability and Neurological Disease”, where experts discuss the role of DNA repair in preserving central nervous system function in greater depth.
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Structural and Evolutionary Adaptations of Nei-Like DNA Glycosylases Proteins Involved in Base Excision Repair of Oxidative DNA Damage in Vertebrates. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1144387. [PMID: 35419164 PMCID: PMC9001079 DOI: 10.1155/2022/1144387] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/03/2022] [Indexed: 12/25/2022]
Abstract
Oxidative stress is a type of stress that damages DNA and can occur from both endogenous and exogenous sources. Damage to DNA caused by oxidative stress can result in base modifications that promote replication errors and the formation of sites of base loss, which pose unique challenges to the preservation of genomic integrity. However, the adaptive evolution of the DNA repair mechanism is poorly understood in vertebrates. This research aimed to explore the evolutionary relationships, physicochemical characteristics, and comparative genomic analysis of the Nei-like glycosylase gene family involved in DNA base repair in the vertebrates. The genomic sequences of NEIL1, NEIL2, and NEIL3 genes were aligned to observe selection constraints in the genes, which were relatively low conserved across vertebrate species. The positive selection signals were identified in these genes across the vertebrate lineages. We identified that only about 2.7% of codons in these genes were subjected to positive selection. We also revealed that positive selection pressure was increased in the Fapy-DNA-glyco and H2TH domain, which are involved in the base excision repair of DNA that has been damaged by oxidative stress. Gene structure, motif, and conserved domain analysis indicated that the Nei-like glycosylase genes in mammals and avians are evolutionarily low conserved compared to other glycosylase genes in other “vertebrates” species. This study revealed that adaptive selection played a critical role in the evolution of Nei-like glycosylase in vertebrate species. Systematic comparative genome analyses will give key insights to elucidate the links between DNA repair and the development of lifespan in various organisms as more diverse vertebrate genome sequences become accessible.
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Oxidative Stress in Human Pathology and Aging: Molecular Mechanisms and Perspectives. Cells 2022; 11:cells11030552. [PMID: 35159361 PMCID: PMC8833991 DOI: 10.3390/cells11030552] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Reactive oxygen and nitrogen species (RONS) are generated through various endogenous and exogenous processes; however, they are neutralized by enzymatic and non-enzymatic antioxidants. An imbalance between the generation and neutralization of oxidants results in the progression to oxidative stress (OS), which in turn gives rise to various diseases, disorders and aging. The characteristics of aging include the progressive loss of function in tissues and organs. The theory of aging explains that age-related functional losses are due to accumulation of reactive oxygen species (ROS), their subsequent damages and tissue deformities. Moreover, the diseases and disorders caused by OS include cardiovascular diseases [CVDs], chronic obstructive pulmonary disease, chronic kidney disease, neurodegenerative diseases and cancer. OS, induced by ROS, is neutralized by different enzymatic and non-enzymatic antioxidants and prevents cells, tissues and organs from damage. However, prolonged OS decreases the content of antioxidant status of cells by reducing the activities of reductants and antioxidative enzymes and gives rise to different pathological conditions. Therefore, the aim of the present review is to discuss the mechanism of ROS-induced OS signaling and their age-associated complications mediated through their toxic manifestations in order to devise effective preventive and curative natural therapeutic remedies.
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43
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Signal-on/signal-off bead-based assays for the multiplexed monitoring of base excision repair activities by flow cytometry. Anal Bioanal Chem 2022; 414:2029-2040. [DOI: 10.1007/s00216-021-03849-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/03/2021] [Accepted: 12/13/2021] [Indexed: 11/01/2022]
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44
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DNA Methyltransferases and DNA Damage. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:349-361. [DOI: 10.1007/978-3-031-11454-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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45
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Onodera A, Kiuchi M, Kokubo K, Nakayama T. Epigenetic regulation of inflammation by CxxC domain‐containing proteins*. Immunol Rev 2022. [DOI: 10.1111/imr.13056
expr 964170082 + 969516512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
- Atsushi Onodera
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
- Institute for Global Prominent Research Chiba University Chiba Japan
| | - Masahiro Kiuchi
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
| | - Kota Kokubo
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
| | - Toshinori Nakayama
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
- AMED‐CREST, AMED Chiba Japan
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46
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De Silva WGM, Han JZR, Yang C, Tongkao-On W, McCarthy BY, Ince FA, Holland AJA, Tuckey RC, Slominski AT, Abboud M, Dixon KM, Rybchyn MS, Mason RS. Evidence for Involvement of Nonclassical Pathways in the Protection From UV-Induced DNA Damage by Vitamin D-Related Compounds. JBMR Plus 2021; 5:e10555. [PMID: 34950826 PMCID: PMC8674768 DOI: 10.1002/jbm4.10555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/29/2021] [Accepted: 09/07/2021] [Indexed: 01/26/2023] Open
Abstract
The vitamin D hormone, 1,25dihydroxyvitamin D3 (1,25(OH)2D3), and related compounds derived from vitamin D3 or lumisterol as a result of metabolism via the enzyme CYP11A1, have been shown, when applied 24 hours before or immediately after UV irradiation, to protect human skin cells and skin from DNA damage due to UV exposure, by reducing both cyclobutane pyrimidine dimers (CPD) and oxidative damage in the form of 8‐oxo‐7,8‐dihydro‐2′‐deoxyguanosine (8‐OHdG). We now report that knockdown of either the vitamin D receptor or the endoplasmic reticulum protein ERp57 by small, interfering RNA (siRNA) abolished the reductions in UV‐induced DNA damage with 20‐hydroxyvitamin D3 or 24‐hydroxylumisterol3, as previously shown for 1,25(OH)2D3. Treatment with 1,25(OH)2D3 reduced oxygen consumption rates in UV‐exposed and sham‐exposed human keratinocytes and reduced phosphorylation of cyclic AMP response binding element protein (CREB). Both these actions have been shown to inhibit skin carcinogenesis after chronic UV exposure, consistent with the anticarcinogenic activity of 1,25(OH)2D3. The requirement for a vitamin D receptor for the photoprotective actions of 1,25(OH)2D3 and of naturally occurring CYP11A1‐derived vitamin D–related compounds may explain why mice lacking the vitamin D receptor in skin are more susceptible to UV‐induced skin cancers, whereas mice lacking the 1α‐hydroxylase and thus unable to make 1,25(OH)2D3 are not more susceptible. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
| | - Jeremy Zhuo Ru Han
- Physiology, School of Medical Sciences and Bosch Institute University of Sydney Sydney NSW Australia
| | - Chen Yang
- Physiology, School of Medical Sciences and Bosch Institute University of Sydney Sydney NSW Australia
| | - Wannit Tongkao-On
- Physiology, School of Medical Sciences and Bosch Institute University of Sydney Sydney NSW Australia
| | - Bianca Yuko McCarthy
- Physiology, School of Medical Sciences and Bosch Institute University of Sydney Sydney NSW Australia
| | - Furkan Akif Ince
- Anatomy & Histology, School of Medical Sciences and Bosch Institute University of Sydney Sydney NSW Australia
| | - Andrew J A Holland
- Department of Paediatric Surgery, The Children's Hospital at Westmead University of Sydney Sydney NSW Australia
| | | | - Andrzej T Slominski
- Department of Dermatology University of Alabama at Birmingham Birmingham AL USA
| | | | - Katie Marie Dixon
- Anatomy & Histology, School of Medical Sciences and Bosch Institute University of Sydney Sydney NSW Australia
| | - Mark Stephen Rybchyn
- Physiology, School of Medical Sciences and Bosch Institute University of Sydney Sydney NSW Australia.,School of Chemical Engineering University of NSW Sydney NSW Australia
| | - Rebecca Sara Mason
- Physiology, School of Medical Sciences and Bosch Institute University of Sydney Sydney NSW Australia.,School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
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47
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Structural Insights into the Specificity of 8-Oxo-7,8-dihydro-2′-deoxyguanosine Bypass by Family X DNA Polymerases. Genes (Basel) 2021; 13:genes13010015. [PMID: 35052363 PMCID: PMC8774566 DOI: 10.3390/genes13010015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 11/23/2022] Open
Abstract
8-oxo-guanine (8OG) is a common base lesion, generated by reactive oxygen species, which has been associated with human diseases such as cancer, aging-related neurodegenerative disorders and atherosclerosis. 8OG is highly mutagenic, due to its dual-coding potential it can pair both with adenine or cytidine. Therefore, it creates a challenge for DNA polymerases striving to correctly replicate and/or repair genomic or mitochondrial DNA. Numerous structural studies provide insights into the mechanistic basis of the specificity of 8OG bypass by DNA polymerases from different families. Here, we focus on how repair polymerases from Family X (Pols β, λ and µ) engage DNA substrates containing the oxidized guanine. We review structures of binary and ternary complexes for the three polymerases, which represent distinct steps in their catalytic cycles—the binding of the DNA substrate and the incoming nucleotide, followed by its insertion and extension. At each of these steps, the polymerase may favor or exclude the correct C or incorrect A, affecting the final outcome, which varies depending on the enzyme.
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48
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Onodera A, Kiuchi M, Kokubo K, Nakayama T. Epigenetic regulation of inflammation by CxxC domain-containing proteins. Immunol Rev 2021; 305:137-151. [PMID: 34935162 DOI: 10.1111/imr.13056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/03/2021] [Accepted: 11/12/2021] [Indexed: 12/14/2022]
Abstract
Epigenetic regulation of gene transcription in the immune system is important for proper control of protective and pathogenic inflammation. Aberrant epigenetic modifications are often associated with dysregulation of the immune cells, including lymphocytes and macrophages, leading to pathogenic inflammation and autoimmune diseases. Two classical epigenetic markers-histone modifications and DNA cytosine methylation, the latter is the 5 position of the cytosine base in the context of CpG dinucleotides-play multiple roles in the immune system. CxxC domain-containing proteins, which basically bind to the non-methylated CpG (i.e., epigenetic "readers"), often function as "writers" of the epigenetic markers via their catalytic domain within the proteins or by interacting with other epigenetic modifiers. We herein report the most recent advances in our understanding of the functions of CxxC domain-containing proteins in the immune system and inflammation, mainly focusing on T cells and macrophages.
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Affiliation(s)
- Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Institute for Global Prominent Research, Chiba University, Chiba, Japan
| | - Masahiro Kiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,AMED-CREST, AMED, Chiba, Japan
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49
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Zhou S, Zhu Q, Liu H, Jiang S, Zhang X, Peng C, Yang G, Li J, Cheng L, Zhong R, Zeng Q, Miao X, Lu Q. Associations of polycyclic aromatic hydrocarbons exposure and its interaction with XRCC1 genetic polymorphism with lung cancer: A case-control study. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118077. [PMID: 34523522 DOI: 10.1016/j.envpol.2021.118077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
Humans are extensively exposed to polycyclic aromatic hydrocarbons (PAHs) daily via multiple pathways. Epidemiological studies have demonstrated that occupational exposure to PAHs increases the risk of lung cancer, but related studies in the general population are limited. Hence, we conducted a case-control study among the Chinese general population to investigate the associations between PAHs exposure and lung cancer risk and analyze the modifications of genetic polymorphisms in DNA repair genes. In this study, we enrolled 122 lung cancer cases and 244 healthy controls in Wuhan, China. Urinary PAHs metabolites were determined by gas chromatography-mass spectrometry, and rs25487 in X-ray repair cross-complementation 1 (XRCC1) gene was genotyped by the Agena Bioscience MassARRAY System. Then, multivariable logistic regression models were performed to estimate the potential associations. We found that urinary hydroxynaphthalene (OH-Nap), hydroxyphenanthrene (OH-Phe) and the sum of hydroxy PAHs (∑OH-PAHs) levels were significantly higher in lung cancer cases than those in controls. After adjusting for gender, age, BMI, smoking status, smoking pack-years, drinking status and family history, urinary ∑OH-Nap and ∑OH-Phe levels were positively associated with lung cancer risk, with dose-response relationships. Compared with those in the lowest tertiles, individuals in the highest tertiles of ∑OH-Nap and ∑OH-Phe had a 2.13-fold (95% CI: 1.10, 4.09) and 2.45-fold (95% CI: 1.23, 4.87) increased risk of lung cancer, respectively. Effects of gender, age, smoking status and smoking pack-years on the associations of PAHs exposure with lung cancer risk were shown in the subgroup analysis. Furthermore, associations of urinary ∑OH-Nap and ∑OH-PAHs levels with lung cancer risk were modified by XRCC1 rs25487 (Pinteraction ≤ 0.025), and were more pronounced in wild-types of rs25487. These findings suggest that environmental exposure to naphthalene and phenanthrene is associated with increased lung cancer risk, and polymorphism of XRCC1 rs25487 might modify the naphthalene exposure-related lung cancer effect.
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Affiliation(s)
- Shuang Zhou
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Qiuqi Zhu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Huimin Liu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Shunli Jiang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China; Key Laboratory of Occupational Health and Environmental Medicine, Department of Public Health, Jining Medical University, 133 Hehua Road, Jining, Shandong, 272067, China
| | - Xu Zhang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Cheng Peng
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Guanlin Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Road, Wuhan, Hubei, 430030, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Road, Wuhan, Hubei, 430030, China
| | - Rong Zhong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Qiang Zeng
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Xiaoping Miao
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Qing Lu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China.
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Higgs EB, Godschalk R, Langie SAS, van Schooten FJ, Hodges NJ. Upregulation of mNEIL3 in Ogg1-null cells is a potential backup mechanism for 8-oxoG repair. Mutagenesis 2021; 36:437-444. [PMID: 34644377 DOI: 10.1093/mutage/geab038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
Reactive oxygen species formation and resultant oxidative damage to DNA are ubiquitous events in cells, the homeostasis of which can be dysregulated in a range of pathological conditions. Base excision repair (BER) is the primary repair mechanism for oxidative genomic DNA damage. One prevalent oxidised base modification, 8-oxoguanine (8-oxoG), is recognised by 8-oxoguanine glycosylase-1 (OGG1) initiating removal and repair via BER. Surprisingly, Ogg1 null mouse embryonic fibroblasts (mOgg1-/- MEFs) do not accumulate 8-oxoG in the genome to the extent expected. This suggests that there are backup repair mechanisms capable of repairing 8-oxoG in the absence of OGG1. In the current study, we identified components of NER (Ercc1, Ercc4, Ercc5), BER (Lig1, Tdg, Nthl1, Mpg, Mgmt, NEIL3), MMR (Mlh1, Msh2, Msh6) and DSB (Brip1, Rad51d, Prkdc) pathways that are transcriptionally elevated in mOgg1-/- MEFs. Interestingly, all three nucleotide excision repair genes identified: Ercc1 (2.5 ± 0.2-fold), Ercc4 (1.5 ± 0.1-fold) and Ercc5 (1.7 ± 0.2-fold) have incision activity. There was also a significant functional increase in NER activity (42.0 ± 7.9%) compared to WT MEFs. We also observed upregulation of both Neil3 mRNA (37.9 ± 1.6-fold) and protein in mOgg1-/- MEFs. This was associated with a 3.4 ± 0.4-fold increase in NEIL3 substrate sites in genomic DNA of cells treated with BSO, consistent with the ability of NEIL3 to remove 8-oxoG oxidation products from genomic DNA. In conclusion, we suggest that in Ogg1-null cells, upregulation of multiple DNA repair proteins including incision components of the NER pathway and Neil3 are important compensatory responses to prevent the accumulation of genomic 8-oxoG.
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Affiliation(s)
- Ellen B Higgs
- School of Biosciences, The University of Birmingham, Birmingham, UK.,Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Roger Godschalk
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Sabine A S Langie
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Frederik-Jan van Schooten
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Nikolas J Hodges
- School of Biosciences, The University of Birmingham, Birmingham, UK
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