1
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Parolini I, Degrassi M, Spadaro F, Caponnetto F, Fecchi K, Mastantuono S, Zhouyiyuan X, Demple B, Cesselli D, Tell G. Intraluminal vesicle trafficking is involved in the secretion of base excision repair protein APE1. FEBS J 2024; 291:2849-2875. [PMID: 38401056 DOI: 10.1111/febs.17088] [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: 07/18/2023] [Revised: 11/24/2023] [Accepted: 01/31/2024] [Indexed: 02/26/2024]
Abstract
The apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) is an essential enzyme of the base excision repair pathway of non-distorting DNA lesions. In response to genotoxic treatments, APE1 is highly secreted (sAPE1) in association with small-extracellular vesicles (EVs). Interestingly, its presence in the serum of patients with hepatocellular or non-small-cell-lung cancers may represent a prognostic biomarker. The mechanism driving APE1 to associate with EVs is unknown, but is of paramount importance in better understanding the biological roles of sAPE1. Because APE1 lacks an endoplasmic reticulum-targeting signal peptide, it can be secreted through an unconventional protein secretion endoplasmic reticulum-Golgi-independent pathway, which includes an endosome-based secretion of intraluminal vesicles, mediated by multivesicular bodies (MVBs). Using HeLa and A549 cell lines, we investigated the role of endosomal sorting complex required for transport protein pathways (either-dependent or -independent) in the constitutive or trichostatin A-induced secretion of sAPE1, by means of manumycin A and GW 4869 treatments. Through an in-depth biochemical analysis of late-endosomes (LEs) and early-endosomes (EEs), we observed that the distribution of APE1 on density gradient corresponded to that of LE-CD63, LE-Rab7, EE-EEA1 and EE-Rab 5. Interestingly, the secretion of sAPE1, induced by cisplatin genotoxic stress, involved an autophagy-based unconventional secretion requiring MVBs. The present study enlightens the central role played by MVBs in the secretion of sAPE1 under various stimuli, and offers new perspectives in understanding the biological relevance of sAPE1 in cancer cells.
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Affiliation(s)
- Isabella Parolini
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Italy
| | - Monica Degrassi
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Italy
| | - Francesca Spadaro
- Core Facilities - Confocal Microscopy Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Federica Caponnetto
- Department of Medicine, University of Udine, Italy
- Institute of Pathology, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Katia Fecchi
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Serena Mastantuono
- Department of Medicine, University of Udine, Italy
- Institute of Pathology, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Xue Zhouyiyuan
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Bruce Demple
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Daniela Cesselli
- Department of Medicine, University of Udine, Italy
- Institute of Pathology, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Italy
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2
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Gao S, Tahara Y, Kool ET, Greenberg MM. Promoter dependent RNA polymerase II bypass of the epimerizable DNA lesion, Fapy•dG and 8-Oxo-2'-deoxyguanosine. Nucleic Acids Res 2024:gkae529. [PMID: 38908029 DOI: 10.1093/nar/gkae529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024] Open
Abstract
Formamidopyrimidine (Fapy•dG) is a major lesion arising from oxidation of dG that is produced from a common chemical precursor of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo). In human cells, replication of single-stranded shuttle vectors containing Fapy•dG is more mutagenic than 8-OxodGuo. Here, we present the first data regarding promoter dependent RNA polymerase II bypass of Fapy•dG. 8-OxodGuo bypass was examined side-by-side. Experiments were carried out using double-stranded shuttle vectors in HeLa cell nuclear lysates and in HEK 293T cells. The lesions do not significantly block transcriptional bypass efficiency. Less than 2% adenosine incorporation occurred in cells when the lesions were base paired with dC. Inhibiting base excision repair in HEK 293T cells significantly increased adenosine incorporation, particularly from Fapy•dG:dC bypass which yielded ∼25% adenosine incorporation. No effect was detected upon transcriptional bypass of either lesion in nucleotide excision repair deficient cells. Transcriptional mutagenesis was significantly higher when shuttle vectors containing dA opposite one of the lesions were employed. For Fapy•dG:dA bypass, adenosine incorporation was greater than 85%; whereas 8-OxodGuo:dA yielded >20% point mutations. The combination of more frequent replication mistakes and greater error-prone Pol II bypass suggest that Fapy•dG is more mutagenic than 8-OxodGuo.
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Affiliation(s)
- Shijun Gao
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yuki Tahara
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
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3
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Gao S, Oden P, Ryan B, Yang H, Freudenthal B, Greenberg M. Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase β. Nucleic Acids Res 2024; 52:5392-5405. [PMID: 38634780 PMCID: PMC11109955 DOI: 10.1093/nar/gkae277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
N6-(2-deoxy-α,β-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido-pyrimidine (Fapy•dG) is formed from a common intermediate and in comparable amounts to the well-studied mutagenic DNA lesion 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo). Fapy•dG preferentially gives rise to G → T transversions and G → A transitions. However, the molecular basis by which Fapy•dG is processed by DNA polymerases during this mutagenic process remains poorly understood. To address this we investigated how DNA polymerase β (Pol β), a model mammalian polymerase, bypasses a templating Fapy•dG, inserts Fapy•dGTP, and extends from Fapy•dG at the primer terminus. When Fapy•dG is present in the template, Pol β incorporates TMP less efficiently than either dCMP or dAMP. Kinetic analysis revealed that Fapy•dGTP is a poor substrate but is incorporated ∼3-times more efficiently opposite dA than dC. Extension from Fapy•dG at the 3'-terminus of a nascent primer is inefficient due to the primer terminus being poorly positioned for catalysis. Together these data indicate that mutagenic bypass of Fapy•dG is likely to be the source of the mutagenic effects of the lesion and not Fapy•dGTP. These experiments increase our understanding of the promutagenic effects of Fapy•dG.
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Affiliation(s)
- Shijun Gao
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Peyton N Oden
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, KS City, KS 66160, USA
| | - Benjamin J Ryan
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, KS City, KS 66160, USA
| | - Haozhe Yang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, KS City, KS 66160, USA
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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4
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Fleming AM, Guerra Castañaza Jenkins BL, Buck BA, Burrows CJ. DNA Damage Accelerates G-Quadruplex Folding in a Duplex-G-Quadruplex-Duplex Context. J Am Chem Soc 2024; 146. [PMID: 38602473 PMCID: PMC11046481 DOI: 10.1021/jacs.4c00960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Molecular details for the impact of DNA damage on folding of potential G-quadruplex sequences (PQSs) to noncanonical DNA structures involved in gene regulation are poorly understood. Here, the effects of DNA base damage and strand breaks on PQS folding kinetics were studied in the context of the VEGF promoter sequence embedded between two DNA duplex anchors, termed a duplex-G-quadruplex-duplex (DGD) motif. This DGD scaffold imposes constraints on the PQS folding process that more closely mimic those found in genomic DNA. Folding kinetics were monitored by circular dichroism (CD) to find folding half-lives ranging from 2 s to 12 min depending on the DNA damage type and sequence position. The presence of Mg2+ ions and G-quadruplex (G4)-binding protein APE1 facilitated the folding reactions. A strand break placing all four G runs required for G4 formation on one side of the break accelerated the folding rate by >150-fold compared to the undamaged sequence. Combined 1D 1H NMR and CD analyses confirmed that isothermal folding of the VEGF-DGD constructs yielded spectral signatures that suggest the formation of G4 motifs and demonstrated a folding dependency on the nature and location of DNA damage. Importantly, the PQS folding half-lives measured are relevant to replication, transcription, and DNA repair time frames.
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Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
| | | | - Bethany A. Buck
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
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5
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Zhao NN, Wang Q, Yang DM, Li DL, Han Y, Zhao S, Zou X, Zhang CY. Elongation and Ligation-Mediated Differential Coding for Label-Free and Locus-Specific Analysis of 8-Oxo-7,8-dihydroguanine in DNA. Anal Chem 2024; 96:5323-5330. [PMID: 38501982 DOI: 10.1021/acs.analchem.4c00387] [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: 03/20/2024]
Abstract
Oxidative DNA damage is closely associated with the occurrence of numerous human diseases and cancers. 8-Oxo-7,8-dihydroguanine (8-oxoG) is the most prevalent form of DNA damage, and it has become not only an oxidative stress biomarker but also a new epigenetic-like biomarker. However, few approaches are available for the locus-specific detection of 8-oxoG because of the low abundance of 8-oxoG damage in DNA and the limited sensitivity of existing assays. Herein, we demonstrate the elongation and ligation-mediated differential coding for label-free and locus-specific analysis of 8-oxoG in DNA. This assay is very simple without the involvement of any specific labeled probes, complicated steps, and large sample consumption. The utilization of Bsu DNA polymerase can specifically initiate a single-base extension reaction to incorporate dATP into the opposite position of 8-oxoG, endowing this assay with excellent selectivity. The introduction of cascade amplification reaction significantly enhances the sensitivity. The proposed method can monitor 8-oxoG with a limit of detection of 8.21 × 10-19 M (0.82 aM), and it can identify as low as 0.001% 8-oxoG damage from a complex mixture with excessive undamaged DNAs. This method can be further applied to measure 8-oxoG levels in the genomic DNA of human cells under diverse oxidative stress, holding prospect potential in the dynamic monitoring of critical 8-oxoG sites, early clinical diagnosis, and gene damage-related biomedical research.
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Affiliation(s)
- Ning-Ning Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Qian Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Dong-Ming Yang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Dong-Ling Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yun Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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6
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Hussen AS, Kravitz HL, Freudenthal BD, Whitaker AM. Oxidative DNA damage on the VEGF G-quadruplex forming promoter is repaired via long-patch BER. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:25-39. [PMID: 37606505 PMCID: PMC10984112 DOI: 10.1002/em.22570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/20/2023] [Indexed: 08/23/2023]
Abstract
In response to oxidative damage, base excision repair (BER) enzymes perturb the structural equilibrium of the VEGF promoter between B-form and G4 DNA conformations, resulting in epigenetic-like modifications of gene expression. However, the mechanistic details remain enigmatic, including the activity and coordination of BER enzymes on the damaged G4 promoter. To address this, we investigated the ability of each BER factor to conduct its repair activity on VEGF promoter G4 DNA substrates by employing pre-steady-state kinetics assays and in vitro coupled BER assays. OGG1 was able to initiate BER on double-stranded VEGF promoter G4 DNA substrates. Moreover, pre-steady-state kinetics revealed that compared to B-form DNA, APE1 repair activity on the G4 was decreased ~two-fold and is the result of slower product release as opposed to inefficient strand cleavage. Interestingly, Pol β performs multiple insertions on G4 substrates via strand displacement DNA synthesis in contrast to a single insertion on B-form DNA. The multiple insertions inhibit ligation of the Pol β products, and hence BER is not completed on the VEGF G4 promoter substrates through canonical short-patch BER. Instead, repair requires the long-patch BER flap-endonuclease activity of FEN1 in response to the multiple insertions by Pol β prior to ligation. Because the BER proteins and their repair activities are a key part of the VEGF transcriptional enhancement in response to oxidative DNA damage of the G4 VEGF promoter, the new insights reported here on BER activity in the context of this promoter are relevant toward understanding the mechanism of transcriptional regulation.
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Affiliation(s)
- Adil S. Hussen
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Haley L. Kravitz
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Bret D. Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Amy M. Whitaker
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
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7
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Yan S, Gaddameedhi S, Sobol RW. Inspiring basic and applied research in genome integrity mechanisms: Dedication to Samuel H. Wilson. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:4-8. [PMID: 38619433 PMCID: PMC11110888 DOI: 10.1002/em.22595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024]
Abstract
This Special Issue (SI) of Environmental and Molecular Mutagenesis (EMM), entitled "Inspiring Basic and Applied Research in Genome Integrity Mechanisms," is to update the community on recent findings and advances on genome integrity mechanisms with emphasis on their importance for basic and environmental health sciences. This SI includes two research articles, one brief research communication, and four reviews that highlight cutting edge research findings and perspectives, from both established leaders and junior trainees, on DNA repair mechanisms. In particular, the authors provided an updated understanding on several distinct enzymes (e.g., DNA polymerase beta, DNA polymerase theta, DNA glycosylase NEIL2) and the associated molecular mechanisms in base excision repair, nucleotide excision repair, and microhomology-mediated end joining of double-strand breaks. In addition, genome-wide sequencing analysis or site-specific mutational signature analysis of DNA lesions from environmental mutagens (e.g., UV light and aflatoxin) provide further characterization and sequence context impact of DNA damage and mutations. This SI is dedicated to the legacy of Dr. Samuel H. Wilson from the U.S. National Institute of Environmental Health Sciences at the National Institutes of Health.
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Affiliation(s)
- Shan Yan
- Department of Biological Sciences and School of Data Science, University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Shobhan Gaddameedhi
- Department of Biological Sciences and Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina
| | - Robert W. Sobol
- Department of Pathology and Laboratory Medicine and Legorreta Cancer Center, Brown University, Providence, Rhode Island
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8
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Chen Y, Simeone A, Melidis L, Cuesta SM, Tannahill D, Balasubramanian S. An Upstream G-Quadruplex DNA Structure Can Stimulate Gene Transcription. ACS Chem Biol 2024; 19:736-742. [PMID: 38417105 PMCID: PMC10949190 DOI: 10.1021/acschembio.3c00775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/01/2024]
Abstract
Four-stranded G-quadruplexes (G4s) are DNA secondary structures that can form in the human genome. G4 structures have been detected in gene promoters and are associated with transcriptionally active chromatin and the recruitment of transcription factors and chromatin remodelers. We adopted a controlled, synthetic biology approach to understand how G4s can influence transcription. We stably integrated G4-forming sequences into the promoter of a synthetic reporter gene and inserted these into the genome of human cells. The integrated G4 sequences were shown to fold into a G4 structure within a cellular genomic context. We demonstrate that G4 structure formation within a gene promoter stimulates transcription compared to the corresponding G4-negative control promoter in a way that is not dependent on primary sequence or inherent G-richness. Systematic variation in the stability of folded G4s showed that in this system, transcriptional levels increased with higher stability of the G4 structure. By creating and manipulating a chromosomally integrated synthetic promoter, we have shown that G4 structure formation in a defined gene promoter can cause gene transcription to increase, which aligns with earlier observational correlations reported in the literature linking G4s to active transcription.
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Affiliation(s)
- Yuqi Chen
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
| | - Angela Simeone
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Cambridge CB2 0RE, U.K.
| | - Larry Melidis
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Cambridge CB2 0RE, U.K.
| | - Sergio Martinez Cuesta
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Cambridge CB2 0RE, U.K.
| | - David Tannahill
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Cambridge CB2 0RE, U.K.
| | - Shankar Balasubramanian
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Cambridge CB2 0RE, U.K.
- School
of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, U.K.
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9
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Neurauter CG, Pannone M, Sousa MMLD, Wang W, Kuśnierczyk A, Luna L, Sætrom P, Scheffler K, Bjørås M. Enhanced glutathione levels confer resistance to apoptotic and ferroptotic programmed cell death in NEIL DNA glycosylase deficient HAP1 cells. Free Radic Biol Med 2024; 213:470-487. [PMID: 38301978 DOI: 10.1016/j.freeradbiomed.2024.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/12/2024] [Accepted: 01/21/2024] [Indexed: 02/03/2024]
Abstract
The NTHL1 and NEIL1-3 DNA glycosylases are major enzymes in the removal of oxidative DNA base lesions, via the base excision repair (BER) pathway. It is expected that lack of these DNA glycosylases activities would render cells vulnerable to oxidative stress, promoting cell death. Intriguingly, we found that single, double, triple, and quadruple DNA glycosylase knockout HAP1 cells are, however, more resistant to oxidative stress caused by genotoxic agents than wild type cells. Furthermore, glutathione depletion in NEIL deficient cells further enhances resistance to cell death induced via apoptosis and ferroptosis. Finally, we observed higher basal level of glutathione and differential expression of NRF2-regulated genes associated with glutathione homeostasis in the NEIL triple KO cells. We propose that lack of NEIL DNA glycosylases causes aberrant transcription and subsequent errors in protein synthesis. This leads to increased endoplasmic reticulum stress and proteotoxic stress. To counteract the elevated intracellular stress, an adaptive response mediated by increased glutathione basal levels, rises in these cells. This study reveals an unforeseen role of NEIL glycosylases in regulation of resistance to oxidative stress, suggesting that modulation of NEIL glycosylase activities is a potential approach to improve the efficacy of e.g. anti-inflammatory therapies.
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Affiliation(s)
- Christine Gran Neurauter
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway.
| | - Marco Pannone
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway; Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Mirta Mittelstedt Leal de Sousa
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway; Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Wei Wang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Anna Kuśnierczyk
- Proteomics and Modomics Experimental Core Facility (PROMEC), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Luisa Luna
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway.
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Katja Scheffler
- Department of Neurology, St.Olavs University Hospital, Trondheim, 7006, Norway; Department of Neuromedicine and Movement Science (INB), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway; Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
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10
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Pan L, Boldogh I. The potential for OGG1 inhibition to be a therapeutic strategy for pulmonary diseases. Expert Opin Ther Targets 2024; 28:117-130. [PMID: 38344773 PMCID: PMC11111349 DOI: 10.1080/14728222.2024.2317900] [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: 08/14/2023] [Accepted: 02/07/2024] [Indexed: 02/15/2024]
Abstract
INTRODUCTION Pulmonary diseases impose a daunting burden on healthcare systems and societies. Current treatment approaches primarily address symptoms, underscoring the urgency for the development of innovative pharmaceutical solutions. A noteworthy focus lies in targeting enzymes recognizing oxidatively modified DNA bases within gene regulatory elements, given their pivotal role in governing gene expression. AREAS COVERED This review delves into the intricate interplay between the substrate-specific binding of 8-oxoguanine DNA glycosylase 1 (OGG1) and epigenetic regulation, with a focal point on elucidating the molecular underpinnings and their biological implications. The absence of OGG1 distinctly attenuates the binding of transcription factors to cis elements, thereby modulating pro-inflammatory or pro-fibrotic transcriptional activity. Through a synergy of experimental insights gained from cell culture studies and murine models, utilizing prototype OGG1 inhibitors (O8, TH5487, and SU0268), a promising panorama emerges. These investigations underscore the absence of cytotoxicity and the establishment of a favorable tolerance profile for these OGG1 inhibitors. EXPERT OPINION Thus, the strategic targeting of the active site pocket of OGG1 through the application of small molecules introduces an innovative trajectory for advancing redox medicine. This approach holds particular significance in the context of pulmonary diseases, offering a refined avenue for their management.
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Affiliation(s)
- Lang Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, USA
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11
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Fleming AM, Jenkins BLGC, Buck BA, Burrows CJ. DNA Damage Accelerates G-Quadruplex Folding in a Duplex-G-Quadruplex-Duplex Context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576387. [PMID: 38293204 PMCID: PMC10827223 DOI: 10.1101/2024.01.20.576387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Molecular details for DNA damage impact on the folding of potential G-quadruplex sequences (PQS) to non-canonical DNA structures that are involved in gene regulation are poorly understood. Here, the effects of DNA base damage and strand breaks on PQS folding kinetics were studied in the context of the VEGF promoter sequence embedded between two DNA duplex anchors, referred to as a duplex-G-quadruplex-duplex (DGD) motif. This DGD scaffold imposes constraints on the PQS folding process that more closely mimic those found in genomic DNA. Folding kinetics were monitored by circular dichroism (CD) to find folding half-lives ranging from 2 s to 12 min depending on the DNA damage type and sequence position. The presence of Mg2+ ions and the G-quadruplex (G4)-binding protein APE1 facilitated the folding reactions. A strand break placing all four G runs required for G4 formation on one side of the break accelerated the folding rate by >150-fold compared to the undamaged sequence. Combined 1D 1H-NMR and CD analyses confirmed that isothermal folding of the VEGF-DGD constructs yielded spectral signatures that suggest formation of G4 motifs, and demonstrated a folding dependency with the nature and location of DNA damage. Importantly, the PQS folding half-lives measured are relevant to replication, transcription, and DNA repair time frames.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
| | | | - Bethany A Buck
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
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12
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Rostami M, Yalin SF, Altiparmak MR, Guven M. Investigation of APE1 and OGG1 expression in chronic hemodialysis patients. Mol Biol Rep 2024; 51:144. [PMID: 38236479 DOI: 10.1007/s11033-023-09152-3] [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: 11/02/2023] [Accepted: 12/13/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND The role of DNA repair mechanisms is of significant importance in diseases characterized by elevated oxidative DNA damage, such as chronic kidney disease. It is imperative to thoroughly understand the functions of molecules associated with DNA repair mechanisms, not only for assessing susceptibility to diseases but also for monitoring disease progression. In this research, we investigated the APE1 and OGG1 gene expression levels, both of which are involved in the base excision repair (BER) mechanism in chronic hemodialysis patients with malignancy (HPM; n = 8) and without malignancy (HP; n = 36) in pre- and post-dialysis period and 37 healty persons. We also assessed how these values correlate with the clinical profiles of the patients. METHODS AND RESULTS We conducted gene expression analysis using real-time polymerase chain reaction (qRT-PCR). No significant differences in APE1 gene expression levels were observed in pre-dialysis when comparing the HP and HPM groups to the control group. The expression levels of the OGG1 gene were significantly lower in both the HP and HPM groups in pre- and post-dialysis periods compared to the control group. Dialysis procedures led to a reduction in APE1 and OGG1 gene expression levels in both HP and HPM groups. CONCLUSIONS The findings of our study elucidate the impact of alterations in the base excision repair (BER) mechanism, including the hemodialysis process, in end-stage renal disease (ESRD).
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Affiliation(s)
- Manouchehr Rostami
- Department of Medical Biology, Cerrahpasa Medicine Faculty, Istanbul University-Cerrahpasa, Istanbul, 34098, Turkey
| | - Serkan Feyyaz Yalin
- Department of Nephrology, Kartal Dr. Lütfi Kırdar City Hospital, Istanbul, Turkey
| | - Mehmet Riza Altiparmak
- Department of Nephrology, Cerrahpaşa Faculty of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Mehmet Guven
- Department of Medical Biology, Cerrahpasa Medicine Faculty, Istanbul University-Cerrahpasa, Istanbul, 34098, Turkey.
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Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM. Biochemical and Structural Characterization of Fapy•dG Replication by Human DNA Polymerase β. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575758. [PMID: 38293220 PMCID: PMC10827042 DOI: 10.1101/2024.01.15.575758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
N6-(2-deoxy-α,β-D-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido-pyrimidine (Fapy•dG) is formed from a common intermediate and in comparable amounts to the well-studied mutagenic DNA lesion 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo). Fapy•dG preferentially gives rise to G → T transversions and G → A transitions. However, the molecular basis by which Fapy•dG is processed by DNA polymerases during this mutagenic process remains poorly understood. To address this we investigated how DNA polymerase β (Pol β), a model mammalian polymerase, bypasses a templating Fapy•dG, inserts Fapy•dGTP, and extends from Fapy•dG at the primer terminus. When Fapy•dG is present in the template, Pol β incorporates TMP less efficiently than either dCMP or dAMP. Kinetic analysis revealed that Fapy•dGTP is a poor substrate but is incorporated ∼3-times more efficiently opposite dA than dC. Extension from Fapy•dG at the 3'-terminus of a nascent primer is inefficient due to the primer terminus being poorly positioned for catalysis. Together these data indicate that mutagenic bypass of Fapy•dG is likely to be the source of the mutagenic effects of the lesion and not Fapy•dGTP. These experiments increase our understanding of the promutagenic effects of Fapy•dG.
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14
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Siqueira PB, de Sousa Rodrigues MM, de Amorim ÍSS, da Silva TG, da Silva Oliveira M, Rodrigues JA, de Souza da Fonseca A, Mencalha AL. The APE1/REF-1 and the hallmarks of cancer. Mol Biol Rep 2024; 51:47. [PMID: 38165468 DOI: 10.1007/s11033-023-08946-9] [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: 08/31/2023] [Accepted: 10/10/2023] [Indexed: 01/03/2024]
Abstract
APE1/REF-1 (apurinic/apyrimidinic endonuclease 1 / redox factor-1) is a protein with two domains, with endonuclease function and redox activity. Its main activity described is acting in DNA repair by base excision repair (BER) pathway, which restores DNA damage caused by oxidation, alkylation, and single-strand breaks. In contrast, the APE1 redox domain is responsible for regulating transcription factors, such as AP-1 (activating protein-1), NF-κB (Nuclear Factor kappa B), HIF-1α (Hypoxia-inducible factor 1-alpha), and STAT3 (Signal Transducers and Activators of Transcription 3). These factors are involved in physiological cellular processes, such as cell growth, inflammation, and angiogenesis, as well as in cancer. In human malignant tumors, APE1 overexpression is associated with lung, colon, ovaries, prostate, and breast cancer progression, more aggressive tumor phenotypes, and worse prognosis. In this review, we explore APE1 and its domain's role in cancer development processes, highlighting the role of APE1 in the hallmarks of cancer. We reviewed original articles and reviews from Pubmed related to APE1 and cancer and found that both domains of APE1/REF-1, but mainly its redox activity, are essential to cancer cells. This protein is often overexpressed in cancer, and its expression and activity are correlated to processes such as proliferation, invasion, inflammation, angiogenesis, and resistance to cell death. Therefore, APE1 participates in essential processes of cancer development. Then, the activity of APE1/REF-1 in these hallmarks suggests that targeting this protein could be a good therapeutic approach.
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Affiliation(s)
- Priscyanne Barreto Siqueira
- Departamento de Biofísica e Biometria, Laboratório de Biologia do Câncer, Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Rio de Janeiro, Brasil.
| | - Mariana Moreno de Sousa Rodrigues
- Departamento de Biofísica e Biometria, Laboratório de Biologia do Câncer, Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Rio de Janeiro, Brasil.
| | - Ísis Salviano Soares de Amorim
- Departamento de Biofísica e Biometria, Laboratório de Biologia do Câncer, Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Rio de Janeiro, Brasil
- Laboratório de Alimentos Funcionais, Universidade Federal do Rio de Janeiro, Instituto de Nutrição Josué de Castro, Rio de Janeiro, Brasil
| | - Thayssa Gomes da Silva
- Departamento de Biofísica e Biometria, Laboratório de Biofotônica, Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Rio de Janeiro, Brasil
| | - Matheus da Silva Oliveira
- Departamento de Biofísica e Biometria, Laboratório de Biologia do Câncer, Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Rio de Janeiro, Brasil
| | - Juliana Alves Rodrigues
- Departamento de Biofísica e Biometria, Laboratório de Biologia do Câncer, Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Rio de Janeiro, Brasil
| | - Adenilson de Souza da Fonseca
- Departamento de Biofísica e Biometria, Laboratório de Biofotônica, Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Rio de Janeiro, Brasil
| | - Andre Luiz Mencalha
- Departamento de Biofísica e Biometria, Laboratório de Biologia do Câncer, Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Rio de Janeiro, Brasil
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15
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Radak Z, Pan L, Zhou L, Mozaffaritabar S, Gu Y, A Pinho R, Zheng X, Ba X, Boldogh I. Epigenetic and "redoxogenetic" adaptation to physical exercise. Free Radic Biol Med 2024; 210:65-74. [PMID: 37977212 DOI: 10.1016/j.freeradbiomed.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Exercise-induced adaptation is achieved by altering the epigenetic landscape of the entire genome leading to the expression of genes involved in various processes including regulatory, metabolic, adaptive, immune, and myogenic functions. Clinical and experimental data suggest that the methylation pattern/levels of promoter/enhancer is not linearly correlated with gene expression and proteome levels during physical activity implying a level of complexity and interplay with other regulatory modulators. It has been shown that a higher level of physical fitness is associated with a slower DNA methylation-based aging clock. There is strong evidence supporting exercise-induced ROS being a key regulatory mediator through overlapping events, both as signaling entities and through oxidative modifications to various protein mediators and DNA molecules. ROS generated by physical activity shapes epigenome both directly and indirectly, a complexity we are beginning to unravel within the epigenetic arrangement. Oxidative modification of guanine to 8-oxoguanine is a non-genotoxic alteration, does not distort DNA helix and serves as an epigenetic-like mark. The reader and eraser of oxidized guanine is the 8-oxoguanine DNA glycosylase 1, contributing to changes in gene expression. In fact, it can modulate methylation patterns of promoters/enhancers consequently leading to multiple phenotypic changes. Here, we provide evidence and discuss the potential roles of exercise-induced ROS in altering cytosine methylation patterns during muscle adaptation processes.
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Affiliation(s)
- Zsolt Radak
- Research Center for Molecular Exercise Science, Hungarian University of Sport Science, 1123, Budapest, Hungary; Faculty of Sport Sciences, Waseda University, Tokorozawa, 359-1192, Japan.
| | - Lang Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
| | - Lei Zhou
- Research Center for Molecular Exercise Science, Hungarian University of Sport Science, 1123, Budapest, Hungary
| | - Soroosh Mozaffaritabar
- Research Center for Molecular Exercise Science, Hungarian University of Sport Science, 1123, Budapest, Hungary
| | - Yaodong Gu
- Faculty of Sports Science, Ningbo University, Ningbo, China
| | - Ricardo A Pinho
- Laboratory of Exercise Biochemistry in Health, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Xu Zheng
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, Jilin, China; Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
| | - Xueqing Ba
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, Jilin, China; Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
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16
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Vlahopoulos S, Pan L, Varisli L, Dancik GM, Karantanos T, Boldogh I. OGG1 as an Epigenetic Reader Affects NFκB: What This Means for Cancer. Cancers (Basel) 2023; 16:148. [PMID: 38201575 PMCID: PMC10778025 DOI: 10.3390/cancers16010148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/16/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
8-oxoguanine glycosylase 1 (OGG1), which was initially identified as the enzyme that catalyzes the first step in the DNA base excision repair pathway, is now also recognized as a modulator of gene expression. What is important for cancer is that OGG1 acts as a modulator of NFκB-driven gene expression. Specifically, oxidant stress in the cell transiently halts enzymatic activity of substrate-bound OGG1. The stalled OGG1 facilitates DNA binding of transactivators, such as NFκB to their cognate sites, enabling the expression of cytokines and chemokines, with ensuing recruitment of inflammatory cells. Recently, we highlighted chief aspects of OGG1 involvement in regulation of gene expression, which hold significance in lung cancer development. However, OGG1 has also been implicated in the molecular underpinning of acute myeloid leukemia. This review analyzes and discusses how these cells adapt through redox-modulated intricate connections, via interaction of OGG1 with NFκB, which provides malignant cells with alternative molecular pathways to transform their microenvironment, enabling adjustment, promoting cell proliferation, metastasis, and evading killing by therapeutic agents.
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Affiliation(s)
- Spiros Vlahopoulos
- First Department of Pediatrics, National and Kapodistrian University of Athens, Thivon & Levadeias 8, Goudi, 11527 Athens, Greece
| | - Lang Pan
- Department of Microbiology and Immunology, School of Medicine, University of Texas Medical Branch at Galveston, 301 University Blvd., Galveston, TX 77555, USA;
| | - Lokman Varisli
- Department of Molecular Biology and Genetics, Science Faculty, Dicle University, Diyarbakir 21280, Turkey;
| | - Garrett M. Dancik
- Department of Computer Science, Eastern Connecticut State University, Willimantic, CT 06226, USA;
| | - Theodoros Karantanos
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA;
| | - Istvan Boldogh
- Department of Microbiology and Immunology, School of Medicine, University of Texas Medical Branch at Galveston, 301 University Blvd., Galveston, TX 77555, USA;
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17
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Kim HJ, Yang J, Herath KHINM, Jeon YJ, Son YO, Kwon D, Kim HJ, Jee Y. Oral Administration of Sargassum horneri Suppresses Particulate Matter-Induced Oxidative DNA Damage in Alveolar Macrophages of Allergic Airway Inflammation: Relevance to PM-Mediated M1/M2 AM Polarization. Mol Nutr Food Res 2023; 67:e2300462. [PMID: 37986167 DOI: 10.1002/mnfr.202300462] [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: 07/04/2023] [Indexed: 11/22/2023]
Abstract
SCOPE Particulate matter (PM) can cause cellular oxidative damage and promote respiratory diseases. It has recently shown that Sargassum horneri ethanol extract (SHE) containing sterols and gallic acid reduces PM-induced oxidative stress in mice lung cells through ROS scavenging and metal chelating. In this study, the role of alveolar macrophages (AMs) is identified that are particularly susceptible to DNA damage due to PM-triggered oxidative stress in lungs of OVA-sensitized mice exposed to PM. METHODS AND RESULTS The study scrutinizes if PM exposure causes oxidative DNA damage to AMs differentially depending on their type of polarization. Further, SHE's potential is investigated in reducing oxidative DNA damage in polarized AMs and restoring AM polarization in PM-induced allergic airway inflammation. The study discovers that PM triggers prolonged oxidative stress to AMs, leading to lipid peroxidation in them and alveolar epithelial cells. Particularly, AMs are polarized to M2 phenotype (F4/80+ CD206+ ) with enhanced oxidative DNA damage when subject to PM-induced oxidative stress. However, SHE repairs oxidative DNA damage in M1- and M2-polarized AMs and reduces AMs polarization imbalance due to PM exposure. CONCLUSION These results suggest the possibility of SHE as beneficial foods against PM-induced allergic airway inflammation via suppression of AM dysfunction.
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Affiliation(s)
- Hyo Jin Kim
- Department of Food Bioengineering, Jeju National University, Jeju, 63243, Republic of Korea
| | - Jiwon Yang
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju, 63243, Republic of Korea
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, Jeju, 63243, Republic of Korea
| | | | - You-Jin Jeon
- Department of Marine Life Science, School of Marine Biomedical Sciences, Jeju National University, Jeju, 63243, Republic of Korea
| | - Young-Ok Son
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju, 63243, Republic of Korea
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, Jeju, 63243, Republic of Korea
| | - Doyoung Kwon
- College of Pharmacy, Jeju National University, Jeju, 63243, Republic of Korea
- Jeju Research Institute of Pharmaceutical Sciences, Jeju National University, Jeju, 63243, Republic of Korea
| | - Hyun Jung Kim
- Department of Food Bioengineering, Jeju National University, Jeju, 63243, Republic of Korea
| | - Youngheun Jee
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju, 63243, Republic of Korea
- Department of Veterinary Medicine and Veterinary Medical Research Institute, Jeju National University, Jeju, 63243, Republic of Korea
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18
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Myres GJ, Kitt JP, Harris JM. Raman Scattering Reveals Ion-Dependent G-Quadruplex Formation in the 15-mer Thrombin-Binding Aptamer upon Association with α-Thrombin. Anal Chem 2023; 95:16160-16168. [PMID: 37870982 DOI: 10.1021/acs.analchem.3c02751] [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: 10/25/2023]
Abstract
The discovery of DNA aptamers that bind biomolecular targets has enabled significant innovations in biosensing. Aptamers form secondary structures that exhibit selective high-affinity interactions with their binding partners. The binding of its target by an aptamer is often accompanied by conformational changes, and sensing by aptamers often relies on these changes to provide readout signals from extrinsic labels to detect target association. Many biosensing applications involve aptamers immobilized to surfaces, but methods to characterize conformations of immobilized aptamers and their in situ response have been lacking. To address this challenge, we have developed a structurally informative Raman spectroscopy method to determine conformations of the 15-mer thrombin-binding aptamer (TBA) immobilized on porous silica surfaces. The TBA is of interest because its binding of α-thrombin depends on the aptamer forming an antiparallel G-quadruplex, which is thought to drive signal changes that allow thrombin-binding to be detected. However, specific metal cations also stabilize the G-quadruplex conformation of the aptamer, even in the absence of its protein target. To develop a deeper understanding of the conformational response of the TBA, we utilize Raman spectroscopy to quantify the effects of the metal cations, K+ (stabilizing) and Li+ (nonstabilizing), on G-quadruplex versus unfolded populations of the TBA. In K+ or Li+ solutions, we then detect the association of α-thrombin with the immobilized aptamer, which can be observed in Raman scattering from the bound protein. The results show that the association of α-thrombin in K+ solutions produces no detectable change in aptamer conformation, which is found in the G-quadruplex form both before and after binding its target. In Li+ solutions, however, where the TBA is unfolded prior to α-thrombin association, protein binding occurs with the formation of a G-quadruplex by the aptamer.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Jay P Kitt
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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19
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Wen T, Kermarrec M, Dumont E, Gillet N, Greenberg MM. DNA-Histone Cross-Link Formation via Hole Trapping in Nucleosome Core Particles. J Am Chem Soc 2023; 145:23702-23714. [PMID: 37856159 PMCID: PMC10652223 DOI: 10.1021/jacs.3c08135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Radical cations (holes) produced in DNA by ionizing radiation and other oxidants yield DNA-protein cross-links (DPCs). Detailed studies of DPC formation in chromatin via this process are lacking. We describe here a comprehensive examination of DPC formation within nucleosome core particles (NCPs), which are the monomeric component of chromatin. DNA holes are introduced at defined sites within NCPs that are constructed from the bottom-up. DPCs form at DNA holes in yields comparable to those of alkali-labile DNA lesions that result from water trapping. DPC-forming efficiency and site preference within the NCP are dependent on translational and rotational positioning. Mass spectrometry and the use of mutant histones reveal that lysine residues in histone N-terminal tails and amino termini are responsible for the DPC formation. These studies are corroborated by computational simulation at the microsecond time scale, showing a wide range of interactions that can precede DPC formation. Three consecutive dGs, which are pervasive in the human genome, including G-quadruplex-forming sequences, are sufficient to produce DPCs that could impact gene expression.
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Affiliation(s)
- Tingyu Wen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Maxime Kermarrec
- Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, ENS de Lyon, CNRS, F-69342 Lyon, France
| | - Elise Dumont
- Institut de Chimie de Nice UMR 7272, Université Côte d'Azur, CNRS, 06108 Nice, France
- Institut Universitaire de France, 5 Rue Descartes, 75005 Paris, France
| | - Natacha Gillet
- Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, ENS de Lyon, CNRS, F-69342 Lyon, France
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
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20
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Kaur B, Sharma P, Arora P, Sood V. QUFIND: tool for comparative prediction and mining of G4 quadruplexes overlapping with CpG islands. Front Genet 2023; 14:1265808. [PMID: 37953924 PMCID: PMC10634401 DOI: 10.3389/fgene.2023.1265808] [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: 08/01/2023] [Accepted: 09/29/2023] [Indexed: 11/14/2023] Open
Abstract
G-quadruplexes (G4s) are secondary structures in DNA that have been shown to be involved in gene regulation. They play a vital role in the cellular processes and several pathogens including bacteria, fungi, and viruses have also been shown to possess G4s that help them in their pathogenesis. Additionally, cross-talk among the CpG islands and G4s has been shown to influence biological processes. The virus-encoded G4s are affected by the mutational landscape leading to the formation/deletion of these G4s. Therefore, understanding and predicting these multivariate effects on traditional and non-traditional quadruplexes forms an important area of research, that is, yet to be investigated. We have designed a user-friendly webserver QUFIND (http://soodlab.com/qufinder/) that can predict traditional as well as non-traditional quadruplexes in a given sequence. QUFIND is connected with ENSEMBL and NCBI so that the sequences can be fetched in a real-time manner. The algorithm is designed in such a way that the user is provided with multiple options to customize the base (A, T, G, or C), size of the stem (2-5), loop length (1-30), number of bulges (1-5) as well as the number of mismatches (0-2) enabling the identification of any of the secondary structure as per their interest. QUFIND is designed to predict both CpG islands as well as G4s in a given sequence. Since G4s are very short as compared to the CpG islands, hence, QUFIND can also predict the overlapping G4s within CpG islands. Therefore, the user has the flexibility to identify either overlapping or non-overlapping G4s along with the CpG islands. Additionally, one section of QUFIND is dedicated to comparing the G4s in two viral sequences. The visualization is designed in such a manner that the user is able to see the unique quadruplexes in both the input sequences. The efficiency of QUFIND is calculated on G4s obtained from G4 high throughput sequencing data (n = 1000) or experimentally validated G4s (n = 329). Our results revealed that QUFIND is able to predict G4-quadruplexes obtained from G4-sequencing data with 90.06% prediction accuracy whereas experimentally validated quadruplexes were predicted with 97.26% prediction accuracy.
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Affiliation(s)
- Baljeet Kaur
- Department of Computer Science, Hansraj College, University of Delhi, Malka Ganj, India
| | - Priya Sharma
- Department of Biochemistry, Jamia Hamdard, Delhi, India
| | - Pooja Arora
- Department of Zoology, Hansraj College, University of Delhi, Malka Ganj, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, Delhi, India
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21
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Sato K, Knipscheer P. G-quadruplex resolution: From molecular mechanisms to physiological relevance. DNA Repair (Amst) 2023; 130:103552. [PMID: 37572578 DOI: 10.1016/j.dnarep.2023.103552] [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: 05/24/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Guanine-rich DNA sequences can fold into stable four-stranded structures called G-quadruplexes or G4s. Research in the past decade demonstrated that G4 structures are widespread in the genome and prevalent in regulatory regions of actively transcribed genes. The formation of G4s has been tightly linked to important biological processes including regulation of gene expression and genome maintenance. However, they can also pose a serious threat to genome integrity especially by impeding DNA replication, and G4-associated somatic mutations have been found accumulated in the cancer genomes. Specialised DNA helicases and single stranded DNA binding proteins that can resolve G4 structures play a crucial role in preventing genome instability. The large variety of G4 unfolding proteins suggest the presence of multiple G4 resolution mechanisms in cells. Recently, there has been considerable progress in our detailed understanding of how G4s are resolved, especially during DNA replication. In this review, we first discuss the current knowledge of the genomic G4 landscapes and the impact of G4 structures on DNA replication and genome integrity. We then describe the recent progress on the mechanisms that resolve G4 structures and their physiological relevance. Finally, we discuss therapeutic opportunities to target G4 structures.
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Affiliation(s)
- Koichi Sato
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
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22
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Tessmer I. The roles of non-productive complexes of DNA repair proteins with DNA lesions. DNA Repair (Amst) 2023; 129:103542. [PMID: 37453245 DOI: 10.1016/j.dnarep.2023.103542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
A multitude of different types of lesions is continuously introduced into the DNA inside our cells, and their rapid and efficient repair is fundamentally important for the maintenance of genomic stability and cellular viability. This is achieved by a number of DNA repair systems that each involve different protein factors and employ versatile strategies to target different types of DNA lesions. Intriguingly, specialized DNA repair proteins have also evolved to form non-functional complexes with their target lesions. These proteins allow the marking of innocuous lesions to render them visible for DNA repair systems and can serve to directly recruit DNA repair cascades. Moreover, they also provide links between different DNA repair mechanisms or even between DNA lesions and transcription regulation. I will focus here in particular on recent findings from single molecule analyses on the alkyltransferase-like protein ATL, which is believed to initiate nucleotide excision repair (NER) of non-native NER target lesions, and the base excision repair (BER) enzyme hOGG1, which recruits the oncogene transcription factor Myc to gene promoters under oxidative stress.
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Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
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23
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Pan L, Vlahopoulos S, Tanner L, Bergwik J, Bacsi A, Radak Z, Egesten A, Ba X, Brasier AR, Boldogh I. Substrate-specific binding of 8-oxoguanine DNA glycosylase 1 (OGG1) reprograms mucosal adaptations to chronic airway injury. Front Immunol 2023; 14:1186369. [PMID: 37614238 PMCID: PMC10442650 DOI: 10.3389/fimmu.2023.1186369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/24/2023] [Indexed: 08/25/2023] Open
Abstract
Recent advances have uncovered the non-random distribution of 7, 8-dihydro-8-oxoguanine (8-oxoGua) induced by reactive oxygen species, which is believed to have epigenetic effects. Its cognate repair protein, 8-oxoguanine DNA glycosylase 1 (OGG1), reads oxidative substrates and participates in transcriptional initiation. When redox signaling is activated in small airway epithelial cells, the DNA repair function of OGG1 is repurposed to transmit acute inflammatory signals accompanied by cell state transitions and modification of the extracellular matrix. Epithelial-mesenchymal and epithelial-immune interactions act cooperatively to establish a local niche that instructs the mucosal immune landscape. If the transitional cell state governed by OGG1 remains responsive to inflammatory mediators instead of differentiation, the collateral damage provides positive feedback to inflammation, ascribing inflammatory remodeling to one of the drivers in chronic pathologies. In this review, we discuss the substrate-specific read through OGG1 has evolved in regulating the innate immune response, controlling adaptations of the airway to environmental and inflammatory injury, with a focus on the reader function of OGG1 in initiation and progression of epithelial to mesenchymal transitions in chronic pulmonary disease.
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Affiliation(s)
- Lang Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Spiros Vlahopoulos
- Horemeio Research Laboratory, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Lloyd Tanner
- Respiratory Medicine, Allergology & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Jesper Bergwik
- Respiratory Medicine, Allergology & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Attila Bacsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Hungary, Debrecen, Hungary
| | - Zsolt Radak
- Research Institute of Sport Science, University of Physical Education, Budapest, Hungary
| | - Arne Egesten
- Respiratory Medicine, Allergology & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Xueqing Ba
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, Jilin, China
| | - Allan R. Brasier
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, United States
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
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24
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Xue Y, Pan L, Vlahopoulos S, Wang K, Zheng X, Radak Z, Bacsi A, Tanner L, Brasier AR, Ba X, Boldogh I. Epigenetic control of type III interferon expression by 8-oxoguanine and its reader 8-oxoguanine DNA glycosylase1. Front Immunol 2023; 14:1161160. [PMID: 37600772 PMCID: PMC10436556 DOI: 10.3389/fimmu.2023.1161160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/23/2023] [Indexed: 08/22/2023] Open
Abstract
Interferons (IFNs) are secreted cytokines with the ability to activate expression of IFN stimulated genes that increase resistance of cells to virus infections. Activated transcription factors in conjunction with chromatin remodelers induce epigenetic changes that reprogram IFN responses. Unexpectedly, 8-oxoguanine DNA glycosylase1 (Ogg1) knockout mice show enhanced stimuli-driven IFN expression that confers increased resistance to viral and bacterial infections and allergen challenges. Here, we tested the hypothesis that the DNA repair protein OGG1 recognizes 8-oxoguanine (8-oxoGua) in promoters modulating IFN expression. We found that functional inhibition, genetic ablation, and inactivation by post-translational modification of OGG1 significantly augment IFN-λ expression in epithelial cells infected by human respiratory syncytial virus (RSV). Mechanistically, OGG1 bound to 8-oxoGua in proximity to interferon response elements, which inhibits the IRF3/IRF7 and NF-κB/RelA DNA occupancy, while promoting the suppressor NF-κB1/p50-p50 homodimer binding to the IFN-λ2/3 promoter. In a mouse model of bronchiolitis induced by RSV infection, functional ablation of OGG1 by a small molecule inhibitor (TH5487) enhances IFN-λ production, decreases immunopathology, neutrophilia, and confers antiviral protection. These findings suggest that the ROS-generated epigenetic mark 8-oxoGua via its reader OGG1 serves as a homeostatic thresholding factor in IFN-λ expression. Pharmaceutical targeting of OGG1 activity may have clinical utility in modulating antiviral response.
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Affiliation(s)
- Yaoyao Xue
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, China
| | - Lang Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Spiros Vlahopoulos
- Horemeio Research Laboratory, First Department of Pediatrics, National and Kapodistrian, University of Athens, Athens, Greece
| | - Ke Wang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, China
| | - Xu Zheng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, China
| | - Zsolt Radak
- Research Institute of Molecular Exercise Science, University of Sport Science, Budapest, Hungary
| | - Attila Bacsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Lloyd Tanner
- Respiratory Medicine, Allergology & Palliative Medicine, Lund University and Skåne University Hospital, Lund, Sweden
| | - Allan R Brasier
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Xueqing Ba
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, China
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
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25
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Lawler NB, Ou A, King JJ, Evans CW, Iyer KS, Smith NM. G4-DNA formation and chromatin remodelling are interdependent in human cells. Chem Sci 2023; 14:7681-7687. [PMID: 37476710 PMCID: PMC10355101 DOI: 10.1039/d3sc02533k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/18/2023] [Indexed: 07/22/2023] Open
Abstract
DNA G-quadruplexes (G4s) have been identified as important biological targets for transcriptional, translational, and epigenetic regulation. The stabilisation of G4s with small molecule ligands has emerged as a technique to regulate gene expression and as a potential therapeutic approach for human diseases. Here, we demonstrate that ligand stabilisation of G4s causes altered chromatin accessibility dependent on the targeting specificity of the molecule. In particular, stabilisation of a target G4 using the highly specific GTC365 ligand resulted in differential accessibility of 61 genomic regions, while the broad-targeting G4 ligand, GQC-05, stabilised many G4s and induced a global shift towards increased accessibility of gene promoter regions. Interestingly, while we observed distinct effects of each ligand on RNA expression levels and the induction of DNA double-stranded breaks, both ligands modified DNA damage response pathways. Our work represents the dual possibility of G4-stabilising ligands for specific or global chromatin modulation via unique targeting characteristics.
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Affiliation(s)
- Nicholas B Lawler
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
- School of Physics, Mathematics and Computing, The University of Western Australia Perth WA Australia
| | - Arnold Ou
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
| | - Jessica J King
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
| | - K Swaminathan Iyer
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
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26
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Xiao S, Fleming AM, Burrows CJ. Sequencing for oxidative DNA damage at single-nucleotide resolution with click-code-seq v2.0. Chem Commun (Camb) 2023; 59:8997-9000. [PMID: 37401666 PMCID: PMC10909242 DOI: 10.1039/d3cc02699j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Oxidative damage to DNA nucleotides has many cellular outcomes that could be aided by the development of sequencing methods. Herein, the previously reported click-code-seq method for sequencing a single damage type is redeveloped to enable the sequencing of many damage types by making simple changes to the protocol (i.e., click-code-seq v2.0).
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Affiliation(s)
- Songjun Xiao
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
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27
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Fleming AM, Burrows CJ. DNA modifications walk a fine line between epigenetics and mutagenesis. Nat Rev Mol Cell Biol 2023; 24:449-450. [PMID: 36813885 PMCID: PMC10330371 DOI: 10.1038/s41580-023-00590-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
In the study of DNA modifications, the disciplines of epigenetics and of DNA damage and repair have evolved separately. The lines are now blurred by the realization that epigenetic modifications require DNA repair pathways for erasure and by the recent discoveries that oxidative DNA damage can upregulate gene expression.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.
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28
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Zhao X, Ma Y, Shi M, Huang M, Xin J, Ci S, Chen M, Jiang T, Hu Z, He L, Pan F, Guo Z. Excessive iron inhibits insulin secretion via perturbing transcriptional regulation of SYT7 by OGG1. Cell Mol Life Sci 2023; 80:159. [PMID: 37209177 PMCID: PMC11072990 DOI: 10.1007/s00018-023-04802-y] [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: 01/01/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/22/2023]
Abstract
Although iron overload is closely related to the occurrence of type 2 diabetes mellitus (T2DM), the specific mechanism is unclear. Here, we found that excessive iron inhibited the secretion of insulin (INS) and impaired islet β cell function through downregulating Synaptotagmin 7 (SYT7) in iron overload model in vivo and in vitro. Our results further demonstrated that 8-oxoguanine DNA glycosylase (OGG1), a key protein in the DNA base excision repair, was an upstream regulator of SYT7. Interestingly, such regulation could be suppressed by excessive iron. Ogg1-null mice, iron overload mice and db/db mice exhibit reduced INS secretion, weakened β cell function and subsequently impaired glucose tolerance. Notably, SYT7 overexpression could rescue these phenotypes. Our data revealed an intrinsic mechanism by which excessive iron inhibits INS secretion through perturbing the transcriptional regulation of SYT7 by OGG1, which suggested that SYT7 was a potential target in clinical therapy for T2DM.
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Affiliation(s)
- Xingqi Zhao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Ying Ma
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Munan Shi
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Miaoling Huang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Jingyu Xin
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Shusheng Ci
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Meimei Chen
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - Tao Jiang
- Department of Geriatrics, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
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29
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Li J, Pan L, Pan W, Li N, Tang B. Recent progress of oxidative stress associated biomarker detection. Chem Commun (Camb) 2023. [PMID: 37194341 DOI: 10.1039/d3cc00878a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Oxidative stress denotes the imbalance between the generation of reactive oxygen species (ROS) and antioxidant defenses in living organisms, participating in various pathophysiological processes and mediating the occurrence of diseases. Typically, the excessive production of ROS under oxidative stress elicits oxidative modification of biomacromolecules, including lipids, proteins and nucleic acids, leading to cell dysfunction and damage. Therefore, the analysis and detection of oxidative stress-associated biomarkers are of considerable importance to accurately reflect and evaluate the oxidative stress status. This review comprehensively elucidates the recent advances and applications of imaging probes for tracking and detecting oxidative stress-related biomarkers such as lipid peroxidation, and protein and DNA oxidation. The existing challenges and future development directions in this field are also discussed.
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Affiliation(s)
- Jingjing Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
| | - Limeng Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
| | - Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
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30
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Xiao Y, Yi H, Zhu J, Chen S, Wang G, Liao Y, Lei Y, Chen L, Zhang X, Ye F. Evaluation of DNA adduct damage using G-quadruplex-based DNAzyme. Bioact Mater 2023; 23:45-52. [DOI: 10.1016/j.bioactmat.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/15/2022] [Accepted: 10/02/2022] [Indexed: 11/11/2022] Open
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31
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Howpay Manage SA, Zhu J, Fleming AM, Burrows CJ. Promoters vs. telomeres: AP-endonuclease 1 interactions with abasic sites in G-quadruplex folds depend on topology. RSC Chem Biol 2023; 4:261-270. [PMID: 37034403 PMCID: PMC10074553 DOI: 10.1039/d2cb00233g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The DNA repair endonuclease APE1 is responsible for the cleavage of abasic sites (AP) in DNA as well as binding AP in promoter G-quadruplex (G4) folds in some genes to regulate transcription. The present studies focused on the topological properties of AP-bearing G4 folds and how they impact APE1 interaction. The human telomere sequence with a tetrahydrofuran model (F) of an AP was folded in K+- or Na+-containing buffers to adopt hybrid- or basket-folds, respectively. Endonuclease and binding assays were performed with APE1 and the G4 substrates, and the data were compared to prior work with parallel-stranded VEGF and NEIL3 promoter G4s to identify topological differences. The APE1-catalyzed endonuclease assays led to the conclusion that telomere G4 folds were slightly better substrates than the promoter G4s, but the yields were all low compared to duplex DNA. In the binding assays, G4 topological differences were observed in which APE1 bound telomere G4s with dissociation constants similar to single-stranded DNA, and promoter G4s were bound with nearly ten-fold lower values similar to duplex DNA. An in-cellulo assay with the telomere G4 in a model promoter bearing a lesion failed to regulate transcription. These data support a hypothesis that G4 topology in gene promoters is a critical feature that APE1 recognizes for gene regulation.
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Affiliation(s)
| | - Judy Zhu
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
| | - Aaron M Fleming
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
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32
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Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
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33
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Pan L, Hao W, Xue Y, Wang K, Zheng X, Luo J, Ba X, Xiang Y, Qin X, Bergwik J, Tanner L, Egesten A, Brasier AR, Boldogh I. 8-Oxoguanine targeted by 8-oxoguanine DNA glycosylase 1 (OGG1) is central to fibrogenic gene activation upon lung injury. Nucleic Acids Res 2023; 51:1087-1102. [PMID: 36651270 PMCID: PMC9943661 DOI: 10.1093/nar/gkac1241] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 01/19/2023] Open
Abstract
Reactive oxygen species (ROS) are implicated in epithelial cell-state transition and deposition of extracellular matrix upon airway injury. Of the many cellular targets of ROS, oxidative DNA modification is a major driving signal. However, the role of oxidative DNA damage in modulation profibrotic processes has not been fully delineated. Herein, we report that oxidative DNA base lesions, 8-oxoG, complexed with 8-oxoguanine DNA glycosylase 1 (OGG1) functions as a pioneer factor, contributing to transcriptional reprogramming within airway epithelial cells. We show that TGFβ1-induced ROS increased 8-oxoG levels in open chromatin, dynamically reconfigure the chromatin state. OGG1 complexed with 8-oxoG recruits transcription factors, including phosphorylated SMAD3, to pro-fibrotic gene promoters thereby facilitating gene activation. Moreover, 8-oxoG levels are elevated in lungs of mice subjected to TGFβ1-induced injury. Pharmacologic targeting of OGG1 with the selective small molecule inhibitor of 8-oxoG binding, TH5487, abrogates fibrotic gene expression and remodeling in this model. Collectively, our study implicates that 8-oxoG substrate-specific binding by OGG1 is a central modulator of transcriptional regulation in response to tissue repair.
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Affiliation(s)
- Lang Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Wenjing Hao
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100871, China
| | - Yaoyao Xue
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ke Wang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xu Zheng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jixian Luo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- School of Life Sciences, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Xueqing Ba
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, Jilin 130024, China
| | - Yang Xiang
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, Hunan 410000, China
| | - Xiaoqun Qin
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, Hunan 410000, China
| | - Jesper Bergwik
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84 Lund, Sweden
| | - Lloyd Tanner
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84 Lund, Sweden
| | - Arne Egesten
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84 Lund, Sweden
| | - Allan R Brasier
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI 53705, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
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34
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Tanner L, Single AB, Bhongir RKV, Heusel M, Mohanty T, Karlsson CAQ, Pan L, Clausson CM, Bergwik J, Wang K, Andersson CK, Oommen RM, Erjefält JS, Malmström J, Wallner O, Boldogh I, Helleday T, Kalderén C, Egesten A. Small-molecule-mediated OGG1 inhibition attenuates pulmonary inflammation and lung fibrosis in a murine lung fibrosis model. Nat Commun 2023; 14:643. [PMID: 36746968 PMCID: PMC9902543 DOI: 10.1038/s41467-023-36314-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Interstitial lung diseases such as idiopathic pulmonary fibrosis (IPF) are caused by persistent micro-injuries to alveolar epithelial tissues accompanied by aberrant repair processes. IPF is currently treated with pirfenidone and nintedanib, compounds which slow the rate of disease progression but fail to target underlying pathophysiological mechanisms. The DNA repair protein 8-oxoguanine DNA glycosylase-1 (OGG1) has significant roles in the modulation of inflammation and metabolic syndromes. Currently, no pharmaceutical solutions targeting OGG1 have been utilized in the treatment of IPF. In this study we show Ogg1-targeting siRNA mitigates bleomycin-induced pulmonary fibrosis in male mice, highlighting OGG1 as a tractable target in lung fibrosis. The small molecule OGG1 inhibitor, TH5487, decreases myofibroblast transition and associated pro-fibrotic gene expressions in fibroblast cells. In addition, TH5487 decreases levels of pro-inflammatory mediators, inflammatory cell infiltration, and lung remodeling in a murine model of bleomycin-induced pulmonary fibrosis conducted in male C57BL6/J mice. OGG1 and SMAD7 interact to induce fibroblast proliferation and differentiation and display roles in fibrotic murine and IPF patient lung tissue. Taken together, these data suggest that TH5487 is a potentially clinically relevant treatment for IPF but further study in human trials is required.
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Affiliation(s)
- L Tanner
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84, Lund, Sweden.
| | - A B Single
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84, Lund, Sweden
| | - R K V Bhongir
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84, Lund, Sweden
| | - M Heusel
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - T Mohanty
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - C A Q Karlsson
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - L Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - C-M Clausson
- Division of Airway Inflammation, Department of Experimental Medical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - J Bergwik
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84, Lund, Sweden
| | - K Wang
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - C K Andersson
- Respiratory Cell Biology, Department of Experimental Medical Sciences Lund, Lund University, SE-221 84, Lund, Sweden
| | - R M Oommen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - J S Erjefält
- Division of Airway Inflammation, Department of Experimental Medical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - J Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - O Wallner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - I Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - T Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Oxcia AB, Norrbackagatan 70C, SE-113 34, Stockholm, Sweden
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - C Kalderén
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Oxcia AB, Norrbackagatan 70C, SE-113 34, Stockholm, Sweden
| | - A Egesten
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84, Lund, Sweden
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Ma Y, Yang Y, Xin J, He L, Hu Z, Gao T, Pan F, Guo Z. RNA G-Quadruplex within the 5'-UTR of FEN1 Regulates mRNA Stability under Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12020276. [PMID: 36829835 PMCID: PMC9952066 DOI: 10.3390/antiox12020276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Reactive oxygen species (ROS) are a group of highly oxidative molecules that induce DNA damage, affecting DNA damage response (DDR) and gene expression. It is now recognized that DNA base excision repair (BER) is one of the important pathways responsible for sensing oxidative stress to eliminate DNA damage, in which FEN1 plays an important role in this process. However, the regulation of FEN1 under oxidative stress is still unclear. Here, we identified a novel RNA G-quadruplex (rG4) sequence in the 5'untranslated region (5'UTR) of FEN1 mRNA. Under oxidative stress, the G bases in the G4-forming sequence can be oxidized by ROS, resulting in structural disruption of the G-quadruplex. ROS or TMPyP4, a G4-structural ligand, disrupted the formation of G4 structure and affected the expression of FEN1. Furthermore, pull-down experiments identified a novel FEN1 rG4-binding protein, heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1), and cellular studies have shown that hnRNPA1 plays an important role in regulating FEN1 expression. This work demonstrates that rG4 acts as a ROS sensor in the 5'UTR of FEN1 mRNA. Taken together, these results suggest a novel role for rG4 in translational control under oxidative stress.
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Affiliation(s)
- Ying Ma
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yang Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jingyu Xin
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Tao Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Correspondence: (F.P.); (Z.G.)
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Correspondence: (F.P.); (Z.G.)
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36
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Gorini F, Ambrosio S, Lania L, Majello B, Amente S. The Intertwined Role of 8-oxodG and G4 in Transcription Regulation. Int J Mol Sci 2023; 24:ijms24032031. [PMID: 36768357 PMCID: PMC9916577 DOI: 10.3390/ijms24032031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
The guanine base in nucleic acids is, among the other bases, the most susceptible to being converted into 8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) when exposed to reactive oxygen species. In double-helix DNA, 8-oxodG can pair with adenine; hence, it may cause a G > T (C > A) mutation; it is frequently referred to as a form of DNA damage and promptly corrected by DNA repair mechanisms. Moreover, 8-oxodG has recently been redefined as an epigenetic factor that impacts transcriptional regulatory elements and other epigenetic modifications. It has been proposed that 8-oxodG exerts epigenetic control through interplay with the G-quadruplex (G4), a non-canonical DNA structure, in transcription regulatory regions. In this review, we focused on the epigenetic roles of 8-oxodG and the G4 and explored their interplay at the genomic level.
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Affiliation(s)
- Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Susanna Ambrosio
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Luigi Lania
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Barbara Majello
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
- Correspondence:
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Wu S, Jiang L, Lei L, Fu C, Huang J, Hu Y, Dong Y, Chen J, Zeng Q. Crosstalk between G-quadruplex and ROS. Cell Death Dis 2023; 14:37. [PMID: 36653351 PMCID: PMC9849334 DOI: 10.1038/s41419-023-05562-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/25/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
The excessive production of reactive oxygen species (ROS) can lead to single nucleic acid base damage, DNA strand breakage, inter- and intra-strand cross-linking of nucleic acids, and protein-DNA cross-linking involved in the pathogenesis of cancer, neurodegenerative diseases, and aging. G-quadruplex (G4) is a stacked nucleic acid structure that is ubiquitous across regulatory regions of multiple genes. Abnormal formation and destruction of G4s due to multiple factors, including cations, helicases, transcription factors (TFs), G4-binding proteins, and epigenetic modifications, affect gene replication, transcription, translation, and epigenetic regulation. Due to the lower redox potential of G-rich sequences and unique structural characteristics, G4s are highly susceptible to oxidative damage. Additionally, the formation, stability, and biological regulatory role of G4s are affected by ROS. G4s are involved in regulating gene transcription, translation, and telomere length maintenance, and are therefore key players in age-related degeneration. Furthermore, G4s also mediate the antioxidant process by forming stress granules and activating Nrf2, which is suggestive of their involvement in developing ROS-related diseases. In this review, we have summarized the crosstalk between ROS and G4s, and the possible regulatory mechanisms through which G4s play roles in aging and age-related diseases.
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Affiliation(s)
- Songjiang Wu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Ling Jiang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Li Lei
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Chuhan Fu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Jinhua Huang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Yibo Hu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Yumeng Dong
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Jing Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China.
| | - Qinghai Zeng
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China.
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Abdallah S, Jampy A, Moison D, Wieckowski M, Messiaen S, Martini E, Campalans A, Radicella JP, Rouiller-Fabre V, Livera G, Guerquin MJ. Foetal exposure to the bisphenols BADGE and BPAF impairs meiosis through DNA oxidation in mouse ovaries. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120791. [PMID: 36464114 DOI: 10.1016/j.envpol.2022.120791] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/16/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Many endocrine disruptors have been proven to impair the meiotic process which is required for the production of healthy gametes. Bisphenol A is emblematic of such disruptors, as it impairs meiotic prophase I and causes oocyte aneuploidy following in utero exposure. However, the mechanisms underlying these deleterious effects remain poorly understood. Furthermore, the increasing use of BPA alternatives raises concerns for public health. Here, we investigated the effects of foetal exposure to two BPA alternatives, bisphenol A Diglycidyl Ether (BADGE) and bisphenol AF (BPAF), on oogenesis in mice. These compounds delay meiosis initiation, increase the number of MLH1 foci per cell and induce oocyte aneuploidy. We further demonstrate that these defects are accompanied by changes in gene expression in foetal premeiotic germ cells and aberrant mRNA splicing of meiotic genes. We observed an increase in DNA oxidation after exposure to BPA alternatives. Specific induction of oxidative DNA damage during foetal germ cell differentiation causes similar defects during oogenesis, as observed in 8-oxoguanine DNA Glycosylase (OGG1)-deficient mice or after in utero exposure to potassium bromate (KBrO3), an inducer of oxidative DNA damage. The supplementation of BPA alternatives with N-acetylcysteine (NAC) counteracts the effects of bisphenols on meiosis. Together, our results propose oxidative DNA lesion as an event that negatively impacts female meiosis with major consequences on oocyte quality. This could be a common mechanism of action for numerous environmental pro-oxidant pollutants, and its discovery, could lead to reconsider the adverse effect of bisphenol mixtures that are simultaneously present in our environment.
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Affiliation(s)
- Sonia Abdallah
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Amandine Jampy
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Delphine Moison
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Margaux Wieckowski
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Sébastien Messiaen
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Emmanuelle Martini
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Anna Campalans
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France
| | - Juan Pablo Radicella
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France
| | - Virginie Rouiller-Fabre
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Gabriel Livera
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Marie-Justine Guerquin
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France.
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39
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OGG1 in the Kidney: Beyond Base Excision Repair. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5774641. [PMID: 36620083 PMCID: PMC9822757 DOI: 10.1155/2022/5774641] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/01/2023]
Abstract
8-Oxoguanine DNA glycosylase (OGG1) is a repair protein for 8-oxoguanine (8-oxoG) in eukaryotic atopic DNA. Through the initial base excision repair (BER) pathway, 8-oxoG is recognized and excised, and subsequently, other proteins are recruited to complete the repair. OGG1 is primarily located in the cytoplasm and can enter the nucleus and mitochondria to repair damaged DNA or to exert epigenetic regulation of gene transcription. OGG1 is involved in a wide range of physiological processes, such as DNA repair, oxidative stress, inflammation, fibrosis, and autophagy. In recent years, studies have found that OGG1 plays an important role in the progression of kidney diseases through repairing DNA, inducing inflammation, regulating autophagy and other transcriptional regulation, and governing protein interactions and functions during disease and injury. In particular, the epigenetic effects of OGG1 in kidney disease have gradually attracted widespread attention. This study reviews the structure and biological functions of OGG1 and the regulatory mechanism of OGG1 in kidney disease. In addition, the possibility of OGG1 as a potential therapeutic target in kidney disease is discussed.
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40
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Sadiku OO, Rodríguez-Seijo A. Metabolic and genetic derangement: a review of mechanisms involved in arsenic and lead toxicity and genotoxicity. Arh Hig Rada Toksikol 2022; 73:244-255. [PMID: 36607725 PMCID: PMC9985351 DOI: 10.2478/aiht-2022-73-3669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/01/2022] [Accepted: 10/01/2022] [Indexed: 01/07/2023] Open
Abstract
Urbanisation and industrialisation are on the rise all over the world. Environmental contaminants such as potentially toxic elements (PTEs) are directly linked with both phenomena. Two PTEs that raise greatest concern are arsenic (As) and lead (Pb) as soil and drinking water contaminants, whether they are naturally occurring or the consequence of human activities. Both elements are potential carcinogens. This paper reviews the mechanisms by which As and Pb impair metabolic processes and cause genetic damage in humans. Despite efforts to ban or limit their use, due to high persistence both continue to pose a risk to human health, which justifies the need for further toxicological research.
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Affiliation(s)
- Olubusayo Olujimi Sadiku
- University of Lagos, College of Medicine, Faculty of Basic Medical Sciences, Department of Medical Laboratory Science, Lagos, Nigeria
| | - Andrés Rodríguez-Seijo
- University of Porto, Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Matosinhos, Portugal
- University of Porto, Faculty of Sciences, Biology Department, Porto, Portugal
- University of Vigo, Department of Plant Biology and Soil Sciences, Ourense, Spain
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41
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Fleming AM, Tran R, Omaga CA, Manage SAH, Burrows CJ, Conboy JC. Second Harmonic Generation Interrogation of the Endonuclease APE1 Binding Interaction with G-Quadruplex DNA. Anal Chem 2022; 94:15027-15032. [PMID: 36269876 PMCID: PMC9945475 DOI: 10.1021/acs.analchem.2c02951] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The binding interaction between the DNA repair enzyme apurinic/apyrimidinic endonuclease-1 (APE1) with promoter G-quadruplex (G4) folds bearing an abasic site (AP) can serve as a gene regulatory switch during oxidative stress. Prior fluorescence-based analysis in solution suggested APE1 binds the VEGF promoter G4 but whether this interaction was specific or not remained an open question. Second harmonic generation (SHG) was used in this work to measure the noncanonical DNA-protein binding interaction in a label-free assay with high sensitivity to demonstrate the interaction is ordered and specific. The binding of APE1 to the VEGF promoter G4 with AP sites modeled by a tetrahydrofuran analogue produced dissociation constants of ∼100 nM that differed from duplex and single-stranded DNA control studies. The SHG measurements confirmed APE1 binds the VEGF G4 folds in a specific manner resolving a remaining question regarding how this endonuclease with gene regulatory features engages G4 folds. The studies demonstrate the power of SHG to interrogate noncanonical DNA-protein interactions providing a foundational example for the use of this analytical method in future biochemical analyses.
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Affiliation(s)
- Aaron M. Fleming
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
| | - Renee Tran
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
| | - Carla A. Omaga
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
| | - Shereen A. Howpay Manage
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
| | - Cynthia J. Burrows
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
| | - John C. Conboy
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
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42
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Hahm JY, Park J, Jang ES, Chi SW. 8-Oxoguanine: from oxidative damage to epigenetic and epitranscriptional modification. Exp Mol Med 2022; 54:1626-1642. [PMID: 36266447 PMCID: PMC9636213 DOI: 10.1038/s12276-022-00822-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/06/2022] [Accepted: 05/26/2022] [Indexed: 12/29/2022] Open
Abstract
In pathophysiology, reactive oxygen species control diverse cellular phenotypes by oxidizing biomolecules. Among these, the guanine base in nucleic acids is the most vulnerable to producing 8-oxoguanine, which can pair with adenine. Because of this feature, 8-oxoguanine in DNA (8-oxo-dG) induces a G > T (C > A) mutation in cancers, which can be deleterious and thus actively repaired by DNA repair pathways. 8-Oxoguanine in RNA (o8G) causes problems in aberrant quality and translational fidelity, thereby it is subjected to the RNA decay pathway. In addition to oxidative damage, 8-oxo-dG serves as an epigenetic modification that affects transcriptional regulatory elements and other epigenetic modifications. With the ability of o8G•A in base pairing, o8G alters structural and functional RNA-RNA interactions, enabling redirection of posttranscriptional regulation. Here, we address the production, regulation, and function of 8-oxo-dG and o8G under oxidative stress. Primarily, we focus on the epigenetic and epitranscriptional roles of 8-oxoguanine, which highlights the significance of oxidative modification in redox-mediated control of gene expression.
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Affiliation(s)
- Ja Young Hahm
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Jongyeun Park
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Eun-Sook Jang
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Sung Wook Chi
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02481 Republic of Korea
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43
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Tanner L, Bergwik J, Bhongir RKV, Pan L, Dong C, Wallner O, Kalderén C, Helleday T, Boldogh I, Adner M, Egesten A. Pharmacological OGG1 inhibition decreases murine allergic airway inflammation. Front Pharmacol 2022; 13:999180. [PMID: 36324676 PMCID: PMC9619105 DOI: 10.3389/fphar.2022.999180] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/05/2022] [Indexed: 12/01/2022] Open
Abstract
Background and aim: Allergic asthma is a complex inflammatory disease involving type 2 innate lymphoid cells, type 2 T helper cells, macrophages, and eosinophils. The disease is characterized by wheezing, dyspnea, coughing, chest tightness and variable airflow limitation for which there is no cure and is symptomatically treated with inhaled corticosteroids and β2-agonists. Molecular mechanisms underlying its complex pathogenesis are not fully understood. However, 8-oxoguanine DNA glycosylase-1 (OGG1), a DNA repair protein may play a central role, as OGG1 deficiency decreases both innate and allergic inflammation. Methods: Using a murine ovalbumin (OVA) model of allergic airway inflammation we assessed the utility of an inhibitor of OGG1 (TH5487) in this disease context. Cytokines and chemokines, promoting immune cell recruitment were measured using a 23-multiplex assay and Western blotting. Additionally, immune cell recruitment to bronchi was measured using flow cytometry. Histological analyses and immunofluorescent staining were used to confirm immune cell influx and goblet cell hyperplasia of the airways. A PCR array was used to assess asthma-related genes in murine lung tissue following TH5487 treatment. Finally, airway hyperresponsiveness was determined using in vivo lung function measurement. Results: In this study, administration of TH5487 to mice with OVA-induced allergic airway inflammation significantly decreased goblet cell hyperplasia and mucus production. TH5487 treatment also decreased levels of activated NF-κB and expression of proinflammatory cytokines and chemokines resulting in significantly lower recruitment of eosinophils and other immune cells to the lungs. Gene expression profiling of asthma and allergy-related proteins after TH5487 treatment revealed differences in several important regulators, including down regulation of Tnfrsf4, Arg1, Ccl12 and Ccl11, and upregulation of the negative regulator of type 2 inflammation, Bcl6. Furthermore, the gene Clca1 was upregulated following TH5487 treatment, which should be explored further due to its ambiguous role in allergic asthma. In addition, the OVA-induced airway hyperresponsiveness was significantly reduced by TH5487 treatment. Conclusion: Taken together, the data presented in this study suggest OGG1 as a clinically relevant pharmacological target for the treatment of allergic inflammation.
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Affiliation(s)
- Lloyd Tanner
- Department of Clinical Sciences Lund, Respiratory Medicine, Allergology, and Palliative Medicine, Lund University and Skåne University Hospital, Lund, Sweden
- *Correspondence: Lloyd Tanner,
| | - Jesper Bergwik
- Department of Clinical Sciences Lund, Respiratory Medicine, Allergology, and Palliative Medicine, Lund University and Skåne University Hospital, Lund, Sweden
| | - Ravi K. V. Bhongir
- Department of Clinical Sciences Lund, Respiratory Medicine, Allergology, and Palliative Medicine, Lund University and Skåne University Hospital, Lund, Sweden
| | - Lang Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, United States
| | - Caijuan Dong
- Unit of Experimental Asthma and Allergy Research, Institute of Environmental Medicine (IMM), Karolinska Institutet, Stockholm, Sweden
| | - Olov Wallner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Christina Kalderén
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Oxcia AB, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Oxcia AB, Stockholm, Sweden
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, United States
| | - Mikael Adner
- Unit of Experimental Asthma and Allergy Research, Institute of Environmental Medicine (IMM), Karolinska Institutet, Stockholm, Sweden
| | - Arne Egesten
- Department of Clinical Sciences Lund, Respiratory Medicine, Allergology, and Palliative Medicine, Lund University and Skåne University Hospital, Lund, Sweden
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44
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Lodato MA, Ziegenfuss JS. The two faces of DNA oxidation in genomic and functional mosaicism during aging in human neurons. FRONTIERS IN AGING 2022; 3:991460. [PMID: 36313183 PMCID: PMC9596766 DOI: 10.3389/fragi.2022.991460] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022]
Abstract
Maintaining genomic integrity in post-mitotic neurons in the human brain is paramount because these cells must survive for an individual's entire lifespan. Due to life-long synaptic plasticity and electrochemical transmission between cells, the brain engages in an exceptionally high level of mitochondrial metabolic activity. This activity results in the generation of reactive oxygen species with 8-oxo-7,8-dihydroguanine (8-oxoG) being one of the most prevalent oxidation products in the cell. 8-oxoG is important for the maintenance and transfer of genetic information into proper gene expression: a low basal level of 8-oxoG plays an important role in epigenetic modulation of neurodevelopment and synaptic plasticity, while a dysregulated increase in 8-oxoG damages the genome leading to somatic mutations and transcription errors. The slow yet persistent accumulation of DNA damage in the background of increasing cellular 8-oxoG is associated with normal aging as well as neurological disorders such as Alzheimer's disease and Parkinson's disease. This review explores the current understanding of how 8-oxoG plays a role in brain function and genomic instability, highlighting new methods being used to advance pathological hallmarks that differentiate normal healthy aging and neurodegenerative disease.
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45
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Konis SMR, Hughes JR, Parsons JL. TRIM26 Maintains Cell Survival in Response to Oxidative Stress through Regulating DNA Glycosylase Stability. Int J Mol Sci 2022; 23:ijms231911613. [PMID: 36232914 PMCID: PMC9569934 DOI: 10.3390/ijms231911613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
Oxidative DNA base lesions in DNA are repaired through the base excision repair (BER) pathway, which consequently plays a vital role in the maintenance of genome integrity and in suppressing mutagenesis. 8-oxoguanine DNA glycosylase (OGG1), endonuclease III-like protein 1 (NTH1), and the endonuclease VIII-like proteins 1-3 (NEIL1-3) are the key enzymes that initiate repair through the excision of the oxidized base. We have previously identified that the E3 ubiquitin ligase tripartite motif 26 (TRIM26) controls the cellular response to oxidative stress through regulating both NEIL1 and NTH1, although its potential, broader role in BER is unclear. We now show that TRIM26 is a central player in determining the response to different forms of oxidative stress. Using siRNA-mediated knockdowns, we demonstrate that the resistance of cells to X-ray radiation and hydrogen peroxide generated as a consequence of trim26 depletion can be reversed through suppression of selective DNA glycosylases. In particular, a knockdown of neil1 or ogg1 can enhance sensitivity and DNA repair rates in response to X-rays, whereas a knockdown of neil1 or neil3 can produce the same effect in response to hydrogen peroxide. Our study, therefore, highlights the importance of TRIM26 in balancing cellular DNA glycosylase levels required for an efficient BER response.
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Affiliation(s)
- Sifaddin M. R. Konis
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Jonathan R. Hughes
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Jason L. Parsons
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6 West Derby Street, Liverpool L7 8TX, UK
- Clatterbridge Cancer Centre NHS Foundation Trust, Clatterbridge Road, Bebington CH63 4JY, UK
- Correspondence: ; Tel.: +44-151-794-8848
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46
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Bangalore DM, Tessmer I. Direct hOGG1-Myc interactions inhibit hOGG1 catalytic activity and recruit Myc to its promoters under oxidative stress. Nucleic Acids Res 2022; 50:10385-10398. [PMID: 36156093 PMCID: PMC9561264 DOI: 10.1093/nar/gkac796] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The base excision repair (BER) glycosylase hOGG1 (human oxoguanine glycosylase 1) is responsible for repairing oxidative lesions in the genome, in particular oxidised guanine bases (oxoG). In addition, a role of hOGG1 in transcription regulation by recruitment of various transcription factors has been reported. Here, we demonstrate direct interactions between hOGG1 and the medically important oncogene transcription factor Myc that is involved in transcription initiation of a large number of genes including inflammatory genes. Using single molecule atomic force microscopy (AFM), we reveal recruitment of Myc to its E-box promoter recognition sequence by hOGG1 specifically under oxidative stress conditions, and conformational changes in hOGG1-Myc complexes at oxoG lesions that suggest loading of Myc at oxoG lesions by hOGG1. Importantly, our data show suppression of hOGG1 catalytic activity in oxoG repair by Myc. Furthermore, mutational analyses implicate the C28 residue in hOGG1 in oxidation induced protein dimerisation and suggest a role of hOGG1 dimerisation under oxidising conditions in hOGG1-Myc interactions. From our data we develop a mechanistic model for Myc recruitment by hOGG1 under oxidising, inflammatory conditions, which may be responsible for the observed enhanced gene expression of Myc target genes.
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Affiliation(s)
- Disha M Bangalore
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
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47
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Manage SAH, Fleming AM, Chen HN, Burrows CJ. Cysteine Oxidation to Sulfenic Acid in APE1 Aids G-Quadruplex Binding While Compromising DNA Repair. ACS Chem Biol 2022; 17:2583-2594. [PMID: 36037088 PMCID: PMC9931449 DOI: 10.1021/acschembio.2c00511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Apurinic/apyrimidinic endonuclease-1 (APE1) is a base excision repair (BER) enzyme that is also engaged in transcriptional regulation. Previous work demonstrated that the enzymatic stalling of APE1 on a promoter G-quadruplex (G4) recruits transcription factors during oxidative stress for gene regulation. Also, during oxidative stress, cysteine (Cys) oxidation is a post-translational modification (PTM) that can change a protein's function. The current study provides a quantitative survey of cysteine oxidation to sulfenic acid in APE1 and how this PTM at specific cysteine residues affects the function of APE1 toward the NEIL3 gene promoter G4 bearing an abasic site. Of the seven cysteine residues in APE1, five (C65, C93, C208, C296, and C310) were prone to carbonate radical anion oxidation to yield sulfenic acids that were identified and quantified by mass spectrometry. Accordingly, five Cys-to-serine (Ser) mutants of APE1 were prepared and found to have attenuated levels of endonuclease activity, depending on the position, while KD values generally decreased for G4 binding, indicating greater affinity. These data support the concept that cysteine oxidation to sulfenic acid can result in modified APE1 that enhances G4 binding at the expense of endonuclease activity during oxidative stress. Cysteine oxidation to sulfenic acid residues should be considered as one of the factors that may trigger a switch from base excision repair activity to transcriptional modulation by APE1.
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Affiliation(s)
- Shereen A. Howpay Manage
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Aaron M. Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Hsiao-Nung Chen
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
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48
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Xue Z, Demple B. Knockout and Inhibition of Ape1: Roles of Ape1 in Base Excision DNA Repair and Modulation of Gene Expression. Antioxidants (Basel) 2022; 11:antiox11091817. [PMID: 36139891 PMCID: PMC9495735 DOI: 10.3390/antiox11091817] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
Apurinic/apyrimidinic endonuclease 1/redox effector-1 (Ape1/Ref-1) is the major apurinic/apyrimidinic (AP) endonuclease in mammalian cells. It functions mainly in the base excision repair pathway to create a suitable substrate for DNA polymerases. Human Ape1 protein can activate some transcription factors to varying degrees, dependent on its N-terminal, unstructured domain, and some of the cysteines within it, apparently via a redox mechanism in some cases. Many cancer studies also suggest that Ape1 has potential for prognosis in terms of the protein level or intracellular localization. While homozygous disruption of the Ape1 structural gene APEX1 in mice causes embryonic lethality, and most studies in cell culture indicate that the expression of Ape1 is essential, some recent studies reported the isolation of viable APEX1 knockout cells with only mild phenotypes. It has not been established by what mechanism the Ape1-null cell lines cope with the endogenous DNA damage that the enzyme normally handles. We review the enzymatic and other activities of Ape1 and the recent studies of the properties of the APEX1 knockout lines. The APEX1 deletions in CH12F3 and HEK293 FT provide an opportunity to test for possible off-target effects of Ape1 inhibition. For this work, we tested the Ape1 endonuclease inhibitor Compound 3 and the redox inhibitor APX2009. Our results confirmed that both APEX1 knockout cell lines are modestly more sensitive to killing by an alkylating agent than their Ape1-proficient cells. Surprisingly, the knockout lines showed equal sensitivity to direct killing by either inhibitor, despite the lack of the target protein. Moreover, the CH12F3 APEX1 knockout was even more sensitive to Compound 3 than its APEX1+ counterpart. Thus, it appears that both Compound 3 and APX2009 have off-target effects. In cases where this issue may be important, it is advisable that more specific endpoints than cell survival be tested for establishing mechanism.
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Affiliation(s)
- Zhouyiyuan Xue
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794-8651, USA
- Molecular and Cellular Biochemistry Program, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Bruce Demple
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794-8651, USA
- Correspondence: ; Tel.: +1-(631)-444-3978
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49
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Akbari M, Nilsen HL, Montaldo NP. Dynamic features of human mitochondrial DNA maintenance and transcription. Front Cell Dev Biol 2022; 10:984245. [PMID: 36158192 PMCID: PMC9491825 DOI: 10.3389/fcell.2022.984245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022] Open
Abstract
Mitochondria are the primary sites for cellular energy production and are required for many essential cellular processes. Mitochondrial DNA (mtDNA) is a 16.6 kb circular DNA molecule that encodes only 13 gene products of the approximately 90 different proteins of the respiratory chain complexes and an estimated 1,200 mitochondrial proteins. MtDNA is, however, crucial for organismal development, normal function, and survival. MtDNA maintenance requires mitochondrially targeted nuclear DNA repair enzymes, a mtDNA replisome that is unique to mitochondria, and systems that control mitochondrial morphology and quality control. Here, we provide an overview of the current literature on mtDNA repair and transcription machineries and discuss how dynamic functional interactions between the components of these systems regulate mtDNA maintenance and transcription. A profound understanding of the molecular mechanisms that control mtDNA maintenance and transcription is important as loss of mtDNA integrity is implicated in normal process of aging, inflammation, and the etiology and pathogenesis of a number of diseases.
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Affiliation(s)
- Mansour Akbari
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Hilde Loge Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Unit for precision medicine, Akershus University Hospital, Nordbyhagen, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Nicola Pietro Montaldo
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- *Correspondence: Nicola Pietro Montaldo,
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50
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Ray S, Abugable AA, Parker J, Liversidge K, Palminha NM, Liao C, Acosta-Martin AE, Souza CDS, Jurga M, Sudbery I, El-Khamisy SF. A mechanism for oxidative damage repair at gene regulatory elements. Nature 2022; 609:1038-1047. [PMID: 36171374 DOI: 10.1038/s41586-022-05217-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/09/2022] [Indexed: 11/09/2022]
Abstract
Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation1,2. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100 bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate-early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.
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Affiliation(s)
- Swagat Ray
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK.,School of Life and Environmental Sciences, Department of Life Sciences, University of Lincoln, Lincoln, UK
| | - Arwa A Abugable
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Jacob Parker
- School of Biosciences, University of Sheffield, Sheffield, UK.,Center for Advanced Parkinson Research, Harvard Medical School, Boston, MA, USA
| | | | - Nelma M Palminha
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Chunyan Liao
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Adelina E Acosta-Martin
- biOMICS Facility, Faculty of Science Mass Spectrometry Centre, University of Sheffield, Sheffield, UK
| | - Cleide D S Souza
- School of Biosciences, University of Sheffield, Sheffield, UK.,Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Mateusz Jurga
- Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK
| | - Ian Sudbery
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Sherif F El-Khamisy
- School of Biosciences, University of Sheffield, Sheffield, UK. .,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK. .,Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK.
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