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Li J, Jia Z, Dong L, Cao H, Huang Y, Xu H, Xie Z, Jiang Y, Wang X, Liu J. DNA damage response in breast cancer and its significant role in guiding novel precise therapies. Biomark Res 2024; 12:111. [PMID: 39334297 PMCID: PMC11437670 DOI: 10.1186/s40364-024-00653-2] [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: 09/05/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
DNA damage response (DDR) deficiency has been one of the emerging targets in treating breast cancer in recent years. On the one hand, DDR coordinates cell cycle and signal transduction, whose dysfunction may lead to cell apoptosis, genomic instability, and tumor development. Conversely, DDR deficiency is an intrinsic feature of tumors that underlies their response to treatments that inflict DNA damage. In this review, we systematically explore various mechanisms of DDR, the rationale and research advances in DDR-targeted drugs in breast cancer, and discuss the challenges in its clinical applications. Notably, poly (ADP-ribose) polymerase (PARP) inhibitors have demonstrated favorable efficacy and safety in breast cancer with high homogenous recombination deficiency (HRD) status in a series of clinical trials. Moreover, several studies on novel DDR-related molecules are actively exploring to target tumors that become resistant to PARP inhibition. Before further clinical application of new regimens or drugs, novel and standardized biomarkers are needed to develop for accurately characterizing the benefit population and predicting efficacy. Despite the promising efficacy of DDR-related treatments, challenges of off-target toxicity and drug resistance need to be addressed. Strategies to overcome drug resistance await further exploration on DDR mechanisms, and combined targeted drugs or immunotherapy will hopefully provide more precise or combined strategies and expand potential responsive populations.
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Affiliation(s)
- Jiayi Li
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Ziqi Jia
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin Dong
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Heng Cao
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yansong Huang
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Hengyi Xu
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhixuan Xie
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Yiwen Jiang
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Xiang Wang
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jiaqi Liu
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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2
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Li C, Fan S, Li P, Bai Y, Wang Y, Cui Y, Li M, Wang R, Shao Y, Wang Y, Zheng S, Wang R, Gao L, Li M, Zheng Y, Wang F, Gao S, Feng S, Wang J, Qu X, Li X. A sophisticated mechanism governs Pol ζ activity in response to replication stress. Nat Commun 2024; 15:7562. [PMID: 39215012 PMCID: PMC11364643 DOI: 10.1038/s41467-024-52112-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024] Open
Abstract
DNA polymerase ζ (Pol ζ) plays an essential role in replicating damaged DNA templates but contributes to mutagenesis due to its low fidelity. Therefore, ensuring tight control of Pol ζ's activity is critical for continuous and accurate DNA replication, yet the specific mechanisms remain unclear. This study reveals a regulation mechanism of Pol ζ activity in human cells. Under normal conditions, an autoinhibition mechanism keeps the catalytic subunit, REV3L, inactive. Upon encountering replication stress, however, ATR-mediated phosphorylation of REV3L's S279 cluster activates REV3L and triggers its degradation via a caspase-mediated pathway. This regulation confines the activity of Pol ζ, balancing its essential role against its mutations causing potential during replication stress. Overall, our findings elucidate a control scheme that fine tunes the low-fidelity polymerase activity of Pol ζ under challenging replication scenarios.
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Affiliation(s)
- Chun Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shuchen Fan
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Pan Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuzhen Bai
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Ye Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yueyun Cui
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Mengdi Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Ruru Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuan Shao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yingying Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shuo Zheng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Rong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Lijun Gao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Miaomiao Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuanyuan Zheng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Fengting Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Sihang Gao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shiguo Feng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Jianing Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xinqi Qu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xialu Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China.
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3
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Arianna GA, Korzhnev DM. Protein Assemblies in Translesion Synthesis. Genes (Basel) 2024; 15:832. [PMID: 39062611 PMCID: PMC11276120 DOI: 10.3390/genes15070832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Translesion synthesis (TLS) is a mechanism of DNA damage tolerance utilized by eukaryotic cells to replicate DNA across lesions that impede the high-fidelity replication machinery. In TLS, a series of specialized DNA polymerases are employed, which recognize specific DNA lesions, insert nucleotides across the damage, and extend the distorted primer-template. This allows cells to preserve genetic integrity at the cost of mutations. In humans, TLS enzymes include the Y-family, inserter polymerases, Polη, Polι, Polκ, Rev1, and the B-family extender polymerase Polζ, while in S. cerevisiae only Polη, Rev1, and Polζ are present. To bypass DNA lesions, TLS polymerases cooperate, assembling into a complex on the eukaryotic sliding clamp, PCNA, termed the TLS mutasome. The mutasome assembly is contingent on protein-protein interactions (PPIs) between the modular domains and subunits of TLS enzymes, and their interactions with PCNA and DNA. While the structural mechanisms of DNA lesion bypass by the TLS polymerases and PPIs of their individual modules are well understood, the mechanisms by which they cooperate in the context of TLS complexes have remained elusive. This review focuses on structural studies of TLS polymerases and describes the case of TLS holoenzyme assemblies in action emerging from recent high-resolution Cryo-EM studies.
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Affiliation(s)
| | - Dmitry M. Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, USA;
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4
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Mórocz M, Qorri E, Pekker E, Tick G, Haracska L. Exploring RAD18-dependent replication of damaged DNA and discontinuities: A collection of advanced tools. J Biotechnol 2024; 380:1-19. [PMID: 38072328 DOI: 10.1016/j.jbiotec.2023.12.001] [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: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/21/2023]
Abstract
DNA damage tolerance (DDT) pathways mitigate the effects of DNA damage during replication by rescuing the replication fork stalled at a DNA lesion or other barriers and also repair discontinuities left in the newly replicated DNA. From yeast to mammalian cells, RAD18-regulated translesion synthesis (TLS) and template switching (TS) represent the dominant pathways of DDT. Monoubiquitylation of the polymerase sliding clamp PCNA by HRAD6A-B/RAD18, an E2/E3 protein pair, enables the recruitment of specialized TLS polymerases that can insert nucleotides opposite damaged template bases. Alternatively, the subsequent polyubiquitylation of monoubiquitin-PCNA by Ubc13-Mms2 (E2) and HLTF or SHPRH (E3) can lead to the switching of the synthesis from the damaged template to the undamaged newly synthesized sister strand to facilitate synthesis past the lesion. When immediate TLS or TS cannot occur, gaps may remain in the newly synthesized strand, partly due to the repriming activity of the PRIMPOL primase, which can be filled during the later phases of the cell cycle. The first part of this review will summarize the current knowledge about RAD18-dependent DDT pathways, while the second part will offer a molecular toolkit for the identification and characterization of the cellular functions of a DDT protein. In particular, we will focus on advanced techniques that can reveal single-stranded and double-stranded DNA gaps and their repair at the single-cell level as well as monitor the progression of single replication forks, such as the specific versions of the DNA fiber and comet assays. This collection of methods may serve as a powerful molecular toolkit to monitor the metabolism of gaps, detect the contribution of relevant pathways and molecular players, as well as characterize the effectiveness of potential inhibitors.
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Affiliation(s)
- Mónika Mórocz
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Erda Qorri
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged H-6720, Hungary.
| | - Emese Pekker
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Doctoral School of Interdisciplinary Medicine, University of Szeged, Korányi fasor 10, 6720 Szeged, Hungary.
| | - Gabriella Tick
- Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Lajos Haracska
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; National Laboratory for Drug Research and Development, Magyar tudósok krt. 2. H-1117 Budapest, Hungary.
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5
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Qu L, Liu SJ, Zhang L, Liu JF, Zhou YJ, Zeng PH, Jing QC, Yin WJ. The Role of m6A-Mediated DNA Damage Repair in Tumor Development and Chemoradiotherapy Resistance. Cancer Control 2024; 31:10732748241247170. [PMID: 38662732 PMCID: PMC11047261 DOI: 10.1177/10732748241247170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Among the post-transcriptional modifications, m6A RNA methylation has gained significant research interest due to its critical role in regulating transcriptional expression. This modification affects RNA metabolism in several ways, including processing, nuclear export, translation, and decay, making it one of the most abundant transcriptional modifications and a crucial regulator of gene expression. The dysregulation of m6A RNA methylation-related proteins in many tumors has been shown to lead to the upregulation of oncoprotein expression, tumor initiation, proliferation, cancer cell progression, and metastasis.Although the impact of m6A RNA methylation on cancer cell growth and proliferation has been extensively studied, its role in DNA repair processes, which are crucial to the pathogenesis of various diseases, including cancer, remains unclear. However, recent studies have shown accumulating evidence that m6A RNA methylation significantly affects DNA repair processes and may play a role in cancer drug resistance. Therefore, a comprehensive literature review is necessary to explore the potential biological role of m6A-modified DNA repair processes in human cancer and cancer drug resistance.In conclusion, m6A RNA methylation is a crucial regulator of gene expression and a potential player in cancer development and drug resistance. Its dysregulation in many tumors leads to the upregulation of oncoprotein expression and tumor progression. Furthermore, the impact of m6A RNA methylation on DNA repair processes, although unclear, may play a crucial role in cancer drug resistance. Therefore, further studies are warranted to better understand the potential biological role of m6A-modified DNA repair processes in human cancer and cancer drug resistance.
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Affiliation(s)
- Li Qu
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hunan Province Clinical Research Center for Accurate Diagnosis and Treatment of High-incidence Sexually Transmitted Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hunan, China
| | - Si jian Liu
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hunan Province Clinical Research Center for Accurate Diagnosis and Treatment of High-incidence Sexually Transmitted Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hunan, China
| | - Ling Zhang
- Department of Clinical Laboratory Medicine, The Affiliated Changsha Central Hospital, Hengyang Medical school, University of South China, Changsha, China
| | - Jia Feng Liu
- Department of Clinical Laboratory Medicine, The Affiliated Changsha Central Hospital, Hengyang Medical school, University of South China, Changsha, China
| | - Ying Jie Zhou
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hunan Province Clinical Research Center for Accurate Diagnosis and Treatment of High-incidence Sexually Transmitted Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hunan, China
| | - Peng Hui Zeng
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hunan Province Clinical Research Center for Accurate Diagnosis and Treatment of High-incidence Sexually Transmitted Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hunan, China
| | - Qian Cheng Jing
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Institute of Otolaryngology Head and Neck Surgery, Hengyang Medical School, University of South China, Changsha, China
| | - Wen Jun Yin
- Department of Clinical Laboratory Medicine, The Affiliated Changsha Central Hospital, Hengyang Medical school, University of South China, Changsha, China
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6
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Martins DJ, Singh JK, Jahjah T, Vessoni AT, Leandro GDS, Silva MM, Biard DSF, Quinet A, Menck CFM. Polymerase iota plays a key role during translesion synthesis of UV-induced lesions in the absence of polymerase eta. Photochem Photobiol 2024; 100:4-18. [PMID: 37926965 DOI: 10.1111/php.13879] [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: 06/22/2023] [Revised: 09/29/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023]
Abstract
Xeroderma pigmentosum (XP) variant cells are deficient in the translesion synthesis (TLS) DNA polymerase Polη (eta). This protein contributes to DNA damage tolerance, bypassing unrepaired UV photoproducts and allowing S-phase progression with minimal delay. In the absence of Polη, backup polymerases perform TLS of UV lesions. However, which polymerase plays this role in human cells remains an open question. Here, we investigated the potential role of Polι (iota) in bypassing ultraviolet (UV) induced photoproducts in the absence of Polη, using NER-deficient (XP-C) cells knocked down for Polι and/or Polη genes. Our results indicate that cells lacking either Polι or Polη have increased sensitivity to UVC radiation. The lack of both TLS polymerases led to increased cell death and defects in proliferation and migration. Loss of both polymerases induces a significant replication fork arrest and G1/S-phase blockage, compared to the lack of Polη alone. In conclusion, we propose that Polι acts as a bona fide backup for Polη in the TLS of UV-photoproducts.
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Affiliation(s)
- Davi Jardim Martins
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Jenny Kaur Singh
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
| | - Tiya Jahjah
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
| | - Alexandre Teixeira Vessoni
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
- Sanofi R&D, Vitry-sur-Seine, France
| | - Giovana da Silva Leandro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Matheus Molina Silva
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Denis Serge François Biard
- Université Paris-Saclay, Institut de Biologie François Jacob, Service d'étude des prions et maladies atypiques, iRCM/IBJF, Fontenay-aux-Roses, France
| | - Annabel Quinet
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
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7
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Wu S, Luo T, Lei X, Yang X. Emerging role of competing endogenous RNA in lung cancer drug resistance. J Chemother 2023:1-20. [PMID: 38124356 DOI: 10.1080/1120009x.2023.2294582] [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: 03/23/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
Lung cancer remains one of the most common malignant cancers worldwide, and its survival rate is extremely low. Chemotherapy, the mainstay of lung cancer treatment, is not as effective as it could be due to the development of cellular resistance. The molecular mechanisms of drug resistance in lung cancer remain to be elucidated. Accumulating evidence suggests that ceRNAs are involved in various carcinogenesis and development. CeRNA is a transcript that regulates each other through competition with miRNA. However, the relationship between ceRNAs and chemoresistance in lung cancer remains unclear. In this narrative review, we provided a summary of treatment approaches that focus on ceRNA networks to overcome drug resistance.
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Affiliation(s)
- Shijie Wu
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, Hengyang, People's Republic of China
| | - Ting Luo
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, Hengyang, People's Republic of China
| | - Xiaoyong Lei
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, Hengyang, People's Republic of China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, Hengyang, People's Republic of China
| | - Xiaoyan Yang
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, Hengyang, People's Republic of China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, Hengyang, People's Republic of China
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8
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Ashton NW, Jaiswal N, Moreno NC, Semenova IV, D'Orlando DA, Latancia MT, McIntyre J, Woodgate R, Bezsonova I. A Novel Interaction Between RAD23A/B and Y-family DNA Polymerases. J Mol Biol 2023; 435:168353. [PMID: 37935254 PMCID: PMC10842004 DOI: 10.1016/j.jmb.2023.168353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/17/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
The Y-family DNA polymerases - Pol ι, Pol η, Pol κ and Rev1 - are most well-known for their roles in the DNA damage tolerance pathway of translesion synthesis (TLS). They function to overcome replication barriers by bypassing DNA damage lesions that cannot be normally replicated, allowing replication forks to continue without stalling. In this work, we demonstrate a novel interaction between each Y-family polymerase and the nucleotide excision repair (NER) proteins, RAD23A and RAD23B. We initially focus on the interaction between RAD23A and Pol ι, and through a series of biochemical, cell-based, and structural assays, find that the RAD23A ubiquitin-binding domains (UBA1 and UBA2) interact with separate sites within the Pol ι catalytic domain. While this interaction involves the ubiquitin-binding cleft of UBA2, Pol ι interacts with a distinct surface on UBA1. We further find that mutating or deleting either UBA domain disrupts the RAD23A-Pol ι interaction, demonstrating that both interactions are necessary for stable binding. We also provide evidence that both RAD23 proteins interact with Pol ι in a similar manner, as well as with each of the Y-family polymerases. These results shed light on the interplay between the different functions of the RAD23 proteins and reveal novel binding partners for the Y-family TLS polymerases.
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Affiliation(s)
- Nicholas W Ashton
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Nancy Jaiswal
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06032, USA.
| | - Natália Cestari Moreno
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Irina V Semenova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06032, USA.
| | - Dana A D'Orlando
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Marcela Teatin Latancia
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Justyna McIntyre
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06032, USA.
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9
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Medina-Rivera M, Phelps S, Sridharan M, Becker J, Lamb N, Kumar C, Sutton M, Bielinsky A, Balakrishnan L, Surtees J. Elevated MSH2 MSH3 expression interferes with DNA metabolism in vivo. Nucleic Acids Res 2023; 51:12185-12206. [PMID: 37930834 PMCID: PMC10711559 DOI: 10.1093/nar/gkad934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023] Open
Abstract
The Msh2-Msh3 mismatch repair (MMR) complex in Saccharomyces cerevisiae recognizes and directs repair of insertion/deletion loops (IDLs) up to ∼17 nucleotides. Msh2-Msh3 also recognizes and binds distinct looped and branched DNA structures with varying affinities, thereby contributing to genome stability outside post-replicative MMR through homologous recombination, double-strand break repair (DSBR) and the DNA damage response. In contrast, Msh2-Msh3 promotes genome instability through trinucleotide repeat (TNR) expansions, presumably by binding structures that form from single-stranded (ss) TNR sequences. We previously demonstrated that Msh2-Msh3 binding to 5' ssDNA flap structures interfered with Rad27 (Fen1 in humans)-mediated Okazaki fragment maturation (OFM) in vitro. Here we demonstrate that elevated Msh2-Msh3 levels interfere with DNA replication and base excision repair in vivo. Elevated Msh2-Msh3 also induced a cell cycle arrest that was dependent on RAD9 and ELG1 and led to PCNA modification. These phenotypes also required Msh2-Msh3 ATPase activity and downstream MMR proteins, indicating an active mechanism that is not simply a result of Msh2-Msh3 DNA-binding activity. This study provides new mechanistic details regarding how excess Msh2-Msh3 can disrupt DNA replication and repair and highlights the role of Msh2-Msh3 protein abundance in Msh2-Msh3-mediated genomic instability.
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Affiliation(s)
- Melisa Medina-Rivera
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Samantha Phelps
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Madhumita Sridharan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jordan Becker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Natalie A Lamb
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Charanya Kumar
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Mark D Sutton
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Anja Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jennifer A Surtees
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
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10
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Zhang X, Zhao Q, Wang T, Long Q, Sun Y, Jiao L, Gullerova M. DNA damage response, a double-edged sword for vascular aging. Ageing Res Rev 2023; 92:102137. [PMID: 38007046 DOI: 10.1016/j.arr.2023.102137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/03/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Vascular aging is a major risk factor for age-related cardiovascular diseases, which have high rates of morbidity and mortality. It is characterized by changes in the blood vessels, such as macroscopically increased vascular diameter and intima-medial thickness, chronic inflammation, vascular calcification, arterial stiffening, and atherosclerosis. DNA damage and the subsequent various DNA damage response (DDR) pathways are important causative factors of vascular aging. Deficient DDR, which may result in the accumulation of unrepaired damaged DNA or mutations, can lead to vascular aging. On the other hand, over-activation of some DDR proteins, such as poly (ADP ribose) polymerase (PARP) and ataxia telangiectasia mutated (ATM), also can enhance the process of vascular aging, suggesting that DDR can have both positive and negative effects on vascular aging. Despite the evidence reviewed in this paper, the role of DDR in vascular aging and potential therapeutic targets remain poorly understood and require further investigation.
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Affiliation(s)
- Xiao Zhang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China
| | - Qing Zhao
- M.D. Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Tao Wang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China
| | - Qilin Long
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Yixin Sun
- First Hospital, Peking University, Beijing, China
| | - Liqun Jiao
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China; Department of Interventional Neuroradiology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
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11
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Tayanloo-Beik A, Hamidpour SK, Nikkhah A, Arjmand R, Mafi AR, Rezaei-Tavirani M, Larijani B, Gilany K, Arjmand B. DNA Damage Responses, the Trump Card of Stem Cells in the Survival Game. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [PMID: 37923882 DOI: 10.1007/5584_2023_791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Stem cells, as a group of undifferentiated cells, are enriched with self-renewal and high proliferative capacity, which have attracted the attention of many researchers as a promising approach in the treatment of many diseases over the past years. However, from the cellular and molecular point of view, the DNA repair system is one of the biggest challenges in achieving therapeutic goals through stem cell technology. DNA repair mechanisms are an advantage for stem cells that are constantly multiplying to deal with various types of DNA damage. However, this mechanism can be considered a trump card in the game of cell survival and treatment resistance in cancer stem cells, which can hinder the curability of various types of cancer. Therefore, getting a deep insight into the DNA repair system can bring researchers one step closer to achieving major therapeutic goals. The remarkable thing about the DNA repair system is that this system is not only under the control of genetic factors, but also under the control of epigenetic factors. Therefore, it is necessary to investigate the role of the DNA repair system in maintaining the survival of cancer stem cells from both aspects.
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Affiliation(s)
- Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Amirabbas Nikkhah
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasta Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Rezazadeh Mafi
- Department of Radiation Oncology, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical sciences, Tehran, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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12
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Gross CA, Walker GC. Evelyn Witkin: Pioneering DNA repair researcher and social justice activist. Mol Cell 2023; 83:3575-3577. [PMID: 37863023 DOI: 10.1016/j.molcel.2023.09.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/22/2023]
Affiliation(s)
- Carol A Gross
- Department of Microbiology and Immunology, Department of Cell and Tissue Biology University of California, San Francisco, San Francisco, CA, USA.
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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13
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Andrés CMC, de la Lastra JMP, Juan CA, Plou FJ, Pérez-Lebeña E. Chemical Insights into Oxidative and Nitrative Modifications of DNA. Int J Mol Sci 2023; 24:15240. [PMID: 37894920 PMCID: PMC10607741 DOI: 10.3390/ijms242015240] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
This review focuses on DNA damage caused by a variety of oxidizing, alkylating, and nitrating species, and it may play an important role in the pathophysiology of inflammation, cancer, and degenerative diseases. Infection and chronic inflammation have been recognized as important factors in carcinogenesis. Under inflammatory conditions, reactive oxygen species (ROS) and reactive nitrogen species (RNS) are generated from inflammatory and epithelial cells, and result in the formation of oxidative and nitrative DNA lesions, such as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-nitroguanine. Cellular DNA is continuously exposed to a very high level of genotoxic stress caused by physical, chemical, and biological agents, with an estimated 10,000 modifications occurring every hour in the genetic material of each of our cells. This review highlights recent developments in the chemical biology and toxicology of 2'-deoxyribose oxidation products in DNA.
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Affiliation(s)
| | - José Manuel Pérez de la Lastra
- Institute of Natural Products and Agrobiology, CSIC-Spanish Research Council, Avda. AstrofísicoFco. Sánchez, 3, 38206 La Laguna, Spain
| | - Celia Andrés Juan
- Cinquima Institute and Department of Organic Chemistry, Faculty of Sciences, Valladolid University, Paseo de Belén, 7, 47011 Valladolid, Spain;
| | - Francisco J. Plou
- Institute of Catalysis and Petrochemistry, CSIC-Spanish Research Council, 28049 Madrid, Spain;
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14
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Hudson KM, Klimczak LJ, Sterling JF, Burkholder AB, Kazanov M, Saini N, Mieczkowski PA, Gordenin DA. Glycidamide-induced hypermutation in yeast single-stranded DNA reveals a ubiquitous clock-like mutational motif in humans. Nucleic Acids Res 2023; 51:9075-9100. [PMID: 37471042 PMCID: PMC10516655 DOI: 10.1093/nar/gkad611] [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: 03/19/2023] [Revised: 06/28/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
Mutagens often prefer specific nucleotides or oligonucleotide motifs that can be revealed by studying the hypermutation spectra in single-stranded (ss) DNA. We utilized a yeast model to explore mutagenesis by glycidamide, a simple epoxide formed endogenously in humans from the environmental toxicant acrylamide. Glycidamide caused ssDNA hypermutation in yeast predominantly in cytosines and adenines. The most frequent mutations in adenines occurred in the nAt→nGt trinucleotide motif. Base substitutions A→G in this motif relied on Rev1 translesion polymerase activity. Inactivating Rev1 did not alter the nAt trinucleotide preference, suggesting it may be an intrinsic specificity of the chemical reaction between glycidamide and adenine in the ssDNA. We found this mutational motif enriched in published sequencing data from glycidamide-treated mouse cells and ubiquitous in human cancers. In cancers, this motif was positively correlated with the single base substitution (SBS) smoking-associated SBS4 signature, with the clock-like signatures SBS1, SBS5, and was strongly correlated with smoking history and with age of tumor donors. Clock-like feature of the motif was also revealed in cells of human skin and brain. Given its pervasiveness, we propose that this mutational motif reflects mutagenic lesions to adenines in ssDNA from a potentially broad range of endogenous and exogenous agents.
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Affiliation(s)
- Kathleen M Hudson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Joan F Sterling
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Adam B Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, 34956, Turkey
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Natalie Saini
- Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Piotr A Mieczkowski
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
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15
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Li X, Gao D, Shen F, Chen H, Zhang Z, He C, Gao A, Lang Y, Zhu X, Zhou J, Shang ZF, Ding WQ, Zhu J. Polymerase iota (POLI) confers radioresistance of esophageal squamous cell carcinoma by regulating RAD51 stability and facilitating homologous recombination. Cell Death Discov 2023; 9:291. [PMID: 37558683 PMCID: PMC10412619 DOI: 10.1038/s41420-023-01541-8] [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: 04/13/2023] [Revised: 06/15/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Radiotherapy resistance is an important and urgent challenge in the clinical management of esophageal squamous carcinoma (ESCC). However, the factors mediating the ESCC resistance to radiotherapy and its underlying molecular mechanisms are not fully clarified. Our previous studies have demonstrated the critical role of DNA polymerase iota (POLI) in ESCC development and progression, here, we aimed to investigate the involvement of POLI in ESCC radiotherapy resistance and elucidate the underlying molecular mechanism. We found that highly expressed POLI was correlated with shorter overall survival of ESCC patients received radiotherapy. Down-regulation of POLI sensitized ESCC to IR, prolonged γH2AX foci in nuclei and comet tails after IR. HR but not NHEJ repair is inhibited in POLI-deficient ESCC cells. POLI stabilizes RAD51 protein via competitively binding with and blocking the interaction between RAD51 and E3 ligase XIAP and XIAP-mediated ubiquitination. Furthermore, loss of POLI leads to the activation of GAS signaling. Our findings provide novel insight into the role of POLI in the development of radioresistance mediated by stabilizing RAD51 protein in ESCC.
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Affiliation(s)
- Xiaoqing Li
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Dexuan Gao
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Fei Shen
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hengrui Chen
- Department of Radiation Oncology, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Zhuqiang Zhang
- Department of Radiation Medicine, Baotou Medical College, Baotou, China
| | - Chao He
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Aidi Gao
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Yue Lang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Xiaozhong Zhu
- Department of Cardiothoracic Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jundong Zhou
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China.
- Department of Radiation Oncology, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China.
| | - Zeng-Fu Shang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China.
| | - Wei-Qun Ding
- Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Ji Zhu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
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16
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Cox MM, Goodman MF, Keck JL, van Oijen A, Lovett ST, Robinson A. Generation and Repair of Postreplication Gaps in Escherichia coli. Microbiol Mol Biol Rev 2023; 87:e0007822. [PMID: 37212693 PMCID: PMC10304936 DOI: 10.1128/mmbr.00078-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
When replication forks encounter template lesions, one result is lesion skipping, where the stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to leave the lesion behind in a postreplication gap. Despite considerable attention in the 6 decades since postreplication gaps were discovered, the mechanisms by which postreplication gaps are generated and repaired remain highly enigmatic. This review focuses on postreplication gap generation and repair in the bacterium Escherichia coli. New information to address the frequency and mechanism of gap generation and new mechanisms for their resolution are described. There are a few instances where the formation of postreplication gaps appears to be programmed into particular genomic locations, where they are triggered by novel genomic elements.
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Affiliation(s)
- Michael M. Cox
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Myron F. Goodman
- Department of Biological Sciences, University of Southern California, University Park, Los Angeles, California, USA
- Department of Chemistry, University of Southern California, University Park, Los Angeles, California, USA
| | - James L. Keck
- Department of Biological Chemistry, University of Wisconsin—Madison School of Medicine, Madison, Wisconsin, USA
| | - Antoine van Oijen
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Susan T. Lovett
- Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Andrew Robinson
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
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17
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Arianna GA, Geddes-Buehre DH, Korzhnev DM. Backbone and ILV side-chain methyl NMR resonance assignments of human Rev7/Rev3-RBM1 and Rev7/Rev3-RBM2 complexes. BIOMOLECULAR NMR ASSIGNMENTS 2023:10.1007/s12104-023-10128-4. [PMID: 37129702 DOI: 10.1007/s12104-023-10128-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
Rev7 is a versatile HORMA (Hop1, Rev7, Mad2) family adaptor protein with multiple roles in mitotic regulation and DNA damage response, and an essential accessory subunit of the translesion synthesis (TLS) DNA polymerase Polζ employed in replication of damaged DNA. Within Polζ, the two copies of Rev7 interact with the two Rev7-bonding motifs (RBM1 and RBM2) of the catalytic subunit Rev3 by a mechanism characteristic of HORMA proteins whereby the "safety-belt" loop of Rev7 closes on the top of the ligand. Here we report the nearly complete backbone and Ile, Val, Leu side-chain methyl NMR resonance assignments of the 27 kDa human Rev7/Rev3-RBM1 and Rev7/Rev3-RBM2 complexes (BMRB deposition numbers 51651 and 51652) that will facilitate future NMR studies of Rev7 dynamics and interactions.
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Affiliation(s)
- Gianluca A Arianna
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Dane H Geddes-Buehre
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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18
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Dyrkheeva NS, Malakhova AA, Zakharenko AL, Okorokova LS, Shtokalo DN, Pavlova SV, Medvedev SP, Zakian SM, Nushtaeva AA, Tupikin AE, Kabilov MR, Khodyreva SN, Luzina OA, Salakhutdinov NF, Lavrik OI. Transcriptomic Analysis of CRISPR/Cas9-Mediated PARP1-Knockout Cells under the Influence of Topotecan and TDP1 Inhibitor. Int J Mol Sci 2023; 24:ijms24065148. [PMID: 36982223 PMCID: PMC10049738 DOI: 10.3390/ijms24065148] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Topoisomerase 1 (TOP1) is an enzyme that regulates DNA topology and is essential for replication, recombination, and other processes. The normal TOP1 catalytic cycle involves the formation of a short-lived covalent complex with the 3' end of DNA (TOP1 cleavage complex, TOP1cc), which can be stabilized, resulting in cell death. This fact substantiates the effectiveness of anticancer drugs-TOP1 poisons, such as topotecan, that block the relegation of DNA and fix TOP1cc. Tyrosyl-DNA phosphodiesterase 1 (TDP1) is able to eliminate TOP1cc. Thus, TDP1 interferes with the action of topotecan. Poly(ADP-ribose) polymerase 1 (PARP1) is a key regulator of many processes in the cell, such as maintaining the integrity of the genome, regulation of the cell cycle, cell death, and others. PARP1 also controls the repair of TOP1cc. We performed a transcriptomic analysis of wild type and PARP1 knockout HEK293A cells treated with topotecan and TDP1 inhibitor OL9-119 alone and in combination. The largest number of differentially expressed genes (DEGs, about 4000 both up- and down-regulated genes) was found in knockout cells. Topotecan and OL9-119 treatment elicited significantly fewer DEGs in WT cells and negligible DEGs in PARP1-KO cells. A significant part of the changes caused by PARP1-KO affected the synthesis and processing of proteins. Differences under the action of treatment with TOP1 or TDP1 inhibitors alone were found in the signaling pathways for the development of cancer, DNA repair, and the proteasome. The drug combination resulted in DEGs in the ribosome, proteasome, spliceosome, and oxidative phosphorylation pathways.
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Affiliation(s)
- Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Anastasia A Malakhova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Aleksandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | | | - Dmitriy N Shtokalo
- AcademGene LLC, 6 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- A.P. Ershov Institute of Informatics Systems SB RAS, 6 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Sophia V Pavlova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Sergey P Medvedev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Suren M Zakian
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Anna A Nushtaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Svetlana N Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Olga A Luzina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Department of Molecular Biology and Biotechnology, Novosibirsk State University, 630090 Novosibirsk, Russia
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19
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Anand J, Chiou L, Sciandra C, Zhang X, Hong J, Wu D, Zhou P, Vaziri C. Roles of trans-lesion synthesis (TLS) DNA polymerases in tumorigenesis and cancer therapy. NAR Cancer 2023; 5:zcad005. [PMID: 36755961 PMCID: PMC9900426 DOI: 10.1093/narcan/zcad005] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/10/2022] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
DNA damage tolerance and mutagenesis are hallmarks and enabling characteristics of neoplastic cells that drive tumorigenesis and allow cancer cells to resist therapy. The 'Y-family' trans-lesion synthesis (TLS) DNA polymerases enable cells to replicate damaged genomes, thereby conferring DNA damage tolerance. Moreover, Y-family DNA polymerases are inherently error-prone and cause mutations. Therefore, TLS DNA polymerases are potential mediators of important tumorigenic phenotypes. The skin cancer-propensity syndrome xeroderma pigmentosum-variant (XPV) results from defects in the Y-family DNA Polymerase Pol eta (Polη) and compensatory deployment of alternative inappropriate DNA polymerases. However, the extent to which dysregulated TLS contributes to the underlying etiology of other human cancers is unclear. Here we consider the broad impact of TLS polymerases on tumorigenesis and cancer therapy. We survey the ways in which TLS DNA polymerases are pathologically altered in cancer. We summarize evidence that TLS polymerases shape cancer genomes, and review studies implicating dysregulated TLS as a driver of carcinogenesis. Because many cancer treatment regimens comprise DNA-damaging agents, pharmacological inhibition of TLS is an attractive strategy for sensitizing tumors to genotoxic therapies. Therefore, we discuss the pharmacological tractability of the TLS pathway and summarize recent progress on development of TLS inhibitors for therapeutic purposes.
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Affiliation(s)
- Jay Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Lilly Chiou
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carly Sciandra
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xingyuan Zhang
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
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20
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Ning K, Kuz CA, Cheng F, Feng Z, Yan Z, Qiu J. Adeno-Associated Virus Monoinfection Induces a DNA Damage Response and DNA Repair That Contributes to Viral DNA Replication. mBio 2023; 14:e0352822. [PMID: 36719192 PMCID: PMC9973366 DOI: 10.1128/mbio.03528-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 02/01/2023] Open
Abstract
Adeno-associated virus (AAV) belongs to the Dependoparvovirus genus of the Parvoviridae family. AAV replication relies on a helper virus, such as adenovirus (Ad). Co-infection of AAV and Ad induces a DNA damage response (DDR), although its function in AAV DNA replication remains unknown. In this study, monoinfection of AAV2 in HEK293T cells expressing a minimal set of Ad helper genes was used to investigate the role of the DDR solely induced by AAV. We found that AAV2 DNA replication, but not single stranded (ss)DNA genome accumulation and Rep expression only, induced a robust DDR in HEK293T cells. The induced DDR featured the phosphorylation of replication protein A32 (RPA32), histone variant H2AX (H2A histone family member X), and all 3 phosphatidylinositol 3-kinase-related kinases (PIKKs). We also found that the kinase ataxia telangiectasia and Rad3-related protein (ATR) plays a major role in AAV2 DNA replication and that Y family DNA repair DNA polymerases η (Pol η) and Pol κ contribute to AAV2 DNA replication both in vitro and in HEK293T cells. Knockout of Pol η and Pol κ in HEK293T cells significantly decreased wild-type AAV2 replication and recombinant AAV2 production. Thus, our study has proven that AAV2 DNA replication induces a DDR, which in turn initiates a DNA repairing process that partially contributes to the viral genome amplification in HEK293T cells. IMPORTANCE Recombinant AAV (rAAV) has emerged as one of the preferred delivery vectors for clinical gene therapy. rAAV production in HEK293 cells by transfection of a rAAV transgene plasmid, an AAV Rep and Cap expression packaging plasmid, and an Ad helper plasmid remains the popular method. Here, we demonstrated that the high fidelity Y family DNA repair DNA polymerase, Pol η, and Pol κ, plays a significant role in AAV DNA replication and rAAV production in HEK293T cells. Understanding the AAV DNA replication mechanism in HEK293T cells could provide clues to increase rAAV vector yield produced from the transfection method. We also provide evidence that the ATR-mediated DNA repair process through Pol η and Pol κ is one of the mechanisms to amplify AAV genome, which could explain AAV replication and rAAV ssDNA genome conversion in mitotic quiescent cells.
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Affiliation(s)
- Kang Ning
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cagla Aksu Kuz
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Fang Cheng
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Zehua Feng
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, USA
| | - Ziying Yan
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, USA
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
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21
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Chi L, Wang H, Yu F, Gao C, Dai H, Si X, Liu L, Wang Z, Zheng J, Ke Y, Liu H, Zhang Q. Recent Progress of Ubiquitin-Specific-Processing Protease 7 Inhibitors. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2023. [DOI: 10.1134/s1068162023020073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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22
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Maloisel L, Ma E, Phipps J, Deshayes A, Mattarocci S, Marcand S, Dubrana K, Coïc E. Rad51 filaments assembled in the absence of the complex formed by the Rad51 paralogs Rad55 and Rad57 are outcompeted by translesion DNA polymerases on UV-induced ssDNA gaps. PLoS Genet 2023; 19:e1010639. [PMID: 36749784 PMCID: PMC9937489 DOI: 10.1371/journal.pgen.1010639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 02/17/2023] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
The bypass of DNA lesions that block replicative polymerases during DNA replication relies on DNA damage tolerance pathways. The error-prone translesion synthesis (TLS) pathway depends on specialized DNA polymerases that incorporate nucleotides in front of base lesions, potentially inducing mutagenesis. Two error-free pathways can bypass the lesions: the template switching pathway, which uses the sister chromatid as a template, and the homologous recombination pathway (HR), which also can use the homologous chromosome as template. The balance between error-prone and error-free pathways controls the mutagenesis level. Therefore, it is crucial to precisely characterize factors that influence the pathway choice to better understand genetic stability at replication forks. In yeast, the complex formed by the Rad51 paralogs Rad55 and Rad57 promotes HR and template-switching at stalled replication forks. At DNA double-strand breaks (DSBs), this complex promotes Rad51 filament formation and stability, notably by counteracting the Srs2 anti-recombinase. To explore the role of the Rad55-Rad57 complex in error-free pathways, we monitored the genetic interactions between Rad55-Rad57, the translesion polymerases Polζ or Polη, and Srs2 following UV radiation that induces mostly single-strand DNA gaps. We found that the Rad55-Rad57 complex was involved in three ways. First, it protects Rad51 filaments from Srs2, as it does at DSBs. Second, it promotes Rad51 filament stability independently of Srs2. Finally, we observed that UV-induced HR is almost abolished in Rad55-Rad57 deficient cells, and is partially restored upon Polζ or Polη depletion. Hence, we propose that the Rad55-Rad57 complex is essential to promote Rad51 filament stability on single-strand DNA gaps, notably to counteract the error-prone TLS polymerases and mutagenesis.
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Affiliation(s)
- Laurent Maloisel
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
- * E-mail: (LM); (EC)
| | - Emilie Ma
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Jamie Phipps
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Alice Deshayes
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Stefano Mattarocci
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Stéphane Marcand
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Karine Dubrana
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Eric Coïc
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
- * E-mail: (LM); (EC)
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23
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Zakharenko AL, Malakhova AA, Dyrkheeva NS, Okorokova LS, Medvedev SP, Zakian SM, Kabilov MR, Tupikin AA, Lavrik OI. PARP1 Gene Knockout Suppresses Expression of DNA Base Excision Repair Genes. DOKL BIOCHEM BIOPHYS 2023; 508:6-11. [PMID: 36653586 PMCID: PMC10042944 DOI: 10.1134/s1607672922700028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 01/20/2023]
Abstract
The effect of PARP1 knockout in HEK293 cells on the gene expression of DNA base excision repair (BER) proteins was studied. It was shown that the expression of all differentially expressed genes (DEGs) of BER was reduced by knockout. The expression of the DNA glycosylase gene NEIL1, which is considered to be one of the common "hubs" for binding BER proteins, has changed the most. The expression of genes of auxiliary subunits of DNA polymerases δ and ε is also significantly reduced. The PARP1 gene knockout cell line obtained is an adequate cell model for studying the activity of the BER process in the absence of PARP1 and testing drugs aimed at inhibiting repair processes. It has been found for the first time that knockout of the PARP1 gene results in a significant change in the level of expression of proteins responsible for ribosome biogenesis and the functioning of the proteasome.
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Affiliation(s)
- A L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Malakhova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin National Medical Research Center of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - N S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - S P Medvedev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin National Medical Research Center of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - S M Zakian
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin National Medical Research Center of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
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24
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Abstract
High-fidelity DNA replication is critical for the faithful transmission of genetic information to daughter cells. Following genotoxic stress, specialized DNA damage tolerance pathways are activated to ensure replication fork progression. These pathways include translesion DNA synthesis, template switching and repriming. In this Review, we describe how DNA damage tolerance pathways impact genome stability, their connection with tumorigenesis and their effects on cancer therapy response. We discuss recent findings that single-strand DNA gap accumulation impacts chemoresponse and explore a growing body of evidence that suggests that different DNA damage tolerance factors, including translesion synthesis polymerases, template switching proteins and enzymes affecting single-stranded DNA gaps, represent useful cancer targets. We further outline how the consequences of DNA damage tolerance mechanisms could inform the discovery of new biomarkers to refine cancer therapies.
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Affiliation(s)
- Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
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25
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Tsegay PS, Hernandez D, Qu F, Olatunji M, Mamun Y, Chapagain P, Liu Y. RNA-guided DNA base damage repair via DNA polymerase-mediated nick translation. Nucleic Acids Res 2022; 51:166-181. [PMID: 36533524 PMCID: PMC9841414 DOI: 10.1093/nar/gkac1178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/28/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
DNA repair is mediated by DNA synthesis guided by a DNA template. Recent studies have shown that DNA repair can also be accomplished by RNA-guided DNA synthesis. However, it remains unknown how RNA can guide DNA synthesis to repair DNA damage. In this study, we revealed the molecular mechanisms underlying RNA-guided DNA synthesis and base damage repair mediated by human repair DNA polymerases. We showed that pol β, pol κ, and pol ι predominantly synthesized one nucleotide, and pol η, pol ν, and pol θ synthesized multi-nucleotides during RNA-guided DNA base damage repair. The steady-state kinetics showed that pol η exhibited more efficient RNA-guided DNA synthesis than pol β. Using molecular dynamics simulation, we further revealed dynamic conformational changes of pol β and pol η and their structural basis to accommodate the RNA template and misoriented triphosphates of an incoming nucleotide. We demonstrated that RNA-guided base damage repair could be accomplished by the RNA-guided DNA strand-displacement synthesis and nick translation leading to nick ligation in a double-strand DNA region. Our study revealed a novel RNA-guided base damage repair pathway during transcription and DNA replication.
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Affiliation(s)
- Pawlos S Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Daniela Hernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Fei Qu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Mustapha Olatunji
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Yasir Mamun
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL, USA,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Yuan Liu
- To whom correspondence should be addressed. Tel: +1 305 348 3628; Fax: +1 305 348 2772;
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26
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Joseph AM, Nahar K, Daw S, Hasan MM, Lo R, Le TBK, Rahman KM, Badrinarayanan A. Mechanistic insight into the repair of C8-linked pyrrolobenzodiazepine monomer-mediated DNA damage. RSC Med Chem 2022; 13:1621-1633. [PMID: 36561066 PMCID: PMC9749960 DOI: 10.1039/d2md00194b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022] Open
Abstract
Pyrrolobenzodiazepines (PBDs) are naturally occurring DNA binding compounds that possess anti-tumor and anti-bacterial activity. Chemical modifications of PBDs can result in improved DNA binding, sequence specificity and enhanced efficacy. More recently, synthetic PBD monomers have shown promise as payloads for antibody drug conjugates and anti-bacterial agents. The precise mechanism of action of these PBD monomers and their role in causing DNA damage remains to be elucidated. Here we characterized the damage-inducing potential of two C8-linked PBD bi-aryl monomers in Caulobacter crescentus and investigated the strategies employed by cells to repair the same. We show that these compounds cause DNA damage and efficiently kill bacteria, in a manner comparable to the extensively used DNA cross-linking agent mitomycin-C (MMC). However, in stark contrast to MMC which employs a mutagenic lesion tolerance pathway, we implicate essential functions for error-free mechanisms in repairing PBD monomer-mediated damage. We find that survival is severely compromised in cells lacking nucleotide excision repair and to a lesser extent, in cells with impaired recombination-based repair. Loss of nucleotide excision repair leads to significant increase in double-strand breaks, underscoring the critical role of this pathway in mediating repair of PBD-induced DNA lesions. Together, our study provides comprehensive insights into how mono-alkylating DNA-targeting therapeutic compounds like PBD monomers challenge cell growth, and identifies the specific mechanisms employed by the cell to counter the same.
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Affiliation(s)
- Asha Mary Joseph
- National Centre for Biological Sciences (Tata Institute of Fundamental Research) Bangalore India
| | - Kazi Nahar
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London Franklin-Wilkins Building, 150 Stamford Street London SE1 9NH UK
| | - Saheli Daw
- National Centre for Biological Sciences (Tata Institute of Fundamental Research) Bangalore India
| | - Md Mahbub Hasan
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London Franklin-Wilkins Building, 150 Stamford Street London SE1 9NH UK
| | - Rebecca Lo
- John Innes Centre, Department of Molecular Microbiology Colney Lane Norwich NR4 7UH UK
| | - Tung B K Le
- John Innes Centre, Department of Molecular Microbiology Colney Lane Norwich NR4 7UH UK
| | - Khondaker Miraz Rahman
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London Franklin-Wilkins Building, 150 Stamford Street London SE1 9NH UK
| | - Anjana Badrinarayanan
- National Centre for Biological Sciences (Tata Institute of Fundamental Research) Bangalore India
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27
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Masłowska KH, Pagès V. Rad5 participates in lesion bypass through its Rev1-binding and ubiquitin ligase domains, but not through its helicase function. Front Mol Biosci 2022; 9:1062027. [DOI: 10.3389/fmolb.2022.1062027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022] Open
Abstract
DNA Damage Tolerance (DDT) functions to bypass replication-blocking lesions and is divided into two distinct pathways: error-prone Translesion Synthesis (TLS) and error-free Damage Avoidance (DA). Rad5 is a multifunctional protein that is involved in these DDT processes. Saccharomyces cerevisiae Rad5 contains three well defined domains: a RING domain that promotes PCNA polyubiquitination, a ssDNA-dependent ATPase/helicase domain, and a Rev1-binding domain. Both the RING domain and the ATPase/helicase domain are conserved in human Rad5 ortholog HLTF. In this study we used domain-specific mutants to address the contribution of each of the Rad5 domains to the lesion tolerance. We demonstrate that the two critical functions of Rad5 during DNA damage tolerance are the activation of template switching through polyubiquitination of PCNA and the recruitment of TLS polymerases, and that loss of one of those functions can be compensated by increased usage of the other. We also show that, unlike previously suggested, the helicase activity does not play any role in lesion tolerance.
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28
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Kalhor S, Fattahi A. Design of amino acid- and carbohydrate-based anticancer drugs to inhibit polymerase η. Sci Rep 2022; 12:18461. [PMID: 36323739 PMCID: PMC9630280 DOI: 10.1038/s41598-022-22810-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
DNA polymerase η (polη) is of significant value for designing new families of anticancer drugs. This protein takes a role in many stages of the cell cycle, including DNA replication, translesion DNA synthesis, and the repairing process of DNA. According to many studies, a high level of expression of polη in most cases has been associated with low rates of patients' survival, regardless of considering the stage of tumor cells. Thus, the design of new drugs with fewer side effects to inhibit polη in cancerous cells has attracted attention in recent years. This project aims to design and explore the alternative inhibitors for polη, which are based on carbohydrates and amino acids. In terms of physicochemical properties, they are similar to the traditional anticancer drugs such as Cytarabine (cytosine arabinose). These alternative inhibitors are supposed to disrupt the DNA replication process in cancerous cells and prevent the tumor cells from mitosis. These newly designed structures, which are based on natural products, are expected to be non-toxic and to have the same chemotherapeutic impact as the traditional agents. The combinatorial use of quantum mechanics studies and molecular dynamic simulation has enabled us to precisely predict the inhibition mechanism of the newly designed structure, which is based on carbohydrates and amino acids, and compare it with that of the traditional chemotherapeutic drugs such as Cytarabine. Our results suggest that the inhibitors containing the natural building blocks of amino acid and carbohydrate could be considered alternative drugs for Cytarabine to block polη.
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Affiliation(s)
- Sepideh Kalhor
- Department of Chemistry, Sharif University of Technology, Tehran, Iran
| | - Alireza Fattahi
- Department of Chemistry, Sharif University of Technology, Tehran, Iran.
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29
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Zhu N, Zhao Y, Mi M, Lu Y, Tan Y, Fang X, Weng S, Yuan Y. REV1: A novel biomarker and potential therapeutic target for various cancers. Front Genet 2022; 13:997970. [PMID: 36246647 PMCID: PMC9560673 DOI: 10.3389/fgene.2022.997970] [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: 07/19/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022] Open
Abstract
Background: REV1 is a member of the translesion synthesis DNA polymerase Y family. It is an essential player in a variety of DNA replication activities, and perform major roles in the production of both spontaneous and DNA damage-induced mutations. This study aimed to explore the role of REV1 as a prognostic biomarker and its potential function regulating the sensitivity of anti-tumor drugs in various cancers. Methods: We analyzed the impact of REV1 gene alterations on patient prognosis and the impact of different REV1 single nucleotide polymorphisms (SNP) on protein structure and function using multiple online prediction servers. REV1 expression was assessed using data from Oncomine, TCGA, and TIMER database. The correlation between REV1 expression and patient prognosis was performed using the PrognoScan and Kaplan-Meier plotter databases. The IC50 values of anti-cancer drugs were downloaded from the Genomics of Drug Sensitivity in Cancer database and the correlation analyses between REV1 expression and each drug pathway’s IC50 value in different tumor types were conducted. Results: Progression free survival was longer in REV1 gene altered group comparing to unaltered group [Median progression free survival (PFS), 107.80 vs. 60.89 months, p value = 7.062e-3]. REV1 SNP rs183737771 (F427L) was predicted to be deleterious SNP. REV1 expression differs in different tumour types. Low REV1 expression is associated with better prognosis in colorectal disease specific survival (DSS), disease-free survival (DFS), gastric overall survival (OS), post progression survival (PPS) and ovarian (OS, PPS) cancer while high REV1 expression is associated with better prognosis in lung [OS, relapse free survival (RFS), first progession (FP), PPS] and breast (DSS, RFS) cancer. In colon adenocarcinoma and rectum adenocarcinoma and lung adenocarcinoma, low expression of REV1 may suggest resistance to drugs in certain pathways. Conversely, high expression of REV1 in acute myeloid leukemia, brain lower grade glioma, small cell lung cancer and thyroid carcinoma may indicate resistance to drugs in certain pathways. Conclusion: REV1 plays different roles in different tumor types, drug susceptibility, and related biological events. REV1 expression is significantly correlated with different prognosis in colorectal, ovarian, lung, breast, and gastric cancer. REV1 expression can be used as predictive marker for various drugs of various pathways in different tumors.
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Affiliation(s)
- Ning Zhu
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yingxin Zhao
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Mi Mi
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yier Lu
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinuo Tan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xuefeng Fang
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shanshan Weng
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Yuan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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30
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Cisneros LH, Vaske C, Bussey KJ. Identification of a signature of evolutionarily conserved stress-induced mutagenesis in cancer. Front Genet 2022; 13:932763. [PMID: 36147501 PMCID: PMC9488704 DOI: 10.3389/fgene.2022.932763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
The clustering of mutations observed in cancer cells is reminiscent of the stress-induced mutagenesis (SIM) response in bacteria. Bacteria deploy SIM when faced with DNA double-strand breaks in the presence of conditions that elicit an SOS response. SIM employs DinB, the evolutionary precursor to human trans-lesion synthesis (TLS) error-prone polymerases, and results in mutations concentrated around DNA double-strand breaks with an abundance that decays with distance. We performed a quantitative study on single nucleotide variant calls for whole-genome sequencing data from 1950 tumors, non-inherited mutations from 129 normal samples, and acquired mutations in 3 cell line models of stress-induced adaptive mutation. We introduce statistical methods to identify mutational clusters, quantify their shapes and tease out the potential mechanism that produced them. Our results show that mutations in both normal and cancer samples are indeed clustered and have shapes indicative of SIM. Clusters in normal samples occur more often in the same genomic location across samples than in cancer suggesting loss of regulation over the mutational process during carcinogenesis. Additionally, the signatures of TLS contribute the most to mutational cluster formation in both patient samples as well as experimental models of SIM. Furthermore, a measure of cluster shape heterogeneity was associated with cancer patient survival with a hazard ratio of 5.744 (Cox Proportional Hazard Regression, 95% CI: 1.824-18.09). Our results support the conclusion that the ancient and evolutionary-conserved adaptive mutation response found in bacteria is a source of genomic instability in cancer. Biological adaptation through SIM might explain the ability of tumors to evolve in the face of strong selective pressures such as treatment and suggests that the conventional 'hit it hard' approaches to therapy could prove themselves counterproductive.
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Affiliation(s)
- Luis H. Cisneros
- NantOmics, LLC, Santa Cruz, CA, United States
- The Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, United States
| | | | - Kimberly J. Bussey
- NantOmics, LLC, Santa Cruz, CA, United States
- The Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, United States
- Precision Medicine, Midwestern University, Glendale, AZ, United States
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31
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Siebler HM, Cui J, Hill SE, Pavlov YI. DNA Polymerase ζ without the C-Terminus of Catalytic Subunit Rev3 Retains Characteristic Activity, but Alters Mutation Specificity of Ultraviolet Radiation in Yeast. Genes (Basel) 2022; 13:1576. [PMID: 36140745 PMCID: PMC9498848 DOI: 10.3390/genes13091576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/16/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022] Open
Abstract
DNA polymerase ζ (pol ζ) plays a central role in replicating damaged genomic DNA. When DNA synthesis stalls at a lesion, it participates in translesion DNA synthesis (TLS), which helps replication proceed. TLS prevents cell death at the expense of new mutations. The current model indicates that pol ζ-dependent TLS events are mediated by Pol31/Pol32 pol ζ subunits, which are shared with replicative polymerase pol δ. Surprisingly, we found that the mutant rev3-ΔC in yeast, which lacks the C-terminal domain (CTD) of the catalytic subunit of pol ζ and, thus, the platform for interaction with Pol31/Pol32, retains most pol ζ functions. To understand the underlying mechanisms, we studied TLS in normal templates or templates with abasic sites in vitro in primer extension reactions with purified four-subunit pol ζ versus pol ζ with Rev3-ΔC. We also examined the specificity of ultraviolet radiation (UVR)-induced mutagenesis in the rev3-ΔC strains. We found that the absence of Rev3 CTD reduces activity levels, but does not alter the basic biochemical properties of pol ζ, and alters the mutation spectrum only at high doses of UVR, alluding to the existence of mechanisms of recruitment of pol ζ to UVR-damaged sites independent of the interaction of Pol31/Pol32 with the CTD of Rev3.
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Affiliation(s)
- Hollie M. Siebler
- Fred & Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Biology, Creighton University, Omaha, NE 68178, USA
| | - Jian Cui
- Fred & Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sarah E. Hill
- Fred & Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Youri I. Pavlov
- Fred & Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Pathology and Microbiology, Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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32
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Abstract
Human cells encode up to 15 DNA polymerases with specialized functions in chromosomal DNA synthesis and damage repair. In contrast, complex DNA viruses, such as those of the herpesviridae family, encode a single B-family DNA polymerase. This disparity raises the possibility that DNA viruses may rely on host polymerases for synthesis through complex DNA geometries. We tested the importance of error-prone Y-family polymerases involved in translesion synthesis (TLS) to human cytomegalovirus (HCMV) infection. We find most Y-family polymerases involved in the nucleotide insertion and bypass of lesions restrict HCMV genome synthesis and replication. In contrast, other TLS polymerases, such as the polymerase ζ complex, which extends past lesions, was required for optimal genome synthesis and replication. Depletion of either the polζ complex or the suite of insertion polymerases demonstrate that TLS polymerases suppress the frequency of viral genome rearrangements, particularly at GC-rich sites and repeat sequences. Moreover, while distinct from HCMV, replication of the related herpes simplex virus type 1 is impacted by host TLS polymerases, suggesting a broader requirement for host polymerases for DNA virus replication. These findings reveal an unexpected role for host DNA polymerases in ensuring viral genome stability.
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33
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Park J. Correlation between the formation of new competing group and spatial scale for biodiversity in the evolutionary dynamics of cyclic competition. CHAOS (WOODBURY, N.Y.) 2022; 32:081101. [PMID: 36049957 DOI: 10.1063/5.0102416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Securing space for species breeding is important in the evolution and maintenance of life in ecological sciences, and an increase in the number of competing species may cause frequent competition and conflict among the population in securing such spaces in a given area. In particular, for cyclically competing species, which can be described by the metaphor of rock-paper-scissors game, most of the previous works in microscopic frameworks have been studied with the initially given three species without any formation of additional competing species, and the phase transition of biodiversity via mobility from coexistence to extinction has never been changed by a change of spatial scale. In this regard, we investigate the relationship between spatial scales and species coexistence in the spatial cyclic game by considering the emergence of a new competing group by mutation. For different spatial scales, our computations reveal that coexistence can be more sensitive to spatial scales and may require larger spaces for frequencies of interactions. By exploiting the calculation of the coexistence probability from Monte-Carlo simulations, we obtain that certain interaction ranges for coexistence can be affected by both spatial scales and mobility, and spatial patterns for coexistence can appear in different ways. Since the issue of spatial scale is important for species survival as competing populations increase, we expect our results to have broad applications in the fields of social and ecological sciences.
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Affiliation(s)
- Junpyo Park
- Department of Applied Mathematics, Kyung Hee University, Yongin 17104, Republic of Korea
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34
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Cheong A, Nagel ZD. Human Variation in DNA Repair, Immune Function, and Cancer Risk. Front Immunol 2022; 13:899574. [PMID: 35935942 PMCID: PMC9354717 DOI: 10.3389/fimmu.2022.899574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
DNA damage constantly threatens genome integrity, and DNA repair deficiency is associated with increased cancer risk. An intuitive and widely accepted explanation for this relationship is that unrepaired DNA damage leads to carcinogenesis due to the accumulation of mutations in somatic cells. But DNA repair also plays key roles in the function of immune cells, and immunodeficiency is an important risk factor for many cancers. Thus, it is possible that emerging links between inter-individual variation in DNA repair capacity and cancer risk are driven, at least in part, by variation in immune function, but this idea is underexplored. In this review we present an overview of the current understanding of the links between cancer risk and both inter-individual variation in DNA repair capacity and inter-individual variation in immune function. We discuss factors that play a role in both types of variability, including age, lifestyle, and environmental exposures. In conclusion, we propose a research paradigm that incorporates functional studies of both genome integrity and the immune system to predict cancer risk and lay the groundwork for personalized prevention.
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35
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Zhu J, Sanford LD, Ren R, Zhang Y, Tang X. Multiple Machine Learning Methods Reveal Key Biomarkers of Obstructive Sleep Apnea and Continuous Positive Airway Pressure Treatment. Front Genet 2022; 13:927545. [PMID: 35910196 PMCID: PMC9326093 DOI: 10.3389/fgene.2022.927545] [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: 04/24/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Obstructive sleep apnea (OSA) is a worldwide health issue that affects more than 400 million people. Given the limitations inherent in the current conventional diagnosis of OSA based on symptoms report, novel diagnostic approaches are required to complement existing techniques. Recent advances in gene sequencing technology have made it possible to identify a greater number of genes linked to OSA. We identified key genes in OSA and CPAP treatment by screening differentially expressed genes (DEGs) using the Gene Expression Omnibus (GEO) database and employing machine learning algorithms. None of these genes had previously been implicated in OSA. Moreover, a new diagnostic model of OSA was developed, and its diagnostic accuracy was verified in independent datasets. By performing Single Sample Gene Set Enrichment Analysis (ssGSEA) and Counting Relative Subsets of RNA Transcripts (CIBERSORT), we identified possible immunologic mechanisms, which led us to conclude that patients with high OSA risk tend to have elevated inflammation levels that can be brought down by CPAP treatment.
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Affiliation(s)
- Jie Zhu
- Sleep Medicine Center, Department of Respiratory and Critical Care Medicine, Mental Health Center, West China Hospital, Sichuan University, Chengdu, China
| | - Larry D. Sanford
- Sleep Research Laboratory, Center for Integrative Neuroscience and Inflammatory Diseases, Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Rong Ren
- Sleep Medicine Center, Department of Respiratory and Critical Care Medicine, Mental Health Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ye Zhang
- Sleep Medicine Center, Department of Respiratory and Critical Care Medicine, Mental Health Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiangdong Tang
- Sleep Medicine Center, Department of Respiratory and Critical Care Medicine, Mental Health Center, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Xiangdong Tang,
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36
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Petljak M, Dananberg A, Chu K, Bergstrom EN, Striepen J, von Morgen P, Chen Y, Shah H, Sale JE, Alexandrov LB, Stratton MR, Maciejowski J. Mechanisms of APOBEC3 mutagenesis in human cancer cells. Nature 2022; 607:799-807. [PMID: 35859169 PMCID: PMC9329121 DOI: 10.1038/s41586-022-04972-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/13/2022] [Indexed: 02/07/2023]
Abstract
The APOBEC3 family of cytosine deaminases has been implicated in some of the most prevalent mutational signatures in cancer1-3. However, a causal link between endogenous APOBEC3 enzymes and mutational signatures in human cancer genomes has not been established, leaving the mechanisms of APOBEC3 mutagenesis poorly understood. Here, to investigate the mechanisms of APOBEC3 mutagenesis, we deleted implicated genes from human cancer cell lines that naturally generate APOBEC3-associated mutational signatures over time4. Analysis of non-clustered and clustered signatures across whole-genome sequences from 251 breast, bladder and lymphoma cancer cell line clones revealed that APOBEC3A deletion diminished APOBEC3-associated mutational signatures. Deletion of both APOBEC3A and APOBEC3B further decreased APOBEC3 mutation burdens, without eliminating them. Deletion of APOBEC3B increased APOBEC3A protein levels, activity and APOBEC3A-mediated mutagenesis in some cell lines. The uracil glycosylase UNG was required for APOBEC3-mediated transversions, whereas the loss of the translesion polymerase REV1 decreased overall mutation burdens. Together, these data represent direct evidence that endogenous APOBEC3 deaminases generate prevalent mutational signatures in human cancer cells. Our results identify APOBEC3A as the main driver of these mutations, indicate that APOBEC3B can restrain APOBEC3A-dependent mutagenesis while contributing its own smaller mutation burdens and dissect mechanisms that translate APOBEC3 activities into distinct mutational signatures.
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Affiliation(s)
- Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevan Chu
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Josefine Striepen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Patrick von Morgen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanyang Chen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hina Shah
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK.
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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37
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Zhao Q, Chen S, Wang G, Du Y, Zhang Z, Yu G, Ren C, Zhang Y, Du J. Exogenous melatonin enhances soybean (Glycine max (L.) Merr.) seedling tolerance to saline-alkali stress by regulating antioxidant response and DNA damage repair. PHYSIOLOGIA PLANTARUM 2022; 174:e13731. [PMID: 35717632 DOI: 10.1111/ppl.13731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/13/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Saline-alkali (SA) stress induces excessive reactive oxygen species (ROS) accumulation in plant cells, resulting in oxidative damages of membranes, lipids, proteins, and nucleic acids. Melatonin has antioxidant protection effects in living organisms and thus has received a lot of attention. This study aimed to investigate the effect and regulating mechanism of melatonin treatment on soybean tolerance to SA stress. In this study, cultivars Heihe 49 (HH49, SA-tolerant) and Henong 95 (HN95, SA-sensitive) were pot-cultured in SA soil, then treated with MT (0-300 μM) at V1 stage. SA stress induced ROS accumulation and DNA damage in the seedling roots of both cultivars, causing G1/S arrest in HN95 and G2/M arrest in HH49. Melatonin treatment enhanced the activity of antioxidant enzymes in soybean seedling roots and reduced ROS accumulation. Additionally, melatonin treatment upregulated DNA damage repair genes, thus enhancing the reduction of DNA oxidative damage under SA stress. The effects of melatonin treatment were manifested as decreased RAPD polymorphism, 8-hydroxy-2'-deoxyguanine (8-OH-dG) level, and relative density of apurinic sites (AP-sites). Meanwhile, melatonin treatment partially alleviated the SA-induced G1/S arrest in HN95 and G2/M arrest in HH49, thus enhancing soybean seedling tolerance to SA stress.
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Affiliation(s)
- Qiang Zhao
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, People's Republic of China
| | - Suyu Chen
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, People's Republic of China
| | - Guangda Wang
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, People's Republic of China
| | - Yanli Du
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, People's Republic of China
| | - Zhaoning Zhang
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, People's Republic of China
| | - Gaobo Yu
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, People's Republic of China
| | - Chunyuan Ren
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, People's Republic of China
| | - Yuxian Zhang
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, People's Republic of China
| | - Jidao Du
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, People's Republic of China
- Research Center of Saline and Alkali Land Improvement Engineering Technology in Heilongjiang Province, Daqing, People's Republic of China
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38
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Post-Translational Modifications of PCNA: Guiding for the Best DNA Damage Tolerance Choice. J Fungi (Basel) 2022; 8:jof8060621. [PMID: 35736104 PMCID: PMC9225081 DOI: 10.3390/jof8060621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
The sliding clamp PCNA is a multifunctional homotrimer mainly linked to DNA replication. During this process, cells must ensure an accurate and complete genome replication when constantly challenged by the presence of DNA lesions. Post-translational modifications of PCNA play a crucial role in channeling DNA damage tolerance (DDT) and repair mechanisms to bypass unrepaired lesions and promote optimal fork replication restart. PCNA ubiquitination processes trigger the following two main DDT sub-pathways: Rad6/Rad18-dependent PCNA monoubiquitination and Ubc13-Mms2/Rad5-mediated PCNA polyubiquitination, promoting error-prone translation synthesis (TLS) or error-free template switch (TS) pathways, respectively. However, the fork protection mechanism leading to TS during fork reversal is still poorly understood. In contrast, PCNA sumoylation impedes the homologous recombination (HR)-mediated salvage recombination (SR) repair pathway. Focusing on Saccharomyces cerevisiae budding yeast, we summarized PCNA related-DDT and repair mechanisms that coordinately sustain genome stability and cell survival. In addition, we compared PCNA sequences from various fungal pathogens, considering recent advances in structural features. Importantly, the identification of PCNA epitopes may lead to potential fungal targets for antifungal drug development.
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39
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Structural and Molecular Kinetic Features of Activities of DNA Polymerases. Int J Mol Sci 2022; 23:ijms23126373. [PMID: 35742812 PMCID: PMC9224347 DOI: 10.3390/ijms23126373] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 02/01/2023] Open
Abstract
DNA polymerases catalyze DNA synthesis during the replication, repair, and recombination of DNA. Based on phylogenetic analysis and primary protein sequences, DNA polymerases have been categorized into seven families: A, B, C, D, X, Y, and RT. This review presents generalized data on the catalytic mechanism of action of DNA polymerases. The structural features of different DNA polymerase families are described in detail. The discussion highlights the kinetics and conformational dynamics of DNA polymerases from all known polymerase families during DNA synthesis.
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40
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Dusek CO, Dash RC, McPherson KS, Calhoun JT, Bezsonova I, Korzhnev DM, Hadden MK. DNA Sequence Specificity Reveals a Role of the HLTF HIRAN Domain in the Recognition of Trinucleotide Repeats. Biochemistry 2022; 61:10.1021/acs.biochem.2c00027. [PMID: 35608245 PMCID: PMC9684356 DOI: 10.1021/acs.biochem.2c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA damage tolerance (DDT) pathways enable cells to cope with a variety of replication blocks that threaten their ability to complete DNA replication. Helicase-like transcription factor (HLTF) plays a central role in the error-free DDT pathway, template switching (TS), by serving as a ubiquitin ligase to polyubiquitinate the DNA sliding clamp PCNA, which promotes TS initiation. HLTF also serves as an ATP-dependent DNA translocase facilitating replication fork remodeling. The HIP116, Rad5p N-terminal (HIRAN) domain of HLTF specifically recognizes the unmodified 3'-end of single-stranded DNA (ssDNA) at stalled replication forks to promote fork regression. Several crystal structures of the HIRAN domain in complex with ssDNA have been reported; however, optimal ssDNA sequences for high-affinity binding with the domain have not been described. Here we elucidated DNA sequence preferences of HLTF HIRAN through systematic studies of its binding to ssDNA substrates using fluorescence polarization assays and a computational analysis of the ssDNA:HIRAN interaction. These studies reveal that the HLTF HIRAN domain preferentially recognizes a (T/C)TG sequence at the 3'-hydroxyl ssDNA end, which occurs in the CTG trinucleotide repeat (TNR) regions that are susceptible to expansion and deletion mutations identified in neuromuscular and neurodegenerative disorders. These findings support a role for HLTF in maintaining the stability of difficult to replicate TNR microsatellite regions.
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Affiliation(s)
- Christopher O Dusek
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
| | - Radha Charan Dash
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
| | - Kerry S McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Jackson T Calhoun
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
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41
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Ling JA, Frevert Z, Washington MT. Recent Advances in Understanding the Structures of Translesion Synthesis DNA Polymerases. Genes (Basel) 2022; 13:genes13050915. [PMID: 35627300 PMCID: PMC9141541 DOI: 10.3390/genes13050915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 12/10/2022] Open
Abstract
DNA damage in the template strand causes replication forks to stall because replicative DNA polymerases are unable to efficiently incorporate nucleotides opposite template DNA lesions. To overcome these replication blocks, cells are equipped with multiple translesion synthesis polymerases that have evolved specifically to incorporate nucleotides opposite DNA lesions. Over the past two decades, X-ray crystallography has provided a wealth of information about the structures and mechanisms of translesion synthesis polymerases. This approach, however, has been limited to ground state structures of these polymerases bound to DNA and nucleotide substrates. Three recent methodological developments have extended our understanding of the structures and mechanisms of these polymerases. These include time-lapse X-ray crystallography, which allows one to identify novel reaction intermediates; full-ensemble hybrid methods, which allow one to examine the conformational flexibility of the intrinsically disordered regions of proteins; and cryo-electron microscopy, which allows one to determine the high-resolution structures of larger protein complexes. In this article, we will discuss how these three methodological developments have added to our understanding of the structures and mechanisms of translesion synthesis polymerases.
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42
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Wang W, Zhou H, Peng L, Yu F, Xu Q, Wang Q, He J, Liu X. Translesion synthesis of apurinic/apyrimidic site analogues by Y-family DNA polymerase Dbh from Sulfolobus acidocaldarius. Acta Biochim Biophys Sin (Shanghai) 2022; 54:637-646. [PMID: 35920197 PMCID: PMC9828665 DOI: 10.3724/abbs.2022045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Apurinic/apyrimidic (AP) sites are severe DNA damages and strongly block DNA extension by major DNA polymerases. Y-family DNA polymerases possess a strong ability to bypass AP sites and continue the DNA synthesis reaction, which is called translesion synthesis (TLS) activity. To investigate the effect of the molecular structure of the AP site on the TLS efficiency of Dbh, a Y-family DNA polymerase from Sulfolobus acidocaldarius, a series of different AP site analogues (various spacers) are used to characterize the bypass efficiency. We find that not only the molecular structure and atomic composition but also the number and position of AP site analogues determine the TLS efficiency of Dbh. Increasing the spacer length decreases TLS activity. The TLS efficiency also decreases when more than one spacer exists on the DNA template. The position of the AP site analogues is also an important factor for TLS. When the spacer is opposite to the first incorporated dNTPs, the TLS efficiency is the lowest, suggesting that AP sites are largely harmful for the formation of hydrogen bonds. These results deepen our understanding of the TLS activity of Y-family DNA polymerases and provide a biochemical basis for elucidating the TLS mechanism in Sulfolobus acidocaldarius cells.
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Affiliation(s)
- Weiwei Wang
- Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghai201800China,University of Chinese Academy of SciencesBeijing100049China
| | - Huan Zhou
- Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghai201800China,University of Chinese Academy of SciencesBeijing100049China
| | - Li Peng
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Feng Yu
- Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghai201800China,University of Chinese Academy of SciencesBeijing100049China
| | - Qin Xu
- Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghai201800China,University of Chinese Academy of SciencesBeijing100049China
| | - Qisheng Wang
- Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghai201800China,University of Chinese Academy of SciencesBeijing100049China,Correspondence address. Tel: +86-21-34204378; E-mail: (X.L.) / Tel: +86-21-33933192; E-mail: (Q.W.) /Tel: +86-21-33933186; E-mail: (J.H.)@
| | - Jianhua He
- Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghai201800China,University of Chinese Academy of SciencesBeijing100049China,Correspondence address. Tel: +86-21-34204378; E-mail: (X.L.) / Tel: +86-21-33933192; E-mail: (Q.W.) /Tel: +86-21-33933186; E-mail: (J.H.)@
| | - Xipeng Liu
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China,Correspondence address. Tel: +86-21-34204378; E-mail: (X.L.) / Tel: +86-21-33933192; E-mail: (Q.W.) /Tel: +86-21-33933186; E-mail: (J.H.)@
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43
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Huang QY, Song D, Wang WW, Peng L, Chen HF, Xiao X, Liu XP. Mechanism Underlying the Bypass of Apurinic/Pyrimidinic Site Analogs by Sulfolobus acidocaldarius DNA Polymerase IV. Int J Mol Sci 2022; 23:ijms23052729. [PMID: 35269871 PMCID: PMC8910976 DOI: 10.3390/ijms23052729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 12/10/2022] Open
Abstract
The spontaneous depurination of genomic DNA occurs frequently and generates apurinic/pyrimidinic (AP) site damage that is mutagenic or lethal to cells. Error-prone DNA polymerases are specifically responsible for the translesion synthesis (TLS) of specific DNA damage, such as AP site damage, generally with relatively low fidelity. The Y-family DNA polymerases are the main error-prone DNA polymerases, and they employ three mechanisms to perform TLS, including template-skipping, dNTP-stabilized misalignment, and misincorporation-misalignment. The bypass mechanism of the dinB homolog (Dbh), an archaeal Y-family DNA polymerase from Sulfolobus acidocaldarius, is unclear and needs to be confirmed. In this study, we show that the Dbh primarily uses template skipping accompanied by dNTP-stabilized misalignment to bypass AP site analogs, and the incorporation of the first nucleotide across the AP site is the most difficult. Furthermore, based on the reported crystal structures, we confirmed that three conserved residues (Y249, R333, and I295) in the little finger (LF) domain and residue K78 in the palm subdomain of the catalytic core domain are very important for TLS. These results deepen our understanding of how archaeal Y-family DNA polymerases deal with intracellular AP site damage and provide a biochemical basis for elucidating the intracellular function of these polymerases.
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Affiliation(s)
- Qin-Ying Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
| | - Dong Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
| | - Wei-Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Li Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
- Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education), Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
- Correspondence: (X.X.); (X.-P.L.)
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
- Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education), Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
- Correspondence: (X.X.); (X.-P.L.)
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44
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Ler AAL, Carty MP. DNA Damage Tolerance Pathways in Human Cells: A Potential Therapeutic Target. Front Oncol 2022; 11:822500. [PMID: 35198436 PMCID: PMC8859465 DOI: 10.3389/fonc.2021.822500] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/30/2021] [Indexed: 12/26/2022] Open
Abstract
DNA lesions arising from both exogenous and endogenous sources occur frequently in DNA. During DNA replication, the presence of unrepaired DNA damage in the template can arrest replication fork progression, leading to fork collapse, double-strand break formation, and to genome instability. To facilitate completion of replication and prevent the generation of strand breaks, DNA damage tolerance (DDT) pathways play a key role in allowing replication to proceed in the presence of lesions in the template. The two main DDT pathways are translesion synthesis (TLS), which involves the recruitment of specialized TLS polymerases to the site of replication arrest to bypass lesions, and homology-directed damage tolerance, which includes the template switching and fork reversal pathways. With some exceptions, lesion bypass by TLS polymerases is a source of mutagenesis, potentially contributing to the development of cancer. The capacity of TLS polymerases to bypass replication-blocking lesions induced by anti-cancer drugs such as cisplatin can also contribute to tumor chemoresistance. On the other hand, during homology-directed DDT the nascent sister strand is transiently utilised as a template for replication, allowing for error-free lesion bypass. Given the role of DNA damage tolerance pathways in replication, mutagenesis and chemoresistance, a more complete understanding of these pathways can provide avenues for therapeutic exploitation. A number of small molecule inhibitors of TLS polymerase activity have been identified that show synergy with conventional chemotherapeutic agents in killing cancer cells. In this review, we will summarize the major DDT pathways, explore the relationship between damage tolerance and carcinogenesis, and discuss the potential of targeting TLS polymerases as a therapeutic approach.
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Affiliation(s)
- Ashlynn Ai Li Ler
- Biochemistry, School of Biological and Chemical Sciences, The National University of Ireland (NUI) Galway, Galway, Ireland
| | - Michael P. Carty
- Biochemistry, School of Biological and Chemical Sciences, The National University of Ireland (NUI) Galway, Galway, Ireland
- DNA Damage Response Laboratory, Centre for Chromosome Biology, NUI Galway, Galway, Ireland
- *Correspondence: Michael P. Carty,
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45
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Dolce V, Dusi S, Giannattasio M, Joseph CR, Fumasoni M, Branzei D. Parental histone deposition on the replicated strands promotes error-free DNA damage tolerance and regulates drug resistance. Genes Dev 2022; 36:167-179. [PMID: 35115379 PMCID: PMC8887126 DOI: 10.1101/gad.349207.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/12/2022] [Indexed: 11/24/2022]
Abstract
In this study, Dolce et al. investigated connections between Ctf4-mediated processes involved in drug resistance, and conducted a suppressor screen of ctf4Δ sensitivity to the methylating agent MMS. Their findings demonstrate a chromatin-based drug resistance mechanism in which defects in parental histone transfer after replication fork passage impair error-free recombination bypass and lead to up-regulation of TLS-mediated mutagenesis and drug resistance. Ctf4 is a conserved replisome component with multiple roles in DNA metabolism. To investigate connections between Ctf4-mediated processes involved in drug resistance, we conducted a suppressor screen of ctf4Δ sensitivity to the methylating agent MMS. We uncovered that mutations in Dpb3 and Dpb4 components of polymerase ε result in the development of drug resistance in ctf4Δ via their histone-binding function. Alleviated sensitivity to MMS of the double mutants was not associated with rescue of ctf4Δ defects in sister chromatid cohesion, replication fork architecture, or template switching, which ensures error-free replication in the presence of genotoxic stress. Strikingly, the improved viability depended on translesion synthesis (TLS) polymerase-mediated mutagenesis, which was drastically increased in ctf4 dpb3 double mutants. Importantly, mutations in Mcm2–Ctf4–Polα and Dpb3–Dpb4 axes of parental (H3–H4)2 deposition on lagging and leading strands invariably resulted in reduced error-free DNA damage tolerance through gap filling by template switch recombination. Overall, we uncovered a chromatin-based drug resistance mechanism in which defects in parental histone transfer after replication fork passage impair error-free recombination bypass and lead to up-regulation of TLS-mediated mutagenesis and drug resistance.
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Affiliation(s)
- Valeria Dolce
- Istituto FIRC (Fondazione Italiana per la Ricerca sul Cancro) di Oncologia Molecolare (IFOM), the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Sabrina Dusi
- Istituto FIRC (Fondazione Italiana per la Ricerca sul Cancro) di Oncologia Molecolare (IFOM), the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Michele Giannattasio
- Istituto FIRC (Fondazione Italiana per la Ricerca sul Cancro) di Oncologia Molecolare (IFOM), the FIRC Institute of Molecular Oncology, 20139 Milan, Italy.,Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, 20122 Milan, Italy
| | - Chinnu Rose Joseph
- Istituto FIRC (Fondazione Italiana per la Ricerca sul Cancro) di Oncologia Molecolare (IFOM), the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Marco Fumasoni
- Istituto FIRC (Fondazione Italiana per la Ricerca sul Cancro) di Oncologia Molecolare (IFOM), the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Dana Branzei
- Istituto FIRC (Fondazione Italiana per la Ricerca sul Cancro) di Oncologia Molecolare (IFOM), the FIRC Institute of Molecular Oncology, 20139 Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 27100 Pavia, Italy
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46
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REV1 promotes lung tumorigenesis by activating the Rad18/SERTAD2 axis. Cell Death Dis 2022; 13:110. [PMID: 35115490 PMCID: PMC8814179 DOI: 10.1038/s41419-022-04567-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/08/2022] [Accepted: 01/19/2022] [Indexed: 11/17/2022]
Abstract
REV1 is the central member of the family of TLS polymerases, which participate in various DNA damage repair and tolerance pathways and play a significant role in maintaining genomic stability. However, the role of REV1 in tumors is rarely reported. In this study, we found that the expression of REV1 was significantly upregulated in lung cancer tissues compared with matched adjacent tissues and was associated with poor prognosis. Functional experiments demonstrated that REV1 silencing decreased the growth and proliferation capacity of lung cancer cells. Mechanistically, REV1 upregulated the expression of SERTAD2 in a Rad18-dependent manner, thereby promoting lung carcinogenesis. A novel REV1 inhibitor, JH-RE-06, suppressed lung tumorigenesis in vivo and in vitro and was shown to be safe and well tolerated. Our study confirmed that REV1 is a potential diagnostic marker and therapeutic target for lung cancer and that JH-RE-06 may be a safe and efficient therapeutic agent for NSCLC.
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47
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van den Boogaard WMC, Komninos DSJ, Vermeij WP. Chemotherapy Side-Effects: Not All DNA Damage Is Equal. Cancers (Basel) 2022; 14:627. [PMID: 35158895 PMCID: PMC8833520 DOI: 10.3390/cancers14030627] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Recent advances have increased survival rates of children and adults suffering from cancer thanks to effective anti-cancer therapy, such as chemotherapy. However, during treatment and later in life they are frequently confronted with the severe negative side-effects of their life-saving treatment. The occurrence of numerous features of accelerated aging, seriously affecting quality of life, has now become one of the most pressing problems associated with (pediatric) cancer treatment. Chemotherapies frequently target and damage the DNA, causing mutations or genome instability, a major hallmark of both cancer and aging. However, there are numerous types of chemotherapeutic drugs that are genotoxic and interfere with DNA metabolism in different ways, each with their own biodistribution, kinetics, and biological fate. Depending on the type of DNA lesion produced (e.g., interference with DNA replication or RNA transcription), the organ or cell type inflicted (e.g., cell cycle or differentiation status, metabolic state, activity of clearance and detoxification mechanisms, the cellular condition or micro-environment), and the degree of exposure, outcomes of cancer treatment can largely differ. These considerations provide a conceptual framework in which different classes of chemotherapeutics contribute to the development of toxicities and accelerated aging of different organ systems. Here, we summarize frequently observed side-effects in (pediatric) ex-cancer patients and discuss which types of DNA damage might be responsible.
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Affiliation(s)
- Winnie M. C. van den Boogaard
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (W.M.C.v.d.B.); (D.S.J.K.)
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, The Netherlands
| | - Daphne S. J. Komninos
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (W.M.C.v.d.B.); (D.S.J.K.)
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, The Netherlands
| | - Wilbert P. Vermeij
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (W.M.C.v.d.B.); (D.S.J.K.)
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, The Netherlands
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48
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Kaszubowski JD, Trakselis MA. Beyond the Lesion: Back to High Fidelity DNA Synthesis. Front Mol Biosci 2022; 8:811540. [PMID: 35071328 PMCID: PMC8766770 DOI: 10.3389/fmolb.2021.811540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
High fidelity (HiFi) DNA polymerases (Pols) perform the bulk of DNA synthesis required to duplicate genomes in all forms of life. Their structural features, enzymatic mechanisms, and inherent properties are well-described over several decades of research. HiFi Pols are so accurate that they become stalled at sites of DNA damage or lesions that are not one of the four canonical DNA bases. Once stalled, the replisome becomes compromised and vulnerable to further DNA damage. One mechanism to relieve stalling is to recruit a translesion synthesis (TLS) Pol to rapidly synthesize over and past the damage. These TLS Pols have good specificities for the lesion but are less accurate when synthesizing opposite undamaged DNA, and so, mechanisms are needed to limit TLS Pol synthesis and recruit back a HiFi Pol to reestablish the replisome. The overall TLS process can be complicated with several cellular Pols, multifaceted protein contacts, and variable nucleotide incorporation kinetics all contributing to several discrete substitution (or template hand-off) steps. In this review, we highlight the mechanistic differences between distributive equilibrium exchange events and concerted contact-dependent switching by DNA Pols for insertion, extension, and resumption of high-fidelity synthesis beyond the lesion.
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Masłowska KH, Villafañez F, Laureti L, Iwai S, Pagès V. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2074-2080. [PMID: 35104879 PMCID: PMC8887424 DOI: 10.1093/nar/gkac044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 12/04/2022] Open
Abstract
The DNA damage response (DDR) preserves the genetic integrity of the cell by sensing and repairing damages after a genotoxic stress. Translesion Synthesis (TLS), an error-prone DNA damage tolerance pathway, is controlled by PCNA ubiquitination. In this work, we raise the question whether TLS is controlled locally or globally. Using a recently developed method that allows to follow the bypass of a single lesion inserted into the yeast genome, we show that (i) TLS is controlled locally at each individual lesion by PCNA ubiquitination, (ii) a single lesion is enough to induce PCNA ubiquitination and (iii) PCNA ubiquitination is imperative for TLS to occur. More importantly, we show that the activation of the DDR that follows a genotoxic stress does not increase TLS at individual lesions. We conclude that unlike the SOS response in bacteria, the eukaryotic DDR does not promote TLS and mutagenesis.
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Affiliation(s)
- Katarzyna H Masłowska
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille 13009, France
| | - Florencia Villafañez
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille 13009, France
| | - Luisa Laureti
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille 13009, France
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, Osaka 560-8531, Japan
| | - Vincent Pagès
- To whom correspondence should be addressed. Tel: +33 4 86 977 384;
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50
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Wang M, Chen S, Ao D. Targeting DNA repair pathway in cancer: Mechanisms and clinical application. MedComm (Beijing) 2021; 2:654-691. [PMID: 34977872 PMCID: PMC8706759 DOI: 10.1002/mco2.103] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023] Open
Abstract
Over the last decades, the growing understanding on DNA damage response (DDR) pathways has broadened the therapeutic landscape in oncology. It is becoming increasingly clear that the genomic instability of cells resulted from deficient DNA damage response contributes to the occurrence of cancer. One the other hand, these defects could also be exploited as a therapeutic opportunity, which is preferentially more deleterious in tumor cells than in normal cells. An expanding repertoire of DDR-targeting agents has rapidly expanded to inhibitors of multiple members involved in DDR pathways, including PARP, ATM, ATR, CHK1, WEE1, and DNA-PK. In this review, we sought to summarize the complex network of DNA repair machinery in cancer cells and discuss the underlying mechanism for the application of DDR inhibitors in cancer. With the past preclinical evidence and ongoing clinical trials, we also provide an overview of the history and current landscape of DDR inhibitors in cancer treatment, with special focus on the combination of DDR-targeted therapies with other cancer treatment strategies.
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Affiliation(s)
- Manni Wang
- Department of BiotherapyCancer CenterWest China HospitalSichuan UniversityChengduChina
| | - Siyuan Chen
- Department of BiotherapyCancer CenterWest China HospitalSichuan UniversityChengduChina
| | - Danyi Ao
- Department of BiotherapyCancer CenterWest China HospitalSichuan UniversityChengduChina
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