1
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Urbancokova A, Hornofova T, Novak J, Salajkova SA, Stemberkova Hubackova S, Uvizl A, Buchtova T, Mistrik M, McStay B, Hodny Z, Bartek J, Vasicova P. Topological stress triggers persistent DNA lesions in ribosomal DNA with ensuing formation of PML-nucleolar compartment. eLife 2024; 12:RP91304. [PMID: 39388244 PMCID: PMC11466457 DOI: 10.7554/elife.91304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024] Open
Abstract
PML, a multifunctional protein, is crucial for forming PML-nuclear bodies involved in stress responses. Under specific conditions, PML associates with nucleolar caps formed after RNA polymerase I (RNAPI) inhibition, leading to PML-nucleolar associations (PNAs). This study investigates PNAs-inducing stimuli by exposing cells to various genotoxic stresses. We found that the most potent inducers of PNAs introduced topological stress and inhibited RNAPI. Doxorubicin, the most effective compound, induced double-strand breaks (DSBs) in the rDNA locus. PNAs co-localized with damaged rDNA, segregating it from active nucleoli. Cleaving the rDNA locus with I-PpoI confirmed rDNA damage as a genuine stimulus for PNAs. Inhibition of ATM, ATR kinases, and RAD51 reduced I-PpoI-induced PNAs, highlighting the importance of ATM/ATR-dependent nucleolar cap formation and homologous recombination (HR) in their triggering. I-PpoI-induced PNAs co-localized with rDNA DSBs positive for RPA32-pS33 but deficient in RAD51, indicating resected DNA unable to complete HR repair. Our findings suggest that PNAs form in response to persistent rDNA damage within the nucleolar cap, highlighting the interplay between PML/PNAs and rDNA alterations due to topological stress, RNAPI inhibition, and rDNA DSBs destined for HR. Cells with persistent PNAs undergo senescence, suggesting PNAs help avoid rDNA instability, with implications for tumorigenesis and aging.
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Affiliation(s)
- Alexandra Urbancokova
- Laboratory of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Terezie Hornofova
- Laboratory of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Josef Novak
- Laboratory of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Sarka Andrs Salajkova
- Laboratory of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Sona Stemberkova Hubackova
- Laboratory of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Alena Uvizl
- Laboratory of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Tereza Buchtova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University OlomoucOlomoucCzech Republic
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University OlomoucOlomoucCzech Republic
| | - Brian McStay
- Centre for Chromosome Biology, College of Science and Engineering, University of GalwayGalwayIreland
| | - Zdenek Hodny
- Laboratory of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Jiri Bartek
- Laboratory of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
- Genome Integrity Unit, Danish Cancer Society Research CenterCopenhagenDenmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska InstitutetStockholmSweden
| | - Pavla Vasicova
- Laboratory of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
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2
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Pozzetti L, Asquith CRM. Pentathiepins are an understudied molecular prism of biological activities. Arch Pharm (Weinheim) 2024:e2400646. [PMID: 39382224 DOI: 10.1002/ardp.202400646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Revised: 09/16/2024] [Accepted: 09/18/2024] [Indexed: 10/10/2024]
Abstract
The pentathiepin core was first synthesized in 1971, and while synthetic techniques have progressed over subsequent decades, the biological applications of this heterocycle have received less attention and are only now becoming more apparent. The first natural product, varacin, was identified in 1991, showing cytotoxicity toward a human colon cancer cell line. More recently, the pentathiepin has acted as a surrogate to replace elemental sulfur, that was discovered as a hit in neurodegenerative animal models. A variety of other medicinal chemistry applications have recently been disclosed. Here, we summarize these indications and highlight the main synthetic pathways to access the pentathiepin core. We offer a concise summary and future perspective of this unique sulfur isosteric replacement.
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Affiliation(s)
- Luca Pozzetti
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Christopher R M Asquith
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
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3
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Lascaux P, Hoslett G, Tribble S, Trugenberger C, Antičević I, Otten C, Torrecilla I, Koukouravas S, Zhao Y, Yang H, Aljarbou F, Ruggiano A, Song W, Peron C, Deangeli G, Domingo E, Bancroft J, Carrique L, Johnson E, Vendrell I, Fischer R, Ng AWT, Ngeow J, D'Angiolella V, Raimundo N, Maughan T, Popović M, Milošević I, Ramadan K. TEX264 drives selective autophagy of DNA lesions to promote DNA repair and cell survival. Cell 2024; 187:5698-5718.e26. [PMID: 39265577 DOI: 10.1016/j.cell.2024.08.020] [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: 10/27/2023] [Revised: 06/04/2024] [Accepted: 08/10/2024] [Indexed: 09/14/2024]
Abstract
DNA repair and autophagy are distinct biological processes vital for cell survival. Although autophagy helps maintain genome stability, there is no evidence of its direct role in the repair of DNA lesions. We discovered that lysosomes process topoisomerase 1 cleavage complexes (TOP1cc) DNA lesions in vertebrates. Selective degradation of TOP1cc by autophagy directs DNA damage repair and cell survival at clinically relevant doses of topoisomerase 1 inhibitors. TOP1cc are exported from the nucleus to lysosomes through a transient alteration of the nuclear envelope and independent of the proteasome. Mechanistically, the autophagy receptor TEX264 acts as a TOP1cc sensor at DNA replication forks, triggering TOP1cc processing by the p97 ATPase and mediating the delivery of TOP1cc to lysosomes in an MRE11-nuclease- and ATR-kinase-dependent manner. We found an evolutionarily conserved role for selective autophagy in DNA repair that enables cell survival, protects genome stability, and is clinically relevant for colorectal cancer patients.
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Affiliation(s)
- Pauline Lascaux
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Gwendoline Hoslett
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Sara Tribble
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Camilla Trugenberger
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ivan Antičević
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Cecile Otten
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Ignacio Torrecilla
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Stelios Koukouravas
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Yichen Zhao
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Hongbin Yang
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ftoon Aljarbou
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Annamaria Ruggiano
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Wei Song
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Cristiano Peron
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Giulio Deangeli
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 2PY, UK
| | - Enric Domingo
- Department of Oncology, Medical Sciences Division, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - James Bancroft
- Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK
| | - Loïc Carrique
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK
| | - Errin Johnson
- Dunn School Bioimaging Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK
| | - Alvin Wei Tian Ng
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore
| | - Joanne Ngeow
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore; Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Vincenzo D'Angiolella
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Nuno Raimundo
- Penn State College of Medicine, Department of Cellular and Molecular Physiology, Hershey, PA 17033, USA; Multidisciplinary Institute for Aging, Center for Innovation in Biomedicine and Biotechnology, University of Coimbra, Coimbra 3000-370, Portugal
| | - Tim Maughan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, UK
| | - Marta Popović
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Ira Milošević
- Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK; Multidisciplinary Institute for Aging, Center for Innovation in Biomedicine and Biotechnology, University of Coimbra, Coimbra 3000-370, Portugal
| | - Kristijan Ramadan
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore.
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4
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Wojtaszek JL, Williams RS. From the TOP: Formation, recognition and resolution of topoisomerase DNA protein crosslinks. DNA Repair (Amst) 2024; 142:103751. [PMID: 39180935 PMCID: PMC11404304 DOI: 10.1016/j.dnarep.2024.103751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
Since the report of "DNA untwisting" activity in 1972, ∼50 years of research has revealed seven topoisomerases in humans (TOP1, TOP1mt, TOP2α, TOP2β, TOP3α, TOP3β and Spo11). These conserved regulators of DNA topology catalyze controlled breakage to the DNA backbone to relieve the torsional stress that accumulates during essential DNA transactions including DNA replication, transcription, and DNA repair. Each topoisomerase-catalyzed reaction involves the formation of a topoisomerase cleavage complex (TOPcc), a covalent protein-DNA reaction intermediate formed between the DNA phosphodiester backbone and a topoisomerase catalytic tyrosine residue. A variety of perturbations to topoisomerase reaction cycles can trigger failure of the enzyme to re-ligate the broken DNA strand(s), thereby generating topoisomerase DNA-protein crosslinks (TOP-DPC). TOP-DPCs pose unique threats to genomic integrity. These complex lesions are comprised of structurally diverse protein components covalently linked to genomic DNA, which are bulky DNA adducts that can directly impact progression of the transcription and DNA replication apparatus. A variety of genome maintenance pathways have evolved to recognize and resolve TOP-DPCs. Eukaryotic cells harbor tyrosyl DNA phosphodiesterases (TDPs) that directly reverse 3'-phosphotyrosyl (TDP1) and 5'-phoshotyrosyl (TDP2) protein-DNA linkages. The broad specificity Mre11-Rad50-Nbs1 and APE2 nucleases are also critical for mitigating topoisomerase-generated DNA damage. These DNA-protein crosslink metabolizing enzymes are further enabled by proteolytic degradation, with the proteasome, Spartan, GCNA, Ddi2, and FAM111A proteases implicated thus far. Strategies to target, unfold, and degrade the protein component of TOP-DPCs have evolved as well. Here we survey mechanisms for addressing Topoisomerase 1 (TOP1) and Topoisomerase 2 (TOP2) DPCs, highlighting systems for which molecular structure information has illuminated function of these critical DNA damage response pathways.
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Affiliation(s)
- Jessica L Wojtaszek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States.
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5
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Johnson D, Allison RM, Cannavo E, Cejka P, Harper JA, Neale MJ. Exploring the removal of Spo11 and topoisomerases from DNA breaks in S. cerevisiae by human Tyrosyl DNA Phosphodiesterase 2. DNA Repair (Amst) 2024; 142:103757. [PMID: 39236418 DOI: 10.1016/j.dnarep.2024.103757] [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: 06/01/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/07/2024]
Abstract
Meiotic recombination is initiated by DNA double-strand breaks (DSBs) created by Spo11, a type-II topoisomerase-like protein that becomes covalently linked to DSB ends. Whilst Spo11 oligos-the products of nucleolytic removal by Mre11-have been detected in several organisms, the lifetime of the covalent Spo11-DSB precursor has not been determined and may be subject to alternative processing. Here, we explore the activity of human Tyrosyl DNA Phosphodiesterase, TDP2-a protein known to repair DNA ends arising from abortive topoisomerase activity-on Spo11 DSBs isolated from S. cerevisiae cells. We demonstrate that TDP2 can remove Spo11 peptides from ssDNA oligos and dsDNA ends even in the presence of competitor genomic DNA. Interestingly, TDP2-processed DSB ends are refractory to resection by Exo1, suggesting that ssDNA generated by Mre11 may be essential in vivo to facilitate HR at Spo11 DSBs even if TDP2 were active. Moreover, although TDP2 can remove Spo11 peptides in vitro, TDP2 expression in meiotic cells was unable to remove Spo11 in vivo-contrasting its ability to aid repair of topoisomerase-induced DNA lesions. These results suggest that Spo11-DNA, but not topoisomerase-DNA cleavage complexes, are inaccessible to the TDP2 enzyme, perhaps due to occlusion by higher-order protein complexes at sites of meiotic recombination.
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Affiliation(s)
- Dominic Johnson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton UK
| | - Rachal M Allison
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton UK
| | - Elda Cannavo
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich 8093, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich 8093, Switzerland
| | - Jon A Harper
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton UK
| | - Matthew J Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton UK.
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6
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Belhadj Z, Akther T, Wang Z, Xie J. Characterization of a deazaflavin analog as a potent inhibitor of multidrug resistance-associated protein 1. Biomed Pharmacother 2024; 178:117167. [PMID: 39032285 DOI: 10.1016/j.biopha.2024.117167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/20/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
Selective inhibition of overexpressed ATP binding cassette (ABC) transporters is an attractive approach to enhancing the efficacy of chemotherapeutics in multidrug resistant cancers. Previously, we reported that the cancer sensitizing effect of deazaflavin analogs, an important chemotype for developing combination treatments with topoisomerase II (TOP2) poisons, is associated with increased intracellular drug accumulation. Here we report the characterization of ZW-1226, a deazaflavin analog, as a potent inhibitor of multidrug resistance-associated protein 1 (MRP1). Specifically, ZW-1226 inhibited MRP1 with a 16-fold higher potency than the most widely used positive control MK-571 in vesicular transport assay and displayed excellent selectivity indices exceeding 100 over other major ABC transporters, including P-glycoprotein (P-gp), breast cancer resistance protein (BCRP), MRP2 and MRP3. Mechanistically, we revealed that its MRP1 inhibitory action requires the participation of GSH. In chemo-sensitization test, ZW-1226 fully reversed the MRP1-mediated drug resistance to TOP2 poisons etoposide (ETP) and doxorubicin (DOX) in H69AR cells and conferred CC50s comparable to those in the sensitive parental NCI-H69 cells. The sensitization was associated with boosted intracellular accumulation of ETP and DOX and elevated endogenous GSH. Moreover, ZW-1226 showed potential to occupy the leukotriene C4 binding site in molecular docking with bovine MRP1, presumably with the help of GSH. Lastly, ZW-1226 exhibited high tissue to plasma partitions in mice but did not alter ETP distribution to normal tissues, suggesting it could be a viable lead with desirable pharmacokinetic properties to warrant further investigation.
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Affiliation(s)
- Zakia Belhadj
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Thamina Akther
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA.
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7
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Anticevic I, Otten C, Popovic M. Tyrosyl-DNA phosphodiesterase 2 (Tdp2) repairs DNA-protein crosslinks and protects against double strand breaks in vivo. Front Cell Dev Biol 2024; 12:1394531. [PMID: 39228401 PMCID: PMC11369425 DOI: 10.3389/fcell.2024.1394531] [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: 03/01/2024] [Accepted: 06/06/2024] [Indexed: 09/05/2024] Open
Abstract
DNA-protein crosslinks pose a significant challenge to genome stability and cell viability. Efficient repair of DPCs is crucial for preserving genomic integrity and preventing the accumulation of DNA damage. Despite recent advances in our understanding of DPC repair, many aspects of this process, especially at the organismal level, remain elusive. In this study, we used zebrafish as a model organism to investigate the role of TDP2 (Tyrosyl-DNA phosphodiesterase 2) in DPC repair. We characterized the two tdp2 orthologs in zebrafish using phylogenetic, syntenic and expression analysis and investigated the phenotypic consequences of tdp2 silencing in zebrafish embryos. We then quantified the effects of tdp2a and tdp2b silencing on cellular DPC levels and DSB accumulation in zebrafish embryos. Our findings revealed that tdp2b is the main ortholog during embryonic development, while both orthologs are ubiquitously present in adult tissues. Notably, the tdp2b ortholog is phylogenetically closer to human TDP2. Silencing of tdp2b, but not tdp2a, resulted in the loss of Tdp2 activity in zebrafish embryos, accompanied by the accumulation of DPCs and DSBs. Our findings contribute to a more comprehensive understanding of DPC repair at the organismal level and underscore the significance of TDP2 in maintaining genome stability.
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Affiliation(s)
| | | | - Marta Popovic
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruder Boskovic, Zagreb, Croatia
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8
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Manguso N, Kim M, Joshi N, Al Mahmud MR, Aldaco J, Suzuki R, Cortes-Ledesma F, Cui X, Yamada S, Takeda S, Giuliano A, You S, Tanaka H. TDP2 is a regulator of estrogen-responsive oncogene expression. NAR Cancer 2024; 6:zcae016. [PMID: 38596431 PMCID: PMC11000318 DOI: 10.1093/narcan/zcae016] [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: 04/28/2023] [Revised: 02/19/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
With its ligand estrogen, the estrogen receptor (ER) initiates a global transcriptional program, promoting cell growth. This process involves topoisomerase 2 (TOP2), a key protein in resolving topological issues during transcription by cleaving a DNA duplex, passing another duplex through the break, and repairing the break. Recent studies revealed the involvement of various DNA repair proteins in the repair of TOP2-induced breaks, suggesting potential alternative repair pathways in cases where TOP2 is halted after cleavage. However, the contribution of these proteins in ER-induced transcriptional regulation remains unclear. We investigated the role of tyrosyl-DNA phosphodiesterase 2 (TDP2), an enzyme for the removal of halted TOP2 from the DNA ends, in the estrogen-induced transcriptome using both targeted and global transcription analyses. MYC activation by estrogen, a TOP2-dependent and transient event, became prolonged in the absence of TDP2 in both TDP2-deficient cells and mice. Bulk and single-cell RNA-seq analyses defined MYC and CCND1 as oncogenes whose estrogen response is tightly regulated by TDP2. These results suggest that TDP2 may inherently participate in the repair of estrogen-induced breaks at specific genomic loci, exerting precise control over oncogenic gene expression.
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Affiliation(s)
- Nicholas Manguso
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Minhyung Kim
- Department of Urology and Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Neeraj Joshi
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Md Rasel Al Mahmud
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Juan Aldaco
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Ryusuke Suzuki
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Felipe Cortes-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Xiaojiang Cui
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Shintaro Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Armando Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Sungyong You
- Department of Urology and Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
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9
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Geraud M, Cristini A, Salimbeni S, Bery N, Jouffret V, Russo M, Ajello AC, Fernandez Martinez L, Marinello J, Cordelier P, Trouche D, Favre G, Nicolas E, Capranico G, Sordet O. TDP1 mutation causing SCAN1 neurodegenerative syndrome hampers the repair of transcriptional DNA double-strand breaks. Cell Rep 2024; 43:114214. [PMID: 38761375 DOI: 10.1016/j.celrep.2024.114214] [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: 03/02/2023] [Revised: 03/05/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024] Open
Abstract
TDP1 removes transcription-blocking topoisomerase I cleavage complexes (TOP1ccs), and its inactivating H493R mutation causes the neurodegenerative syndrome SCAN1. However, the molecular mechanism underlying the SCAN1 phenotype is unclear. Here, we generate human SCAN1 cell models using CRISPR-Cas9 and show that they accumulate TOP1ccs along with changes in gene expression and genomic distribution of R-loops. SCAN1 cells also accumulate transcriptional DNA double-strand breaks (DSBs) specifically in the G1 cell population due to increased DSB formation and lack of repair, both resulting from abortive removal of transcription-blocking TOP1ccs. Deficient TDP1 activity causes increased DSB production, and the presence of mutated TDP1 protein hampers DSB repair by a TDP2-dependent backup pathway. This study provides powerful models to study TDP1 functions under physiological and pathological conditions and unravels that a gain of function of the mutated TDP1 protein, which prevents DSB repair, rather than a loss of TDP1 activity itself, could contribute to SCAN1 pathogenesis.
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Affiliation(s)
- Mathéa Geraud
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Agnese Cristini
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Simona Salimbeni
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France; Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Nicolas Bery
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Virginie Jouffret
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France; BigA Core Facility, Centre de Biologie Intégrative (CBI), Université de Toulouse, 31062 Toulouse, France
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Andrea Carla Ajello
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Lara Fernandez Martinez
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Pierre Cordelier
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Didier Trouche
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Estelle Nicolas
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy.
| | - Olivier Sordet
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France.
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10
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Trifault B, Mamontova V, Cossa G, Ganskih S, Wei Y, Hofstetter J, Bhandare P, Baluapuri A, Nieto B, Solvie D, Ade CP, Gallant P, Wolf E, Larsen DH, Munschauer M, Burger K. Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts. Nucleic Acids Res 2024; 52:3050-3068. [PMID: 38224452 PMCID: PMC11014278 DOI: 10.1093/nar/gkae022] [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: 07/13/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/16/2024] Open
Abstract
RNA-binding proteins emerge as effectors of the DNA damage response (DDR). The multifunctional non-POU domain-containing octamer-binding protein NONO/p54nrb marks nuclear paraspeckles in unperturbed cells, but also undergoes re-localization to the nucleolus upon induction of DNA double-strand breaks (DSBs). However, NONO nucleolar re-localization is poorly understood. Here we show that the topoisomerase II inhibitor etoposide stimulates the production of RNA polymerase II-dependent, DNA damage-inducible antisense intergenic non-coding RNA (asincRNA) in human cancer cells. Such transcripts originate from distinct nucleolar intergenic spacer regions and form DNA-RNA hybrids to tether NONO to the nucleolus in an RNA recognition motif 1 domain-dependent manner. NONO occupancy at protein-coding gene promoters is reduced by etoposide, which attenuates pre-mRNA synthesis, enhances NONO binding to pre-mRNA transcripts and is accompanied by nucleolar detention of a subset of such transcripts. The depletion or mutation of NONO interferes with detention and prolongs DSB signalling. Together, we describe a nucleolar DDR pathway that shields NONO and aberrant transcripts from DSBs to promote DNA repair.
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Affiliation(s)
- Barbara Trifault
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Victoria Mamontova
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Giacomo Cossa
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Yuanjie Wei
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Julia Hofstetter
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Pranjali Bhandare
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Blanca Nieto
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, Copenhagen, Denmark
| | - Daniel Solvie
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Carsten P Ade
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Peter Gallant
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, Copenhagen, Denmark
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Kaspar Burger
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
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11
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Elkhadragy L, Myers A, Long W. Role of the Atypical MAPK ERK3 in Cancer Growth and Progression. Cancers (Basel) 2024; 16:1381. [PMID: 38611058 PMCID: PMC11011113 DOI: 10.3390/cancers16071381] [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: 03/02/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Extracellular signal-regulated kinase 3 (ERK3) is an atypical mitogen-activated protein kinase (MAPK) whose structural and regulatory features are distinct from those of conventional MAPKs, such as ERK1/2. Since its identification in 1991, the regulation, substrates and functions of ERK3 have remained largely unknown. However, recent years have witnessed a wealth of new findings about ERK3 signaling. Several important biological functions for ERK3 have been revealed, including its role in neuronal morphogenesis, inflammation, metabolism, endothelial cell tube formation and epithelial architecture. In addition, ERK3 has been recently shown to play important roles in cancer cell proliferation, migration, invasion and chemoresistance in multiple types of cancers. Furthermore, accumulating studies have uncovered various molecular mechanisms by which the expression level, protein stability and activity of ERK3 are regulated. In particular, several post-translational modifications (PTMs), including ubiquitination, hydroxylation and phosphorylation, have been shown to regulate the stability and activity of ERK3 protein. In this review, we discuss recent findings regarding biochemical and cellular functions of ERK3, with a main focus on its roles in cancers, as well as the molecular mechanisms of regulating its expression and activity.
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Affiliation(s)
- Lobna Elkhadragy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA; (L.E.); (A.M.)
- Department of Radiology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Amanda Myers
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA; (L.E.); (A.M.)
| | - Weiwen Long
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA; (L.E.); (A.M.)
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12
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Belhadj Z, Offei S, Jacobson BA, Cambron D, Kratzke RA, Wang Z, Xie J. Cancer sensitizing effect of deazaflavin analogs is associated with increased intracellular drug accumulation. Eur J Pharm Sci 2024; 193:106686. [PMID: 38159687 DOI: 10.1016/j.ejps.2023.106686] [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: 07/26/2023] [Revised: 12/06/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
As part of our efforts geared towards developing mechanism-based cancer sensitizing agents, we have previously synthesized and characterized novel deazaflavin analogs as potent tyrosyl DNA phosphodiesterase 2 (TDP2) inhibitors for combination treatments with topoisomerase II (TOP2) poisons. Interestingly, the sensitizing effect of a few analogs toward TOP2 poison etoposide (ETP) was associated with a significant increase in intracellular drug accumulation, which could be an alternative mechanism to boost the clinical efficacy of ETP in cancer chemotherapies. Hence, we evaluated more deazaflavin TDP2 inhibitors for their impact on drug retention in cancer cells. We found that all but one tested TDP2 inhibitors substantially increased the ETP retention in DT40 cells. Particularly, we identified an exceptionally potent analog, ZW-1226, which at 3 nM increased the intracellular ETP by 13-fold. Significantly, ZW-1226 also stimulated cellular accumulation of two other anticancer drugs, TOP2 poison teniposide and antifolate pemetrexed, and produced an effect more pronounced than those of ABC transporter inhibitors verapamil and elacridar in human leukemic CCRF-CEM cells toward ETP. Lastly, ZW-1226 potentiated the action of ETP in the sensitive human CCRF-CEM cells and a few resistant non-small-cell lung cancer (NSCLC) cells, including H460 and H838 cells. Collectively, the results of this study strongly suggest that deazaflavin analog ZW-1226 could be an effective cancer sensitizing agent which warrants further investigation.
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Affiliation(s)
- Zakia Belhadj
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samuel Offei
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Blake A Jacobson
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Daniel Cambron
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Robert A Kratzke
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA.
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13
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Yamazaki K, Iguchi T, Kanoh Y, Takayasu K, Ngo TTT, Onuki A, Kawaji H, Oshima S, Kanda T, Masai H, Sasanuma H. Homologous recombination contributes to the repair of acetaldehyde-induced DNA damage. Cell Cycle 2024; 23:369-384. [PMID: 38571319 PMCID: PMC11174073 DOI: 10.1080/15384101.2024.2335028] [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: 11/04/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Acetaldehyde, a chemical that can cause DNA damage and contribute to cancer, is prevalently present in our environment, e.g. in alcohol, tobacco, and food. Although aldehyde potentially promotes crosslinking reactions among biological substances including DNA, RNA, and protein, it remains unclear what types of DNA damage are caused by acetaldehyde and how they are repaired. In this study, we explored mechanisms involved in the repair of acetaldehyde-induced DNA damage by examining the cellular sensitivity to acetaldehyde in the collection of human TK6 mutant deficient in each genome maintenance system. Among the mutants, mismatch repair mutants did not show hypersensitivity to acetaldehyde, while mutants deficient in base and nucleotide excision repair pathways or homologous recombination (HR) exhibited higher sensitivity to acetaldehyde than did wild-type cells. We found that acetaldehyde-induced RAD51 foci representing HR intermediates were prolonged in HR-deficient cells. These results indicate a pivotal role of HR in the repair of acetaldehyde-induced DNA damage. These results suggest that acetaldehyde causes complex DNA damages that require various types of repair pathways. Mutants deficient in the removal of protein adducts from DNA ends such as TDP1-/- and TDP2-/- cells exhibited hypersensitivity to acetaldehyde. Strikingly, the double mutant deficient in both TDP1 and RAD54 showed similar sensitivity to each single mutant. This epistatic relationship between TDP1-/- and RAD54-/- suggests that the protein-DNA adducts generated by acetaldehyde need to be removed for efficient repair by HR. Our study would help understand the molecular mechanism of the genotoxic and mutagenic effects of acetaldehyde.
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Affiliation(s)
- Kosuke Yamazaki
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tomohiro Iguchi
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yutaka Kanoh
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kazuto Takayasu
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Trinh Thi To Ngo
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Ayaka Onuki
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hideya Kawaji
- Research Center for Genome and Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Shunji Oshima
- Sustainable Technology Laboratories, Asahi Quality & Innovations Ltd, Ibaraki, Japan
| | | | - Hisao Masai
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hiroyuki Sasanuma
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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14
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Essawy MM, Campbell C. Enzymatic Processing of DNA-Protein Crosslinks. Genes (Basel) 2024; 15:85. [PMID: 38254974 PMCID: PMC10815813 DOI: 10.3390/genes15010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
DNA-protein crosslinks (DPCs) represent a unique and complex form of DNA damage formed by covalent attachment of proteins to DNA. DPCs are formed through a variety of mechanisms and can significantly impede essential cellular processes such as transcription and replication. For this reason, anti-cancer drugs that form DPCs have proven effective in cancer therapy. While cells rely on numerous different processes to remove DPCs, the molecular mechanisms responsible for orchestrating these processes remain obscure. Having this insight could potentially be harnessed therapeutically to improve clinical outcomes in the battle against cancer. In this review, we describe the ways cells enzymatically process DPCs. These processing events include direct reversal of the DPC via hydrolysis, nuclease digestion of the DNA backbone to delete the DPC and surrounding DNA, proteolytic processing of the crosslinked protein, as well as covalent modification of the DNA-crosslinked proteins with ubiquitin, SUMO, and Poly(ADP) Ribose (PAR).
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Affiliation(s)
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA;
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15
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Brown GGB, Gittens WH, Allison RM, Oliver AW, Neale MJ. CC-seq: Nucleotide-Resolution Mapping of Spo11 DNA Double-Strand Breaks in S. cerevisiae Cells. Methods Mol Biol 2024; 2818:3-22. [PMID: 39126464 DOI: 10.1007/978-1-0716-3906-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
During meiosis, Spo11 generates DNA double-strand breaks to induce recombination, becoming covalently attached to the 5' ends on both sides of the break during this process. Such Spo11 "covalent complexes" are transient in wild-type cells, but accumulate in nuclease mutants unable to initiate repair. The CC-seq method presented here details how to map the location of these Spo11 complexes genome-wide with strand-specific nucleotide-resolution accuracy in synchronized Saccharomyces cerevisiae meiotic cells.
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Affiliation(s)
- George G B Brown
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
| | - Will H Gittens
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Rachal M Allison
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Matthew J Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
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16
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Bakman AS, Boichenko SS, Kuznetsova AA, Ishchenko AA, Saparbaev M, Kuznetsov NA. Coordination between human DNA polymerase β and apurinic/apyrimidinic endonuclease 1 in the course of DNA repair. Biochimie 2024; 216:126-136. [PMID: 37806619 DOI: 10.1016/j.biochi.2023.10.007] [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: 07/13/2023] [Revised: 09/08/2023] [Accepted: 10/06/2023] [Indexed: 10/10/2023]
Abstract
Coordination of enzymatic activities in the course of base excision repair (BER) is essential to ensure complete repair of damaged bases. Two major mechanisms underlying the coordination of BER are known today: the "passing the baton" model and a model of preassembled stable multiprotein repair complexes called "repairosomes." In this work, we aimed to elucidate the coordination between human apurinic/apyrimidinic (AP) endonuclease APE1 and DNA polymerase Polβ in BER through studying an impact of APE1 on Polβ-catalyzed nucleotide incorporation into different model substrates that mimic different single-strand break (SSB) intermediates arising along the BER pathway. It was found that APE1's impact on separate stages of Polβ's catalysis depends on the nature of a DNA substrate. In this complex, APE1 removed 3' blocking groups and corrected Polβ-catalyzed DNA synthesis in a coordinated manner. Our findings support the hypothesis that Polβ not only can displace APE1 from damaged DNA within the "passing the baton" model but also performs the gap-filling reaction in the ternary complex with APE1 according to the "repairosome" model. Taken together, our results provide new insights into coordination between APE1 and Polβ during the BER process.
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Affiliation(s)
- Artemiy S Bakman
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad, Lavrentyeva, Novosibirsk, 630090, Russia
| | - Stanislav S Boichenko
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk, 630090, Russia
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad, Lavrentyeva, Novosibirsk, 630090, Russia
| | - Alexander A Ishchenko
- Group «Mechanisms of DNA Repair and Carcinogenesis», Gustave Roussy Cancer Campus, CNRS UMR9019, Université Paris-Saclay, 94805, Villejuif, France
| | - Murat Saparbaev
- Group «Mechanisms of DNA Repair and Carcinogenesis», Gustave Roussy Cancer Campus, CNRS UMR9019, Université Paris-Saclay, 94805, Villejuif, France
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad, Lavrentyeva, Novosibirsk, 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk, 630090, Russia.
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17
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Essawy M, Chesner L, Alshareef D, Ji S, Tretyakova N, Campbell C. Ubiquitin signaling and the proteasome drive human DNA-protein crosslink repair. Nucleic Acids Res 2023; 51:12174-12184. [PMID: 37843153 PMCID: PMC10711432 DOI: 10.1093/nar/gkad860] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 09/11/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are large cytotoxic DNA lesions that form following exposure to chemotherapeutic drugs and environmental chemicals. Nucleotide excision repair (NER) and homologous recombination (HR) promote survival following exposure to DPC-inducing agents. However, it is not known how cells recognize DPC lesions, or what mechanisms selectively target DPC lesions to these respective repair pathways. To address these questions, we examined DPC recognition and repair by transfecting a synthetic DPC lesion comprised of the human oxoguanine glycosylase (OGG1) protein crosslinked to double-stranded M13MP18 into human cells. In wild-type cells, this lesion is efficiently repaired, whereas cells deficient in NER can only repair this lesion if an un-damaged homologous donor is co-transfected. Transfected DPC is subject to rapid K63 polyubiquitination. In NER proficient cells, the DPC is subject to K48 polyubiquitination, and is removed via a proteasome-dependent mechanism. In NER-deficient cells, the DNA-conjugated protein is not subject to K48 polyubiquitination. Instead, the K63 tag remains attached, and is only lost when a homologous donor molecule is present. Taken together, these results support a model in which selective addition of polyubiquitin chains to DNA-crosslinked protein leads to selective recruitment of the proteasome and the cellular NER and recombinational DNA repair machinery.
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Affiliation(s)
- Maram Essawy
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
| | - Lisa Chesner
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
| | - Duha Alshareef
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
| | - Shaofei Ji
- Department of Medicinal Chemistry, University of Minnesota, Minnesota, MN 55455, USA
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minnesota, MN 55455, USA
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
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18
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D’Alessandro G, Morales-Juarez DA, Richards SL, Nitiss KC, Serrano-Benitez A, Wang J, Thomas JC, Gupta V, Voigt A, Belotserkovskaya R, Goh CG, Bowden AR, Galanty Y, Beli P, Nitiss JL, Zagnoli-Vieira G, Jackson SP. RAD54L2 counters TOP2-DNA adducts to promote genome stability. SCIENCE ADVANCES 2023; 9:eadl2108. [PMID: 38055822 PMCID: PMC10699776 DOI: 10.1126/sciadv.adl2108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
The catalytic cycle of topoisomerase 2 (TOP2) enzymes proceeds via a transient DNA double-strand break (DSB) intermediate termed the TOP2 cleavage complex (TOP2cc), in which the TOP2 protein is covalently bound to DNA. Anticancer agents such as etoposide operate by stabilizing TOP2ccs, ultimately generating genotoxic TOP2-DNA protein cross-links that require processing and repair. Here, we identify RAD54 like 2 (RAD54L2) as a factor promoting TOP2cc resolution. We demonstrate that RAD54L2 acts through a novel mechanism together with zinc finger protein associated with tyrosyl-DNA phosphodiesterase 2 (TDP2) and TOP2 (ZATT/ZNF451) and independent of TDP2. Our work suggests a model wherein RAD54L2 recognizes sumoylated TOP2 and, using its ATPase activity, promotes TOP2cc resolution and prevents DSB exposure. These findings suggest RAD54L2-mediated TOP2cc resolution as a potential mechanism for cancer therapy resistance and highlight RAD54L2 as an attractive candidate for drug discovery.
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Affiliation(s)
- Giuseppina D’Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Sean L. Richards
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Juanjuan Wang
- Institute of Molecular Biology (IMB), Chromatin Biology & Proteomics, Mainz, Germany
| | - John C. Thomas
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Andrea Voigt
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Rimma Belotserkovskaya
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chen Gang Goh
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anne Ramsay Bowden
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Yaron Galanty
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Chromatin Biology & Proteomics, Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | | | - Guido Zagnoli-Vieira
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Stephen P. Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
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19
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Zhang H, Xiong Y, Sun Y, Park JM, Su D, Feng X, Keast S, Tang M, Huang M, Wang C, Srivastava M, Yang C, Zhu D, Chen Z, Li S, Yin L, Pommier Y, Chen J. RAD54L2-mediated DNA damage avoidance pathway specifically preserves genome integrity in response to topoisomerase 2 poisons. SCIENCE ADVANCES 2023; 9:eadi6681. [PMID: 38055811 PMCID: PMC10699775 DOI: 10.1126/sciadv.adi6681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Type II topoisomerases (TOP2) form transient TOP2 cleavage complexes (TOP2ccs) during their catalytic cycle to relieve topological stress. TOP2ccs are covalently linked TOP2-DNA intermediates that are reversible but can be trapped by TOP2 poisons. Trapped TOP2ccs block transactions on DNA and generate genotoxic stress, which are the mechanisms of action of TOP2 poisons. How cells avoid TOP2cc accumulation remains largely unknown. In this study, we uncovered RAD54 like 2 (RAD54L2) as a key factor that mediates a TOP2-specific DNA damage avoidance pathway. RAD54L2 deficiency conferred unique sensitivity to treatment with TOP2 poisons. RAD54L2 interacted with TOP2A/TOP2B and ZATT/ZNF451 and promoted the turnover of TOP2 from DNA with or without TOP2 poisons. Additionally, inhibition of proteasome activity enhanced the chromatin binding of RAD54L2, which in turn led to the removal of TOP2 from chromatin. In conclusion, we propose that RAD54L2-mediated TOP2 turnover is critically important for the avoidance of potential TOP2-linked DNA damage under physiological conditions and in response to TOP2 poisons.
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Affiliation(s)
- Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yun Xiong
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Jeong-Min Park
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sarah Keast
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Min Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chang Yang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dandan Zhu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ling Yin
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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20
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Chatzinikolaou G, Stratigi K, Siametis A, Goulielmaki E, Akalestou-Clocher A, Tsamardinos I, Topalis P, Austin C, Bouwman BA, Crosetto N, Altmüller J, Garinis GA. XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes. SCIENCE ADVANCES 2023; 9:eadi2095. [PMID: 37939182 PMCID: PMC10631727 DOI: 10.1126/sciadv.adi2095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Co-transcriptional RNA-DNA hybrids can not only cause DNA damage threatening genome integrity but also regulate gene activity in a mechanism that remains unclear. Here, we show that the nucleotide excision repair factor XPF interacts with the insulator binding protein CTCF and the cohesin subunits SMC1A and SMC3, leading to R-loop-dependent DNA looping upon transcription activation. To facilitate R-loop processing, XPF interacts and recruits with TOP2B on active gene promoters, leading to double-strand break accumulation and the activation of a DNA damage response. Abrogation of TOP2B leads to the diminished recruitment of XPF, CTCF, and the cohesin subunits to promoters of actively transcribed genes and R-loops and the concurrent impairment of CTCF-mediated DNA looping. Together, our findings disclose an essential role for XPF with TOP2B and the CTCF/cohesin complex in R-loop processing for transcription activation with important ramifications for DNA repair-deficient syndromes associated with transcription-associated DNA damage.
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Affiliation(s)
- Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Athanasios Siametis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Evi Goulielmaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Alexia Akalestou-Clocher
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Ioannis Tsamardinos
- Computer Science Department of University of Crete, Heraklion, Crete, Greece
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Caroline Austin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Britta A. M. Bouwman
- Division of Microbiology, Tumor and Cell Biology, Karolinska Institutet and Science for Life Laboratory, Stockholm 17177, Sweden
| | - Nicola Crosetto
- Division of Microbiology, Tumor and Cell Biology, Karolinska Institutet and Science for Life Laboratory, Stockholm 17177, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157 Milan, Italy
| | - Janine Altmüller
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Core Facility Genomics, Charitéplatz 1, 10117 Berlin, Germany
| | - George A. Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
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21
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Petsalaki E, Balafouti S, Kyriazi AA, Zachos G. The abscission checkpoint senses chromatin bridges through Top2α recruitment to DNA knots. J Cell Biol 2023; 222:e202303123. [PMID: 37638884 PMCID: PMC10461104 DOI: 10.1083/jcb.202303123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/13/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023] Open
Abstract
In response to chromatin bridges, the abscission checkpoint delays completion of cytokinesis to prevent chromosome breakage or tetraploidization. Here, we show that spontaneous or replication stress-induced chromatin bridges exhibit "knots" of catenated and overtwisted DNA next to the midbody. Topoisomerase IIα (Top2α) forms abortive Top2-DNA cleavage complexes (Top2ccs) on DNA knots; furthermore, impaired Top2α-DNA cleavage activity correlates with chromatin bridge breakage in cytokinesis. Proteasomal degradation of Top2ccs is required for Rad17 localization to Top2-generated double-strand DNA ends on DNA knots; in turn, Rad17 promotes local recruitment of the MRN complex and downstream ATM-Chk2-INCENP signaling to delay abscission and prevent chromatin breakage. In contrast, dicentric chromosomes that do not exhibit knotted DNA fail to activate the abscission checkpoint in human cells. These findings are the first to describe a mechanism by which the abscission checkpoint detects chromatin bridges, through generation of abortive Top2ccs on DNA knots, to preserve genome integrity.
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Affiliation(s)
- Eleni Petsalaki
- Department of Biology, University of Crete, Heraklion, Greece
| | - Sofia Balafouti
- Department of Biology, University of Crete, Heraklion, Greece
| | | | - George Zachos
- Department of Biology, University of Crete, Heraklion, Greece
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22
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El-Khamisy SF. Oxidative DNA damage and repair at non-coding regulatory regions. Trends Cell Biol 2023; 33:939-949. [PMID: 37029073 DOI: 10.1016/j.tcb.2023.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 04/09/2023]
Abstract
DNA breaks at protein-coding sequences are well-established threats to tissue homeostasis and maintenance. They arise from the exposure to intracellular and environmental genotoxins, causing damage in one or two strands of the DNA. DNA breaks have been also reported in non-coding regulatory regions such as enhancers and promoters. They arise from essential cellular processes required for gene transcription, cell identity and function. One such process that has attracted recent attention is the oxidative demethylation of DNA and histones, which generates abasic sites and DNA single-strand breaks. Here, we discuss how oxidative DNA breaks at non-coding regulatory regions are generated and the recently reported role of NuMA (nuclear mitotic apparatus) protein in promoting transcription and repair at these regions.
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Affiliation(s)
- Sherif F El-Khamisy
- School of Biosciences, The Healthy Lifespan and Neuroscience Institutes, Firth Court, University of Sheffield, Sheffield, UK; Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK.
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23
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Son SH, Kim MY, Choi S, Kim JS, Lee YS, Lee S, Lee YJ, Lee JY, Lee SE, Lim YS, Ha DH, Oh E, Won YB, Ji CJ, Park MA, Kim B, Byun KT, Chung MS, Jeong J, Choi D, Baek EJ, Cho EH, Kim SB, Je AR, Kweon HS, Park HS, Park D, Bae JS, Jang SJ, Yun CO, Chae JH, Lee JW, Lee SJ, Kim CG, Kang HC, Uversky VN, Kim CG. A Cell-Penetrant Peptide Disrupting the Transcription Factor CP2c Complexes Induces Cancer-Specific Synthetic Lethality. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2305096. [PMID: 37845006 PMCID: PMC10667816 DOI: 10.1002/advs.202305096] [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: 07/25/2023] [Revised: 09/23/2023] [Indexed: 10/18/2023]
Abstract
Despite advances in precision oncology, cancer remains a global public health issue. In this report, proof-of-principle evidence is presented that a cell-penetrable peptide (ACP52C) dissociates transcription factor CP2c complexes and induces apoptosis in most CP2c oncogene-addicted cancer cells through transcription activity-independent mechanisms. CP2cs dissociated from complexes directly interact with and degrade YY1, leading to apoptosis via the MDM2-p53 pathway. The liberated CP2cs also inhibit TDP2, causing intrinsic genome-wide DNA strand breaks and subsequent catastrophic DNA damage responses. These two mechanisms are independent of cancer driver mutations but are hindered by high MDM2 p60 expression. However, resistance to ACP52C mediated by MDM2 p60 can be sensitized by CASP2 inhibition. Additionally, derivatives of ACP52C conjugated with fatty acid alone or with a CASP2 inhibiting peptide show improved pharmacokinetics and reduced cancer burden, even in ACP52C-resistant cancers. This study enhances the understanding of ACP52C-induced cancer-specific apoptosis induction and supports the use of ACP52C in anticancer drug development.
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Affiliation(s)
- Seung Han Son
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Min Young Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Sungwoo Choi
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Ji Sook Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
- Department of Pathology, Hanyang University College of Medicine, Seoul, 04763, South Korea
| | - Yong Sang Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Sangwon Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Yeon Ju Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Jin Youn Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Seol Eui Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Young Su Lim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Dae Hyun Ha
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Eonju Oh
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Young-Bin Won
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Chang-Jun Ji
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Mi Ae Park
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Boram Kim
- Department of Biotechnology and Research Institute for Biomedical and Health Science, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, 27478, South Korea
| | - Kyu Tae Byun
- Department of Biotechnology and Research Institute for Biomedical and Health Science, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, 27478, South Korea
| | - Min Sung Chung
- Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, South Korea
| | - Jaemin Jeong
- Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, South Korea
| | - Dongho Choi
- Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, South Korea
| | - Eun Jung Baek
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, 04763, South Korea
| | - Eung-Ho Cho
- Department of Surgery, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, South Korea
| | - Sang-Bum Kim
- Department of Surgery, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, South Korea
| | - A Reum Je
- Center for Research Equipment, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Hee-Seok Kweon
- Center for Research Equipment, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | | | - Dongsun Park
- Department of Biology Education, Korea National University of Education, Cheongju, Chungbuk, 29173, South Korea
| | - June Sung Bae
- Department of Research and Development, OncoClew Co. Ltd, Seoul, 04778, South Korea
| | - Se Jin Jang
- Department of Research and Development, OncoClew Co. Ltd, Seoul, 04778, South Korea
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, 05505, South Korea
| | - Chae-Ok Yun
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Ji Hyung Chae
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Su-Jae Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Chan Gil Kim
- Department of Biotechnology and Research Institute for Biomedical and Health Science, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, 27478, South Korea
| | - Ho Chul Kang
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer`s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
- CGK Biopharma Co. Ltd., Seoul, 04763, South Korea
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24
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Zakharenko AL, Dyrkheeva NS, Luzina OA, Filimonov AS, Mozhaitsev ES, Malakhova AA, Medvedev SP, Zakian SM, Salakhutdinov NF, Lavrik OI. Usnic Acid Derivatives Inhibit DNA Repair Enzymes Tyrosyl-DNA Phosphodiesterases 1 and 2 and Act as Potential Anticancer Agents. Genes (Basel) 2023; 14:1931. [PMID: 37895279 PMCID: PMC10606488 DOI: 10.3390/genes14101931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/04/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 and 2 (Tdp1 and Tdp2) are DNA repair enzymes that repair DNA damage caused by various agents, including anticancer drugs. Thus, these enzymes resist anticancer therapy and could be the reason for resistance to such widely used drugs such as topotecan and etoposide. In the present work, we found compounds capable of inhibiting both enzymes among derivatives of (-)-usnic acid. Both (+)- and (-)-enantiomers of compounds act equally effectively against Tdp1 with IC50 values in the range of 0.02-0.2 μM; only (-)-enantiomers inhibited Tdp2 with IC50 values in the range of 6-9 μM. Surprisingly, the compounds protect HEK293FT wild type cells from the cytotoxic effect of etoposide (CC50 3.0-3.9 μM in the presence of compounds and 2.4 μM the presence of DMSO) but potentiate it against Tdp2 knockout cells (CC50 1.2-1.6 μM in the presence of compounds against 2.3 μM in the presence of DMSO). We assume that the sensitizing effect of the compounds in the absence of Tdp2 is associated with the effective inhibition of Tdp1, which could take over the functions of Tdp2.
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Affiliation(s)
- Alexandra L. Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (N.S.D.); (O.I.L.)
| | - Nadezhda S. Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (N.S.D.); (O.I.L.)
| | - Olga A. Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (O.A.L.); (A.S.F.); (E.S.M.); (N.F.S.)
| | - Aleksandr S. Filimonov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (O.A.L.); (A.S.F.); (E.S.M.); (N.F.S.)
| | - Evgenii S. Mozhaitsev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (O.A.L.); (A.S.F.); (E.S.M.); (N.F.S.)
| | - Anastasia A. Malakhova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.M.); (S.P.M.); (S.M.Z.)
| | - Sergey P. Medvedev
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.M.); (S.P.M.); (S.M.Z.)
| | - Suren M. Zakian
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.M.); (S.P.M.); (S.M.Z.)
| | - Nariman F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (O.A.L.); (A.S.F.); (E.S.M.); (N.F.S.)
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (N.S.D.); (O.I.L.)
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25
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Anticevic I, Otten C, Vinkovic L, Jukic L, Popovic M. Tyrosyl-DNA phosphodiesterase 1 (TDP1) and SPRTN protease repair histone 3 and topoisomerase 1 DNA-protein crosslinks in vivo. Open Biol 2023; 13:230113. [PMID: 37788708 PMCID: PMC10547559 DOI: 10.1098/rsob.230113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/14/2023] [Indexed: 10/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are frequent and damaging DNA lesions that affect all DNA transactions, which in turn can lead to the formation of double-strand breaks, genomic instability and cell death. At the organismal level, impaired DPC repair (DPCR) is associated with cancer, ageing and neurodegeneration. Despite the severe consequences of DPCs, little is known about the processes underlying repair pathways at the organism level. SPRTN is a protease that removes most cellular DPCs during replication, whereas tyrosyl-DNA phosphodiesterase 1 repairs one of the most abundant enzymatic DPCs, topoisomerase 1-DPC (TOP1-DPC). How these two enzymes repair DPCs at the organism level is currently unknown. We perform phylogenetic, syntenic, structural and expression analysis to compare tyrosyl-DNA phosphodiesterase 1 (TDP1) orthologues between human, mouse and zebrafish. Using the zebrafish animal model and human cells, we demonstrate that TDP1 and SPRTN repair endogenous, camptothecin- and formaldehyde-induced DPCs, including histone H3- and TOP1-DPCs. We show that resolution of H3-DNA crosslinks depends on upstream proteolysis by SPRTN and subsequent peptide removal by TDP1 in RPE1 cells and zebrafish embryos, whereas SPRTN and TDP1 function in different pathways in the repair of endogenous TOP1-DPCs and total DPCs. Furthermore, we have found increased TDP2 expression in TDP1-deficient cells and embryos. Understanding the role of TDP1 in DPCR at the cellular and organismal levels could provide an impetus for the development of new drugs and combination therapies with TOP1-DPC inducing drugs.
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Affiliation(s)
- Ivan Anticevic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Cecile Otten
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Vinkovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Jukic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Marta Popovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
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26
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Zagnoli-Vieira G, Brazina J, Van Den Bogaert K, Huybrechts W, Molenaers G, Caldecott KW, Van Esch H. Inactivating TDP2 missense mutation in siblings with congenital abnormalities reminiscent of fanconi anemia. Hum Genet 2023; 142:1417-1427. [PMID: 37558815 PMCID: PMC10449949 DOI: 10.1007/s00439-023-02589-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/15/2023] [Indexed: 08/11/2023]
Abstract
Mutations in TDP2, encoding tyrosyl-DNA phosphodiesterase 2, have been associated with a syndromal form of autosomal recessive spinocerebellar ataxia, type 23 (SCAR23). This is a very rare and progressive neurodegenerative disorder described in only nine patients to date, and caused by splice site or nonsense mutations that result in greatly reduced or absent TDP2 protein. TDP2 is required for the rapid repair of DNA double-strand breaks induced by abortive DNA topoisomerase II (TOP2) activity, important for genetic stability in post-mitotic cells such as neurons. Here, we describe a sibship that is homozygous for the first TDP2 missense mutation (p.Glu152Lys) and which presents with clinical features overlapping both SCAR23 and Fanconi anemia (FA). We show that in contrast to previously reported SCAR23 patients, fibroblasts derived from the current patient retain significant levels of TDP2 protein. However, this protein is catalytically inactive, resulting in reduced rates of repair of TOP2-induced DNA double-strand breaks and cellular hypersensitivity to the TOP2 poison, etoposide. The TDP2-mutated patient-derived fibroblasts do not display increased chromosome breakage following treatment with DNA crosslinking agents, but both TDP2-mutated and FA cells exhibit increased chromosome breakage in response to etoposide. This suggests that the FA pathway is required in response to TOP2-induced DNA lesions, providing a possible explanation for the clinical overlap between FA and the current TDP2-mutated patients. When reviewing the relatively small number of patients with SCAR23 that have been reported, it is clear that the phenotype of such patients can extend beyond neurological features, indicating that the TDP2 protein influences not only neural homeostasis but also other tissues as well.
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Affiliation(s)
- Guido Zagnoli-Vieira
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK.
| | - Jan Brazina
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Wim Huybrechts
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Guy Molenaers
- Pediatric Orthopedics, Department of Orthopedics, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium.
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Shimizu N, Hamada Y, Morozumi R, Yamamoto J, Iwai S, Sugiyama KI, Ide H, Tsuda M. Repair of topoisomerase 1-induced DNA damage by tyrosyl-DNA phosphodiesterase 2 (TDP2) is dependent on its magnesium binding. J Biol Chem 2023; 299:104988. [PMID: 37392847 PMCID: PMC10407441 DOI: 10.1016/j.jbc.2023.104988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 07/03/2023] Open
Abstract
Topoisomerases are enzymes that relax DNA supercoiling during replication and transcription. Camptothecin, a topoisomerase 1 (TOP1) inhibitor, and its analogs trap TOP1 at the 3'-end of DNA as a DNA-bound intermediate, resulting in DNA damage that can kill cells. Drugs with this mechanism of action are widely used to treat cancers. It has previously been shown that tyrosyl-DNA phosphodiesterase 1 (TDP1) repairs TOP1-induced DNA damage generated by camptothecin. In addition, tyrosyl-DNA phosphodiesterase 2 (TDP2) plays critical roles in repairing topoisomerase 2 (TOP2)-induced DNA damage at the 5'-end of DNA and in promoting the repair of TOP1-induced DNA damage in the absence of TDP1. However, the catalytic mechanism by which TDP2 processes TOP1-induced DNA damage has not been elucidated. In this study, we found that a similar catalytic mechanism underlies the repair of TOP1- and TOP2-induced DNA damage by TDP2, with Mg2+-TDP2 binding playing a role in both repair mechanisms. We show chain-terminating nucleoside analogs are incorporated into DNA at the 3'-end and abort DNA replication to kill cells. Furthermore, we found that Mg2+-TDP2 binding also contributes to the repair of incorporated chain-terminating nucleoside analogs. Overall, these findings reveal the role played by Mg2+-TDP2 binding in the repair of both 3'- and 5'-blocking DNA damage.
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Affiliation(s)
- Naoto Shimizu
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yusaku Hamada
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ryosuke Morozumi
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Kei-Ichi Sugiyama
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Hiroshi Ide
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
| | - Masataka Tsuda
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.
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28
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Marini V, Nikulenkov F, Samadder P, Juul S, Knudsen BR, Krejci L. MUS81 cleaves TOP1-derived lesions and other DNA-protein cross-links. BMC Biol 2023; 21:110. [PMID: 37194054 DOI: 10.1186/s12915-023-01614-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND DNA-protein cross-links (DPCs) are one of the most deleterious DNA lesions, originating from various sources, including enzymatic activity. For instance, topoisomerases, which play a fundamental role in DNA metabolic processes such as replication and transcription, can be trapped and remain covalently bound to DNA in the presence of poisons or nearby DNA damage. Given the complexity of individual DPCs, numerous repair pathways have been described. The protein tyrosyl-DNA phosphodiesterase 1 (Tdp1) has been demonstrated to be responsible for removing topoisomerase 1 (Top1). Nevertheless, studies in budding yeast have indicated that alternative pathways involving Mus81, a structure-specific DNA endonuclease, could also remove Top1 and other DPCs. RESULTS This study shows that MUS81 can efficiently cleave various DNA substrates modified by fluorescein, streptavidin or proteolytically processed topoisomerase. Furthermore, the inability of MUS81 to cleave substrates bearing native TOP1 suggests that TOP1 must be either dislodged or partially degraded prior to MUS81 cleavage. We demonstrated that MUS81 could cleave a model DPC in nuclear extracts and that depletion of TDP1 in MUS81-KO cells induces sensitivity to the TOP1 poison camptothecin (CPT) and affects cell proliferation. This sensitivity is only partially suppressed by TOP1 depletion, indicating that other DPCs might require the MUS81 activity for cell proliferation. CONCLUSIONS Our data indicate that MUS81 and TDP1 play independent roles in the repair of CPT-induced lesions, thus representing new therapeutic targets for cancer cell sensitisation in combination with TOP1 inhibitors.
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Affiliation(s)
- Victoria Marini
- Department of Biology, Masaryk University, Kamenice 5/B07, Brno, 62500, Czech Republic
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekařská 53, Brno, 60200, Czech Republic
| | - Fedor Nikulenkov
- Department of Biology, Masaryk University, Kamenice 5/B07, Brno, 62500, Czech Republic
| | - Pounami Samadder
- Department of Biology, Masaryk University, Kamenice 5/B07, Brno, 62500, Czech Republic
| | - Sissel Juul
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, Aarhus, 8000, Denmark
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, Aarhus, 8000, Denmark
| | - Lumir Krejci
- Department of Biology, Masaryk University, Kamenice 5/B07, Brno, 62500, Czech Republic.
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekařská 53, Brno, 60200, Czech Republic.
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/C04, Brno, 625 00, Czech Republic.
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29
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Yang H, Qin C, Wu M, Wang FT, Wang W, Agama K, Pommier Y, Hu DX, An LK. Synthesis and Biological Activities of 11- and 12-Substituted Benzophenanthridinone Derivatives as DNA Topoisomerase IB and Tyrosyl-DNA Phosphodiesterase 1 Inhibitors. ChemMedChem 2023; 18:e202200593. [PMID: 36932053 PMCID: PMC10233710 DOI: 10.1002/cmdc.202200593] [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: 11/04/2022] [Revised: 03/06/2023] [Indexed: 03/19/2023]
Abstract
Herein, a series of 11- or 12-substituted benzophenanthridinone derivatives was designed and synthesized for the discovery of dual topoisomerase IB (TOP1) and tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors. Enzyme-based assays indicated that two compounds 12 and 38 showed high TOP1 inhibitory potency (+++), and four compounds 35, 37, 39 and 43 showed good TDP1 inhibition with IC50 values ranging from 10 to 18 μM. 38 could induce cellular TOP1cc formation, resulting in the highest cytotoxicity against HCT-116 cells (0.25 μM). The most potent TDP1 inhibitor 43 (10 μM) could induce cellular TDP1cc formation and enhance topotecan-induced DNA damage and showed strong synergistic cytotoxicity with topotecan in both MCF-7 and MCF-7/TDP1 cells.
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Affiliation(s)
- Hao Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
- School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, P. R. China
| | - Chao Qin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
| | - Min Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
| | - Fang-Ting Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
| | - Wenjie Wang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keli Agama
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - De-Xuan Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, 510006, P. R. China
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30
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Ranga A, Gupta A, Yadav L, Kumar S, Jain P. Advancing beyond reverse transcriptase inhibitors: The new era of hepatitis B polymerase inhibitors. Eur J Med Chem 2023; 257:115455. [PMID: 37216809 DOI: 10.1016/j.ejmech.2023.115455] [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: 02/28/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023]
Abstract
Hepatitis B virus (HBV) is a genetically diverse blood-borne virus responsible for chronic hepatitis B. The HBV polymerase plays a key role in viral genome replication within the human body and has been identified as a potential drug target for chronic hepatitis B therapeutics. However, available nucleotide reverse transcriptase inhibitors only target the reverse transcriptase domain of the HBV polymerase; they also pose resistance issues and require lifelong treatment that can burden patients financially. In this study, various chemical classes are reviewed that have been developed to target different domains of the HBV polymerase: Terminal protein, which plays a vital role in the formation of the viral DNA; Reverse transcriptase, which is responsible for the synthesis of the viral DNA from RNA, and; Ribonuclease H, which is responsible for degrading the RNA strand in the RNA-DNA duplex formed during the reverse transcription process. Host factors that interact with the HBV polymerase to achieve HBV replication are also reviewed; these host factors can be targeted by inhibitors to indirectly inhibit polymerase functionality. A detailed analysis of the scope and limitations of these inhibitors from a medicinal chemistry perspective is provided. The structure-activity relationship of these inhibitors and the factors that may affect their potency and selectivity are also examined. This analysis will be useful in supporting the further development of these inhibitors and in designing new inhibitors that can inhibit HBV replication more efficiently.
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Affiliation(s)
- Abhishek Ranga
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Aarti Gupta
- Department of Pharmaceutical Biotechnology, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Laxmi Yadav
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Sachin Kumar
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India.
| | - Priti Jain
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India.
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31
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Saha LK, Saha S, Yang X, Huang SYN, Sun Y, Jo U, Pommier Y. Replication-associated formation and repair of human topoisomerase IIIα cleavage complexes. Nat Commun 2023; 14:1925. [PMID: 37024461 PMCID: PMC10079683 DOI: 10.1038/s41467-023-37498-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
Topoisomerase IIIα (TOP3A) belongs to the conserved Type IA family of DNA topoisomerases. Here we report that human TOP3A is associated with DNA replication forks and that a "self-trapping" TOP3A mutant (TOP3A-R364W) generates cellular TOP3A DNA cleavage complexes (TOP3Accs). We show that trapped TOP3Accs that interfere with replication, induce DNA damage and genome instability. To elucidate how TOP3Accs are repaired, we explored the role of Spartan (SPRTN), the metalloprotease associated with DNA replication, which digests proteins forming DNA-protein crosslinks (DPCs). We find that SPRTN-deficient cells show elevated TOP3Accs, whereas overexpression of SPRTN lowers cellular TOP3Accs. SPRTN is deubiquitinated and epistatic with TDP2 in response to TOP3Accs. In addition, we found that MRE11 can excise TOP3Accs, and that cell cycle determines the preference for the SPRTN-TDP2 vs. the ATM-MRE11 pathways, in S vs. G2, respectively. Our study highlights the prevalence of TOP3Accs repair mechanisms to ensure normal DNA replication.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Ukhyun Jo
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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32
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Park JM, Zhang H, Nie L, Wang C, Huang M, Feng X, Tang M, Chen Z, Xiong Y, Lee N, Li S, Yin L, Hart T, Chen J. Genome-Wide CRISPR Screens Reveal ZATT as a Synthetic Lethal Target of TOP2-Poison Etoposide That Can Act in a TDP2-Independent Pathway. Int J Mol Sci 2023; 24:ijms24076545. [PMID: 37047518 PMCID: PMC10095316 DOI: 10.3390/ijms24076545] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Etoposide (ETO) is an anticancer drug that targets topoisomerase II (TOP2). It stabilizes a normally transient TOP2–DNA covalent complex (TOP2cc), thus leading to DNA double-strand breaks (DSBs). Tyrosyl-DNA phosphodiesterases two (TDP2) is directly involved in the repair of TOP2cc by removing phosphotyrosyl peptides from 5′-termini of DSBs. Recent studies suggest that additional factors are required for TOP2cc repair, which include the proteasome and the zinc finger protein associated with TDP2 and TOP2, named ZATT. ZATT may alter the conformation of TOP2cc in a way that renders the accessibility of TDP2 for TOP2cc removal. In this study, our genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screens revealed that ZATT also has a TDP2-independent role in promoting cell survival following ETO treatment. ZATT KO cells showed relatively higher ETO sensitivity than TDP2-KO cells, and ZATT/TDP2 DKO cells displayed additive hypersensitivity to ETO treatment. The study using a series of deletion mutants of ZATT determined that the N-terminal 1–168 residues of ZATT are required for interaction with TOP2 and this interaction is critical to ETO sensitivity. Moreover, depletion of ZATT resulted in accelerated TOP2 degradation after ETO or cycloheximide (CHX) treatment, suggesting that ZATT may increase TOP2 stability and likely participate in TOP2 turnover. Taken together, this study suggests that ZATT is a critical determinant that dictates responses to ETO treatment and targeting. ZATT is a promising strategy to increase ETO efficacy for cancer therapy.
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Affiliation(s)
- Jeong-Min Park
- Department of Stem Cell Transplantation Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (J.-M.P.)
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (H.Z.)
| | - Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (H.Z.)
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (H.Z.)
| | - Min Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (H.Z.)
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (H.Z.)
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (H.Z.)
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (H.Z.)
| | - Yun Xiong
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Namsoo Lee
- Department of Stem Cell Transplantation Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (J.-M.P.)
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (H.Z.)
| | - Ling Yin
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (H.Z.)
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (H.Z.)
- Correspondence:
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33
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Dai XJ, Xue LP, Ji SK, Zhou Y, Gao Y, Zheng YC, Liu HM, Liu HM. Triazole-fused pyrimidines in target-based anticancer drug discovery. Eur J Med Chem 2023; 249:115101. [PMID: 36724635 DOI: 10.1016/j.ejmech.2023.115101] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/31/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023]
Abstract
In recent decades, the development of targeted drugs has featured prominently in the treatment of cancer, which is among the major causes of mortality globally. Triazole-fused pyrimidines, a widely-used class of heterocycles in medicinal chemistry, have attracted considerable interest as potential anticancer agents that target various cancer-associated targets in recent years, demonstrating them as valuable templates for discovering novel anticancer candidates. The current review concentrates on the latest advancements of triazole-pyrimidines as target-based anticancer agents, including works published between 2007 and the present (2007-2022). The structure-activity relationships (SARs) and multiple pathways are also reviewed to shed light on the development of more effective and biotargeted anticancer candidates.
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Affiliation(s)
- Xing-Jie Dai
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan Province, China
| | - Lei-Peng Xue
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan Province, China
| | - Shi-Kun Ji
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan Province, China
| | - Ying Zhou
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan Province, China
| | - Ya Gao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan Province, China
| | - Yi-Chao Zheng
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan Province, China
| | - Hui-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan Province, China.
| | - Hong-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan Province, China
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34
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Yang H, Yao W, Yang J. Overview of the development of HBV small molecule inhibitors. Eur J Med Chem 2023; 249:115128. [PMID: 36709647 DOI: 10.1016/j.ejmech.2023.115128] [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: 12/09/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/28/2023]
Abstract
Like tuberculosis and Acquired Immune Deficiency Syndrome (AIDS), hepatitis B is a globally recognized major public health threat. Although there are many small-molecule drugs for the treatment of hepatitis B, the approved drugs cannot eradicate the pathogenic culprit covalently closed circular DNA in patients, so the patients need long-term medication to control HBV amplification. Driven by a high unmet medical need, many pharmaceutical companies and research institutions have been engaged in the development of anti-HBV drugs to achieve a functional cure for chronic hepatitis B as soon as possible. This review summarizes the pathogenesis of hepatitis B virus and the research progress in the development of anti-HBV small molecule drugs, and introduces the cccDNA formation and transcription inhibitors and core inhibitors in detail, especially emphasizes the role of chinese herbal medicine in the treatment of chronic hepatitis B. Furthermore, this review proposes three potential strategies for cccDNA eradication in the future. We believe this review will provide meaningful guidance to achieve a functional cure for viral hepatitis B in the future.
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Affiliation(s)
- Huihui Yang
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266001, China
| | - Weiwei Yao
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266001, China
| | - Jinfei Yang
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266001, China.
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35
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Najnin RA, Al Mahmud MR, Rahman MM, Takeda S, Sasanuma H, Tanaka H, Murakawa Y, Shimizu N, Akter S, Takagi M, Sunada T, Akamatsu S, He G, Itou J, Toi M, Miyaji M, Tsutsui KM, Keeney S, Yamada S. ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen. Cell Rep 2023; 42:111909. [PMID: 36640339 PMCID: PMC10023214 DOI: 10.1016/j.celrep.2022.111909] [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: 07/27/2022] [Revised: 10/27/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
ATM gene mutation carriers are predisposed to estrogen-receptor-positive breast cancer (BC). ATM prevents BC oncogenesis by activating p53 in every cell; however, much remains unknown about tissue-specific oncogenesis after ATM loss. Here, we report that ATM controls the early transcriptional response to estrogens. This response depends on topoisomerase II (TOP2), which generates TOP2-DNA double-strand break (DSB) complexes and rejoins the breaks. When TOP2-mediated ligation fails, ATM facilitates DSB repair. After estrogen exposure, TOP2-dependent DSBs arise at the c-MYC enhancer in human BC cells, and their defective repair changes the activation profile of enhancers and induces the overexpression of many genes, including the c-MYC oncogene. CRISPR/Cas9 cleavage at the enhancer also causes c-MYC overexpression, indicating that this DSB causes c-MYC overexpression. Estrogen treatment induced c-Myc protein overexpression in mammary epithelial cells of ATM-deficient mice. In conclusion, ATM suppresses the c-Myc-driven proliferative effects of estrogens, possibly explaining such tissue-specific oncogenesis.
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Affiliation(s)
- Rifat Ara Najnin
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Kyoto 606-8501, Japan
| | - Md Rasel Al Mahmud
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Kyoto 606-8501, Japan
| | - Md Maminur Rahman
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Kyoto 606-8501, Japan
| | - Shunichi Takeda
- Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Kyoto 606-8501, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; IFOM-the FIRC Institute of Molecular Oncology, Milan, Italy; Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Institute for Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
| | - Naoto Shimizu
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Kyoto 606-8501, Japan
| | - Salma Akter
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Kyoto 606-8501, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Takuro Sunada
- Department of Urology, Graduate School of Medicine, Kyoto University, 54 Shougoin Kawahara-cho, Kyoto 606-8507, Japan
| | - Shusuke Akamatsu
- Department of Urology, Graduate School of Medicine, Kyoto University, 54 Shougoin Kawahara-cho, Kyoto 606-8507, Japan
| | - Gang He
- Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Junji Itou
- Breast Cancer Unit, Kyoto University Hospital, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Masakazu Toi
- Breast Cancer Unit, Kyoto University Hospital, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Mary Miyaji
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Kimiko M Tsutsui
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shintaro Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Kyoto 606-8501, Japan; Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Rahmoon MA, Elghaish RA, Ibrahim AA, Alaswad Z, Gad MZ, El-Khamisy SF, Elserafy M. High Glucose Increases DNA Damage and Elevates the Expression of Multiple DDR Genes. Genes (Basel) 2023; 14:144. [PMID: 36672885 PMCID: PMC9858638 DOI: 10.3390/genes14010144] [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: 10/22/2022] [Revised: 12/19/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
The DNA Damage Response (DDR) pathways sense DNA damage and coordinate robust DNA repair and bypass mechanisms. A series of repair proteins are recruited depending on the type of breaks and lesions to ensure overall survival. An increase in glucose levels was shown to induce genome instability, yet the links between DDR and glucose are still not well investigated. In this study, we aimed to identify dysregulation in the transcriptome of normal and cancerous breast cell lines upon changing glucose levels. We first performed bioinformatics analysis using a microarray dataset containing the triple-negative breast cancer (TNBC) MDA-MB-231 and the normal human mammary epithelium MCF10A cell lines grown in high glucose (HG) or in the presence of the glycolysis inhibitor 2-deoxyglucose (2DG). Interestingly, multiple DDR genes were significantly upregulated in both cell lines grown in HG. In the wet lab, we remarkably found that HG results in severe DNA damage to TNBC cells as observed using the comet assay. In addition, several DDR genes were confirmed to be upregulated using qPCR analysis in the same cell line. Our results propose a strong need for DDR pathways in the presence of HG to oppose the severe DNA damage induced in cells.
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Affiliation(s)
- Mai A. Rahmoon
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- Department of Pharmaceutical Biology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Reem A. Elghaish
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Aya A. Ibrahim
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Zina Alaswad
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Mohamed Z. Gad
- Department of Biochemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Sherif F. El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- The Healthy Lifespan Institute and Institute of Neuroscience, School of Bioscience, University of Sheffield, Sheffield S10 2TN, UK
- The Institute of Cancer Therapeutics, University of Bradford, Bradford BD7 1 DP, UK
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
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37
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Sun Y, Nitiss JL, Pommier Y. Editorial: The repair of DNA-protein crosslinks. Front Mol Biosci 2023; 10:1203479. [PMID: 37187895 PMCID: PMC10175854 DOI: 10.3389/fmolb.2023.1203479] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Affiliation(s)
- Yilun Sun
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss, ; Yves Pommier,
| | - John L. Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss, ; Yves Pommier,
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss, ; Yves Pommier,
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38
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Chen J, Zhao B, Zou J, Yang J, Yang L, Zhang J, Chen W, Huang D, Zhong Y. Macromolecular NO-Donor Micelles for Targeted and Augmented Chemotherapy against Prostate Cancer. Adv Healthc Mater 2023; 12:e2202266. [PMID: 36415059 DOI: 10.1002/adhm.202202266] [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: 09/05/2022] [Revised: 11/01/2022] [Indexed: 11/24/2022]
Abstract
Mitoxantrone (MTO) is clinically utilized for treating hormone-refractory prostate cancer (PCa), however, the therapeutic outcome is far from optimal due to the lack of proper drug carrier as well as the inherent MTO detoxification mechanisms of DNA lesion repair and anti-oxidation. Herein, a bombesin-installed nanoplatform combining the chemotherapeutic MTO and the chemotherapeutic sensitizer of nitric oxide (NO) is developed based on MTO-loaded macromolecular NO-donor-containing polymeric micelles (BN-NMMTO ) for targeted NO-sensitized chemotherapy against PCa. BN-NMMTO actively target and accumulates in PCa sites and are internalized into the tumor cells. The macromolecular NO-donor of BN-NMMTO undergoes a reductive reaction to unleash NO upon intracellular glutathione (GSH), accompanying by micelle swelling and MTO release. The targeted intracellular MTO release induces DNA lesion and reactive oxygen species (ROS) generation in tumor cells without damage to the normal cells, and MTO's cytotoxicity is further augmented by NO release via the inhibition of both DNA repair and anti-oxidation pathways as compared with traditional MTO therapies.
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Affiliation(s)
- Jiaxin Chen
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China
| | - Bingbing Zhao
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China
| | - Junhui Zou
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China
| | - Jiachen Yang
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China
| | - Lifen Yang
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China
| | - Junmei Zhang
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China
| | - Wei Chen
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China.,Engineering Research Center for Smart Pharmaceutical Manufacturing Technologies, Ministry of Education, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China
| | - Dechun Huang
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China.,Engineering Research Center for Smart Pharmaceutical Manufacturing Technologies, Ministry of Education, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China
| | - Yinan Zhong
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China
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39
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Akter S, Shimba A, Ikuta K, Mahmud MRA, Yamada S, Sasanuma H, Tsuda M, Sone M, Ago Y, Murai K, Tanaka H, Takeda S. Physiological concentrations of glucocorticoids induce pathological DNA double-strand breaks. Genes Cells 2023; 28:53-67. [PMID: 36415926 DOI: 10.1111/gtc.12993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022]
Abstract
Steroid hormones induce the transcription of target genes by activating nuclear receptors. Early transcriptional response to various stimuli, including hormones, involves the active catalysis of topoisomerase II (TOP2) at transcription regulatory sequences. TOP2 untangles DNAs by transiently generating double-strand breaks (DSBs), where TOP2 covalently binds to DSB ends. When TOP2 fails to rejoin, called "abortive" catalysis, the resulting DSBs are repaired by tyrosyl-DNA phosphodiesterase 2 (TDP2) and non-homologous end-joining (NHEJ). A steroid, cortisol, is the most important glucocorticoid, and dexamethasone (Dex), a synthetic glucocorticoid, is widely used for suppressing inflammation in clinics. We here revealed that clinically relevant concentrations of Dex and physiological concentrations of cortisol efficiently induce DSBs in G1 phase cells deficient in TDP2 and NHEJ. The DSB induction depends on glucocorticoid receptor (GR) and TOP2. Considering the specific role of TDP2 in removing TOP2 adducts from DSB ends, induced DSBs most likely represent stalled TOP2-DSB complexes. Inhibition of RNA polymerase II suppressed the DSBs formation only modestly in the G1 phase. We propose that cortisol and Dex frequently generate DSBs through the abortive catalysis of TOP2 at transcriptional regulatory sequences, including promoters or enhancers, where active TOP2 catalysis occurs during early transcriptional response.
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Affiliation(s)
- Salma Akter
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akihiro Shimba
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koichi Ikuta
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Md Rasel Al Mahmud
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shintaro Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masakatsu Sone
- Department of Metabolic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Metabolism and Endocrinology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Yukio Ago
- Department of Cellular and Molecular Pharmacology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenichi Murai
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Shenzhen University School of Medicine, Shenzhen University, Shenzhen, Guangdong, China
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TDP1-independent pathways in the process and repair of TOP1-induced DNA damage. Nat Commun 2022; 13:4240. [PMID: 35869071 PMCID: PMC9307636 DOI: 10.1038/s41467-022-31801-7] [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: 09/13/2021] [Accepted: 06/29/2022] [Indexed: 11/15/2022] Open
Abstract
Anticancer drugs, such as camptothecin (CPT), trap topoisomerase I (TOP1) on DNA and form TOP1 cleavage complexes (TOP1cc). Alternative repair pathways have been suggested in the repair of TOP1cc. However, how these pathways work with TDP1, a key repair enzyme that specifically hydrolyze the covalent bond between TOP1 catalytic tyrosine and the 3’-end of DNA and contribute to the repair of TOP1cc is poorly understood. Here, using unbiased whole-genome CRISPR screens and generation of co-deficient cells with TDP1 and other genes, we demonstrate that MUS81 is an important factor that mediates the generation of excess double-strand breaks (DSBs) in TDP1 KO cells. APEX1/2 are synthetic lethal with TDP1. However, deficiency of APEX1/2 does not reduce DSB formation in TDP1 KO cells. Together, our data suggest that TOP1cc can be either resolved directly by TDP1 or be converted into DSBs and repaired further by the Homologous Recombination (HR) pathway. Here the authors find that MUS81 mediates excess DNA double strand break (DSB) generation in TDP1 KO cells after camptothecin treatment. They show that TOP1 cleavage complexes can be either resolved directly by TDP1 or be converted into DSBs and repaired further by the Homologous Recombination pathway.
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41
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Uusküla-Reimand L, Wilson MD. Untangling the roles of TOP2A and TOP2B in transcription and cancer. SCIENCE ADVANCES 2022; 8:eadd4920. [PMID: 36322662 PMCID: PMC9629710 DOI: 10.1126/sciadv.add4920] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/12/2022] [Indexed: 06/09/2023]
Abstract
Type II topoisomerases (TOP2) are conserved regulators of chromatin topology that catalyze reversible DNA double-strand breaks (DSBs) and are essential for maintaining genomic integrity in diverse dynamic processes such as transcription, replication, and cell division. While controlled TOP2-mediated DSBs are an elegant solution to topological constraints of DNA, DSBs also contribute to the emergence of chromosomal translocations and mutations that drive cancer. The central importance of TOP2 enzymes as frontline chemotherapeutic targets is well known; however, their precise biological functions and impact in cancer development are still poorly understood. In this review, we provide an updated overview of TOP2A and TOP2B in the regulation of chromatin topology and transcription, and discuss the recent discoveries linking TOP2 activities with cancer pathogenesis.
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Affiliation(s)
- Liis Uusküla-Reimand
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D. Wilson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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42
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GOF Mutant p53 in Cancers: A Therapeutic Challenge. Cancers (Basel) 2022; 14:cancers14205091. [PMID: 36291874 PMCID: PMC9600758 DOI: 10.3390/cancers14205091] [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: 09/24/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary In normal cells, p53 is a protein which regulates the cell cycle progression to ensure normal cell division, growth, and development. However, in cancer, changes in the p53 DNA sequence, called genetic mutation, results in the protein either losing its normal function or exhibiting advanced pro-tumorigenic functions that lead to cancer. Importantly, cancers with mutations in the p53 protein often represent ones which are more aggressive and more resistant to chemotherapy. As a result, many studies have and continue to investigate multiple ways to target mutant p53-bearing cancer using targeted therapy, gene therapy, immunotherapy, and combination therapies. Knowledge of these strategies is important in improving the overall therapeutic response of cancers with mutant p53. This review highlights new strategies and discusses the progression of such therapies. Abstract TP53 is mutated in the majority of human cancers. Mutations can lead to loss of p53 expression or expression of mutant versions of the p53 protein. These mutant p53 proteins have oncogenic potential. They can inhibit any remaining WTp53 in a dominant negative manner, or they can acquire new functions that promote tumour growth, invasion, metastasis and chemoresistance. In this review we explore some of the mechanisms that make mutant p53 cells resistant to chemotherapy. As mutant p53 tumours are resistant to many traditional chemotherapies, many have sought to explore new ways of targeting mutant p53 tumours and reinstate chemosensitivity. These approaches include targeting of mutant p53 stability, mutant p53 binding partners and downstream pathways, p53 vaccines, restoration of WTp53 function, and WTp53 gene delivery. The current advances and challenges of these strategies are discussed.
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Sun Y, Soans E, Mishina M, Petricci E, Pommier Y, Nitiss KC, Nitiss JL. Requirements for MRN endonuclease processing of topoisomerase II-mediated DNA damage in mammalian cells. Front Mol Biosci 2022; 9:1007064. [PMID: 36213114 PMCID: PMC9537633 DOI: 10.3389/fmolb.2022.1007064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022] Open
Abstract
During a normal topoisomerase II (TOP2) reaction, the enzyme forms a covalent enzyme DNA intermediate consisting of a 5′ phosphotyrosyl linkage between the enzyme and DNA. While the enzyme typically rejoins the transient breakage after strand passage, a variety of conditions including drugs targeting TOP2 can inhibit DNA resealing, leading to enzyme-mediated DNA damage. A critical aspect of the repair of TOP2-mediated damage is the removal of the TOP2 protein covalently bound to DNA. While proteolysis plays a role in repairing this damage, nucleolytic enzymes must remove the phosphotyrosyl-linked peptide bound to DNA. The MRN complex has been shown to participate in the removal of TOP2 protein from DNA following cellular treatment with TOP2 poisons. In this report we used an optimized ICE (In vivo Complex of Enzyme) assay to measure covalent TOP2/DNA complexes. In agreement with previous independent reports, we find that the absence or inhibition of the MRE11 endonuclease results in elevated levels of both TOP2α and TOP2β covalent complexes. We also examined levels of TOP2 covalent complexes in cells treated with the proteasome inhibitor MG132. Although MRE11 inhibition plus MG132 was not synergistic in etoposide-treated cells, ectopic overexpression of MRE11 resulted in removal of TOP2 even in the presence of MG132. We also found that VCP/p97 inhibition led to elevated TOP2 covalent complexes and prevented the removal of TOP2 covalent complexes by MRE11 overexpression. Our results demonstrate the existence of multiple pathways for proteolytic processing of TOP2 prior to nucleolytic processing, and that MRE11 can process TOP2 covalent complexes even when the proteasome is inhibited. The interactions between VCP/p97 and proteolytic processing of TOP2 covalent complexes merit additional investigation.
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Affiliation(s)
- Yilun Sun
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss,
| | - Eroica Soans
- St. Jude Children’s Research Hospital Memphis, Memphis, TN, United States
| | - Margarita Mishina
- St. Jude Children’s Research Hospital Memphis, Memphis, TN, United States
| | | | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Karin C. Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
| | - John L. Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss,
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A Review of Medicinal Plants of the Himalayas with Anti-Proliferative Activity for the Treatment of Various Cancers. Cancers (Basel) 2022; 14:cancers14163898. [PMID: 36010892 PMCID: PMC9406073 DOI: 10.3390/cancers14163898] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Drugs are used to treat cancer. Most drugs available in the market are chemosynthetic drugs and have side effects on the patient during and after the treatment, in addition to cancer itself. For instance, hair loss, loss of skin color and texture, loss of energy, nausea, infertility, etc. To overcome these side effects, naturally obtained drugs from medicinal plants are preferred. Our review paper aims to encourage the study of anticancer medicinal plants by giving detailed information on thirty-three medicinal plants and parts that constitute the phytochemicals responsible for the treatment of cancer. The development of plant-based drugs could be a game changer in treating cancer as well as boosting the immune system. Abstract Cancer is a serious and significantly progressive disease. Next to cardiovascular disease, cancer has become the most common cause of mortality in the entire world. Several factors, such as environmental factors, habitual activities, genetic factors, etc., are responsible for cancer. Many cancer patients seek alternative and/or complementary treatments because of the high death rate linked with cancer and the adverse side effects of chemotherapy and radiation therapy. Traditional medicine has a long history that begins with the hunt for botanicals to heal various diseases, including cancer. In the traditional medicinal system, several plants used to treat diseases have many bioactive compounds with curative capability, thereby also helping in disease prevention. Plants also significantly contributed to the modern pharmaceutical industry throughout the world. In the present review, we have listed 33 medicinal plants with active and significant anticancer activity, as well as their anticancer compounds. This article will provide a basic set of information for researchers interested in developing a safe and nontoxic active medicinal plant-based treatment for cancer. The research will give a scientific foundation for the traditional usage of these medicinal herbs to treat cancer.
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Discovery, enantioselective synthesis of myrtucommulone E analogues as tyrosyl-DNA phosphodiesterase 2 inhibitors and their biological activities. Eur J Med Chem 2022; 238:114445. [DOI: 10.1016/j.ejmech.2022.114445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/26/2022] [Accepted: 05/05/2022] [Indexed: 11/20/2022]
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Bhat S, Kazim SN. HBV cccDNA-A Culprit and Stumbling Block for the Hepatitis B Virus Infection: Its Presence in Hepatocytes Perplexed the Possible Mission for a Functional Cure. ACS OMEGA 2022; 7:24066-24081. [PMID: 35874215 PMCID: PMC9301636 DOI: 10.1021/acsomega.2c02216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Hepatitis B virus infection (HBV) is still a big health problem across the globe. It has been linked to the development of liver cirrhosis and hepatocellular carcinoma and can trigger different types of liver damage. Existing medicines are unable to disable covalently closed circular DNA (cccDNA), which may result in HBV persistence and recurrence. The current therapeutic goal is to achieve a functional cure, which means HBV-DNA no longer exists when treatment stops and the absence of HBsAg seroclearance. However, due to the presence of integrated HBV DNA and cccDNA functional treatment is now regarded to be difficult. In order to uncover pathways for potential therapeutic targets and identify medicines that could result in large rates of functional cure, a thorough understanding of the virus' biology is required. The proteins of the virus and episomal cccDNA are thought to be critical for the management and support of the HBV replication cycle as they interact directly with the host proteome to establish the best atmosphere for the virus while evading immune detection. The breakthroughs of host dependence factors, cccDNA transcription, epigenetic regulation, and immune-mediated breakdown have all produced significant progress in our understanding of cccDNA biology during the past decade. There are some strategies where cccDNA can be targeted either in a direct or indirect way and are presently at the point of discovery or preclinical or early clinical advancement. Editing of genomes, techniques targeting host dependence factors or epigenetic gene maintenance, nucleocapsid modulators, miRNA, siRNA, virion secretory inhibitors, and immune-mediated degradation are only a few examples. Though cccDNA approaches for direct targeting are still in the early stages of development, the assembly of capsid modulators and immune-reliant treatments have made it to the clinic. Clinical trials are currently being conducted to determine their efficiency and safety in patients, as well as their effect on viral cccDNA. The influence of recent breakthroughs in the development of new treatment techniques on cccDNA biology is also summarized in this review.
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Affiliation(s)
- Sajad
Ahmad Bhat
- Jamia Millia Islamia Central University, Centre for Interdisciplinary Research in Basic Sciences, New Delhi 110025, India
| | - Syed Naqui Kazim
- Jamia Millia Islamia Central University, Centre for Interdisciplinary Research in Basic Sciences, New Delhi 110025, India
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47
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Leng X, Duxin JP. Targeting DNA-Protein Crosslinks via Post-Translational Modifications. Front Mol Biosci 2022; 9:944775. [PMID: 35860355 PMCID: PMC9289515 DOI: 10.3389/fmolb.2022.944775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Covalent binding of proteins to DNA forms DNA-protein crosslinks (DPCs), which represent cytotoxic DNA lesions that interfere with essential processes such as DNA replication and transcription. Cells possess different enzymatic activities to counteract DPCs. These include enzymes that degrade the adducted proteins, resolve the crosslinks, or incise the DNA to remove the crosslinked proteins. An important question is how DPCs are sensed and targeted for removal via the most suited pathway. Recent advances have shown the inherent role of DNA replication in triggering DPC removal by proteolysis. However, DPCs are also efficiently sensed and removed in the absence of DNA replication. In either scenario, post-translational modifications (PTMs) on DPCs play essential and versatile roles in orchestrating the repair routes. In this review, we summarize the current knowledge of the mechanisms that trigger DPC removal via PTMs, focusing on ubiquitylation, small ubiquitin-related modifier (SUMO) conjugation (SUMOylation), and poly (ADP-ribosyl)ation (PARylation). We also briefly discuss the current knowledge gaps and emerging hypotheses in the field.
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Perry M, Ghosal G. Mechanisms and Regulation of DNA-Protein Crosslink Repair During DNA Replication by SPRTN Protease. Front Mol Biosci 2022; 9:916697. [PMID: 35782873 PMCID: PMC9240642 DOI: 10.3389/fmolb.2022.916697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
DNA-protein crosslinks (DPCs) are deleterious DNA lesions that occur when proteins are covalently crosslinked to the DNA by the action of variety of agents like reactive oxygen species, aldehydes and metabolites, radiation, and chemotherapeutic drugs. Unrepaired DPCs are blockades to all DNA metabolic processes. Specifically, during DNA replication, replication forks stall at DPCs and are vulnerable to fork collapse, causing DNA breakage leading to genome instability and cancer. Replication-coupled DPC repair involves DPC degradation by proteases such as SPRTN or the proteasome and the subsequent removal of DNA-peptide adducts by nucleases and canonical DNA repair pathways. SPRTN is a DNA-dependent metalloprotease that cleaves DPC substrates in a sequence-independent manner and is also required for translesion DNA synthesis following DPC degradation. Biallelic mutations in SPRTN cause Ruijs-Aalfs (RJALS) syndrome, characterized by hepatocellular carcinoma and segmental progeria, indicating the critical role for SPRTN and DPC repair pathway in genome maintenance. In this review, we will discuss the mechanism of replication-coupled DPC repair, regulation of SPRTN function and its implications in human disease and cancer.
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Affiliation(s)
- Megan Perry
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States,Fred and Pamela Buffett Cancer Center, Omaha, NE, United States,*Correspondence: Gargi Ghosal,
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Chowdhury SR, Das SK, Banerjee B, Paul Chowdhuri S, Majumder HK, Das BB. TDP1 knockout Leishmania donovani accumulate topoisomerase 1-linked DNA damage and are hypersensitive to clinically used antileishmanial drugs. FASEB J 2022; 36:e22265. [PMID: 35319800 DOI: 10.1096/fj.202101668rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 11/11/2022]
Abstract
Leishmania donovani, a unicellular protozoan parasite, causes a wide range of human diseases including fatal visceral leishmaniasis. Tyrosyl DNA-phosphodiesterase 1 (TDP1) hydrolyzes the phosphodiester bond between DNA 3'-end and a tyrosyl moiety of trapped topoisomerase I-DNA covalent complexes (Top1cc). We have previously shown Leishmania harbors a TDP1 gene (LdTDP1), however, the biological role of TDP1 remains largely unknown. In the present study, we have generated TDP1 knockout L. donovani (LdTDP1-/- ) promastigotes and have shown that LdTDP1-/- parasites are deficient in 3'-phosphodiesterase activities and were hypersensitive to Top1-poison like camptothecin (CPT), DNA alkylation agent like methyl methanesulfonate, and oxidative DNA lesions generated by hydrogen peroxide but were not sensitive to etoposide. We also detected elevated levels of CPT-induced reactive oxygen species triggering cell cycle arrest and cell death in LdTDP1-/- promastigotes. LdTDP1-/- promastigotes accumulate a significant change in the membrane morphology with the accumulation of membrane pores, which is associated with oxidative stress and lipid peroxidation. To our surprise, we detected that LdTDP1-/- parasites were hypersensitive to antileishmanial drugs like amphotericin B and miltefosine, which could be rescued by complementation of wild-type TDP1 gene in the LdTDP1-/- parasites. Notably, multidrug-resistant L. donovani clinical isolates showed a marked reduction in TDP1 expression and were sensitive to Top1 poisons. Taken together, our study provides a new role of LdTDP1 in protecting L. donovani parasites from oxidative stress-induced DNA damage and resistance to amphotericin B and miltefosine.
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Affiliation(s)
- Somenath Roy Chowdhury
- Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subhendu K Das
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Bijoylaxmi Banerjee
- Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Srijita Paul Chowdhuri
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Hemanta K Majumder
- Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Benu Brata Das
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, India
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Pommier Y, Nussenzweig A, Takeda S, Austin C. Human topoisomerases and their roles in genome stability and organization. Nat Rev Mol Cell Biol 2022; 23:407-427. [PMID: 35228717 PMCID: PMC8883456 DOI: 10.1038/s41580-022-00452-3] [Citation(s) in RCA: 148] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2022] [Indexed: 12/15/2022]
Abstract
Human topoisomerases comprise a family of six enzymes: two type IB (TOP1 and mitochondrial TOP1 (TOP1MT), two type IIA (TOP2A and TOP2B) and two type IA (TOP3A and TOP3B) topoisomerases. In this Review, we discuss their biochemistry and their roles in transcription, DNA replication and chromatin remodelling, and highlight the recent progress made in understanding TOP3A and TOP3B. Because of recent advances in elucidating the high-order organization of the genome through chromatin loops and topologically associating domains (TADs), we integrate the functions of topoisomerases with genome organization. We also discuss the physiological and pathological formation of irreversible topoisomerase cleavage complexes (TOPccs) as they generate topoisomerase DNA–protein crosslinks (TOP-DPCs) coupled with DNA breaks. We discuss the expanding number of redundant pathways that repair TOP-DPCs, and the defects in those pathways, which are increasingly recognized as source of genomic damage leading to neurological diseases and cancer. Topoisomerases have essential roles in transcription, DNA replication, chromatin remodelling and, as recently revealed, 3D genome organization. However, topoisomerases also generate DNA–protein crosslinks coupled with DNA breaks, which are increasingly recognized as a source of disease-causing genomic damage.
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