1
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Sasatani M, Xi Y, Daino K, Ishikawa A, Masuda Y, Kajimura J, Piao J, Zaharieva EK, Honda H, Zhou G, Hamasaki K, Kusunoki Y, Shimura T, Kakinuma S, Shimada Y, Doi K, Ishikawa‐Fujiwara T, Sotomaru Y, Kamiya K. Rev1 overexpression accelerates N-methyl-N-nitrosourea (MNU)-induced thymic lymphoma by increasing mutagenesis. Cancer Sci 2024; 115:1808-1819. [PMID: 38572512 PMCID: PMC11145157 DOI: 10.1111/cas.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/28/2024] [Accepted: 03/10/2024] [Indexed: 04/05/2024] Open
Abstract
Rev1 has two important functions in the translesion synthesis pathway, including dCMP transferase activity, and acts as a scaffolding protein for other polymerases involved in translesion synthesis. However, the role of Rev1 in mutagenesis and tumorigenesis in vivo remains unclear. We previously generated Rev1-overexpressing (Rev1-Tg) mice and reported that they exhibited a significantly increased incidence of intestinal adenoma and thymic lymphoma (TL) after N-methyl-N-nitrosourea (MNU) treatment. In this study, we investigated mutagenesis of MNU-induced TL tumorigenesis in wild-type (WT) and Rev1-Tg mice using diverse approaches, including whole-exome sequencing (WES). In Rev1-Tg TLs, the mutation frequency was higher than that in WT TL in most cases. However, no difference in the number of nonsynonymous mutations in the Catalogue of Somatic Mutations in Cancer (COSMIC) genes was observed, and mutations involved in Notch1 and MAPK signaling were similarly detected in both TLs. Mutational signature analysis of WT and Rev1-Tg TLs revealed cosine similarity with COSMIC mutational SBS5 (aging-related) and SBS11 (alkylation-related). Interestingly, the total number of mutations, but not the genotypes of WT and Rev1-Tg, was positively correlated with the relative contribution of SBS5 in individual TLs, suggesting that genetic instability could be accelerated in Rev1-Tg TLs. Finally, we demonstrated that preleukemic cells could be detected earlier in Rev1-Tg mice than in WT mice, following MNU treatment. In conclusion, Rev1 overexpression accelerates mutagenesis and increases the incidence of MNU-induced TL by shortening the latency period, which may be associated with more frequent DNA damage-induced genetic instability.
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Grants
- Network-Type Joint Usage/Research Center for Radiation Disaster Medical Science at Hiroshima University, Nagasaki University, and Fukushima Medical University
- NIFS10KOBS015 National Institute for Fusion Science Collaborative Research Program
- NIFS13KOBA028 National Institute for Fusion Science Collaborative Research Program
- NIFS20KOCA004 National Institute for Fusion Science Collaborative Research Program
- Initiative for Realizing Diversity in the Research Environment (Specific Correspondence Type), a support project for the Development of Human Resources in Science and Technology conducted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 20710043 Japan Society for the Promotion of Science, JSPS KAKENHI
- 22310037 Japan Society for the Promotion of Science, JSPS KAKENHI
- 22710055 Japan Society for the Promotion of Science, JSPS KAKENHI
- JPMX08S08080294 Nuclear Energy S&T and Human Resource Development Project
- Initiative for Realizing Diversity in the Research Environment (Specific Correspondence Type), a support project for the Development of Human Resources in Science and Technology conducted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Japan Society for the Promotion of Science, JSPS KAKENHI
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Affiliation(s)
- Megumi Sasatani
- Department of Experimental OncologyResearch Institute for Radiation Biology and Medicine, Hiroshima UniversityHiroshimaJapan
| | - Yang Xi
- Department of Experimental OncologyResearch Institute for Radiation Biology and Medicine, Hiroshima UniversityHiroshimaJapan
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science CenterNingbo UniversityNingboChina
| | - Kazuhiro Daino
- Department of Radiation Effects ResearchInstitute for Radiological Sciences, National Institutes for Quantum Science and TechnologyChibaJapan
| | - Atsuko Ishikawa
- Department of Radiation Effects ResearchInstitute for Radiological Sciences, National Institutes for Quantum Science and TechnologyChibaJapan
| | - Yuji Masuda
- Department of Experimental OncologyResearch Institute for Radiation Biology and Medicine, Hiroshima UniversityHiroshimaJapan
- Department of Genome DynamicsResearch Institute of Environmental Medicine, Nagoya UniversityNagoyaJapan
- Department of Molecular Pharmaco‐BiologyNagoya University Graduate School of MedicineNagoyaJapan
| | - Junko Kajimura
- Department of Experimental OncologyResearch Institute for Radiation Biology and Medicine, Hiroshima UniversityHiroshimaJapan
- Biosample Research Center, Radiation Effects Research FoundationHiroshimaJapan
| | - Jinlian Piao
- Department of Experimental OncologyResearch Institute for Radiation Biology and Medicine, Hiroshima UniversityHiroshimaJapan
- Gastroenterological and Transplant Surgery, Graduate School of Biomedical & Health SciencesHiroshima UniversityHiroshimaJapan
| | - Elena Karamfilova Zaharieva
- Department of Experimental OncologyResearch Institute for Radiation Biology and Medicine, Hiroshima UniversityHiroshimaJapan
| | - Hiroaki Honda
- Institute of Laboratory Animals, Tokyo Women's Medical UniversityTokyoJapan
| | - Guanyu Zhou
- Department of Experimental OncologyResearch Institute for Radiation Biology and Medicine, Hiroshima UniversityHiroshimaJapan
| | - Kanya Hamasaki
- Department of Molecular BiosciencesRadiation Effects Research FoundationHiroshimaJapan
| | - Yoichiro Kusunoki
- Department of Molecular BiosciencesRadiation Effects Research FoundationHiroshimaJapan
| | - Tsutomu Shimura
- Department of Environmental HealthNational Institute of Public HealthSaitamaJapan
| | - Shizuko Kakinuma
- Department of Radiation Effects ResearchInstitute for Radiological Sciences, National Institutes for Quantum Science and TechnologyChibaJapan
| | | | - Kazutaka Doi
- Department of Radiation Regulatory Science ResearchInstitute for Radiological Sciences, National Institutes for Quantum Science and TechnologyChibaJapan
| | | | - Yusuke Sotomaru
- Natural Science Center for Basic Research and DevelopmentHiroshima UniversityHiroshimaJapan
| | - Kenji Kamiya
- Department of Experimental OncologyResearch Institute for Radiation Biology and Medicine, Hiroshima UniversityHiroshimaJapan
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2
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Gielecińska A, Kciuk M, Kołat D, Kruczkowska W, Kontek R. Polymorphisms of DNA Repair Genes in Thyroid Cancer. Int J Mol Sci 2024; 25:5995. [PMID: 38892180 PMCID: PMC11172789 DOI: 10.3390/ijms25115995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The incidence of thyroid cancer, one of the most common forms of endocrine cancer, is increasing rapidly worldwide in developed and developing countries. Various risk factors can increase susceptibility to thyroid cancer, but particular emphasis is put on the role of DNA repair genes, which have a significant impact on genome stability. Polymorphisms of these genes can increase the risk of developing thyroid cancer by affecting their function. In this article, we present a concise review on the most common polymorphisms of selected DNA repair genes that may influence the risk of thyroid cancer. We point out significant differences in the frequency of these polymorphisms between various populations and their potential relationship with susceptibility to the disease. A more complete understanding of these differences may lead to the development of effective prevention strategies and targeted therapies for thyroid cancer. Simultaneously, there is a need for further research on the role of polymorphisms of previously uninvestigated DNA repair genes in the context of thyroid cancer, which may contribute to filling the knowledge gaps on this subject.
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Affiliation(s)
- Adrianna Gielecińska
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland; (A.G.); (R.K.)
- Doctoral School of Exact and Natural Sciences, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
| | - Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland; (A.G.); (R.K.)
- Doctoral School of Exact and Natural Sciences, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
| | - Damian Kołat
- Department of Functional Genomics, Medical University of Lodz, 90-752 Lodz, Poland;
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, 90-136 Lodz, Poland
| | - Weronika Kruczkowska
- Faculty of Biomedical Sciences, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland;
| | - Renata Kontek
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland; (A.G.); (R.K.)
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3
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Khodaverdian V, Sano T, Maggs L, Tomarchio G, Dias A, Clairmont C, Tran M, McVey M. REV1 Coordinates a Multi-Faceted Tolerance Response to DNA Alkylation Damage and Prevents Chromosome Shattering in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580051. [PMID: 38405884 PMCID: PMC10888836 DOI: 10.1101/2024.02.13.580051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
When replication forks encounter damaged DNA, cells utilize DNA damage tolerance mechanisms to allow replication to proceed. These include translesion synthesis at the fork, postreplication gap filling, and template switching via fork reversal or homologous recombination. The extent to which these different damage tolerance mechanisms are utilized depends on cell, tissue, and developmental context-specific cues, the last two of which are poorly understood. To address this gap, we have investigated damage tolerance responses following alkylation damage in Drosophila melanogaster. We report that translesion synthesis, rather than template switching, is the preferred response to alkylation-induced damage in diploid larval tissues. Furthermore, we show that the REV1 protein plays a multi-faceted role in damage tolerance in Drosophila. Drosophila larvae lacking REV1 are hypersensitive to methyl methanesulfonate (MMS) and have highly elevated levels of γ-H2Av foci and chromosome aberrations in MMS-treated tissues. Loss of the REV1 C-terminal domain (CTD), which recruits multiple translesion polymerases to damage sites, sensitizes flies to MMS. In the absence of the REV1 CTD, DNA polymerases eta and zeta become critical for MMS tolerance. In addition, flies lacking REV3, the catalytic subunit of polymerase zeta, require the deoxycytidyl transferase activity of REV1 to tolerate MMS. Together, our results demonstrate that Drosophila prioritize the use of multiple translesion polymerases to tolerate alkylation damage and highlight the critical role of REV1 in the coordination of this response to prevent genome instability.
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Affiliation(s)
- Varandt Khodaverdian
- Department of Biology, Tufts University, Medford, MA 02155
- Current address: Yarrow Biotechnology, New York, NY
| | - Tokio Sano
- Department of Biology, Tufts University, Medford, MA 02155
| | - Lara Maggs
- Department of Biology, Tufts University, Medford, MA 02155
| | - Gina Tomarchio
- Current address: Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ana Dias
- Department of Biology, Tufts University, Medford, MA 02155
| | - Connor Clairmont
- Department of Biology, Tufts University, Medford, MA 02155
- Current address: Vertex Pharmaceuticals, Boston, MA
| | - Mai Tran
- Department of Biology, Tufts University, Medford, MA 02155
| | - Mitch McVey
- Department of Biology, Tufts University, Medford, MA 02155
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4
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Tian LF, Gao H, Yang S, Liu YP, Li M, Xu W, Yan XX. Structure and function of extreme TLS DNA polymerase TTEDbh from Thermoanaerobacter tengcongensis. Int J Biol Macromol 2023; 253:126770. [PMID: 37683741 DOI: 10.1016/j.ijbiomac.2023.126770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Translesion synthesis (TLS) is a kind of DNA repair that maintains the stability of the genome and ensures the normal growth of life in cells under emergencies. Y-family DNA polymerases, as a kind of error-prone DNA polymerase, mainly perform TLS. Previous studies have suggested that the occurrence of tumors is associated with the overexpression of human DNA polymerase of the Y family. And the combination of Y-family DNA polymerase inhibitors is promising for cancer therapy. Here we report the functional and structural characterization of a member of the Y-family DNA polymerases, TTEDbh. We determine TTEDbh is an extreme TLS polymerase that can cross oxidative damage sites, and further identify the amino acids and novel structures that are critical for DNA binding, synthesis, fidelity, and oxidative damage bypass. Moreover, previously unnoticed structural elements with important functions have been discovered and analyzed. These studies provide a more experimental basis for further elucidating the molecular mechanisms of DNA polymerase in the Y family. It could also shed light on the design of drugs to target tumors.
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Affiliation(s)
- Li-Fei Tian
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongwei Gao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyu Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Ping Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingzhou Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqing Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Xiao-Xue Yan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Mellis IA, Bodkin N, Melzer ME, Goyal Y. Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553318. [PMID: 37645989 PMCID: PMC10462021 DOI: 10.1101/2023.08.14.553318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Cells and tissues have a remarkable ability to adapt to genetic perturbations via a variety of molecular mechanisms. Nonsense-induced transcriptional compensation, a form of transcriptional adaptation, has recently emerged as one such mechanism, in which nonsense mutations in a gene can trigger upregulation of related genes, possibly conferring robustness at cellular and organismal levels. However, beyond a handful of developmental contexts and curated sets of genes, to date, no comprehensive genome-wide investigation of this behavior has been undertaken for mammalian cell types and contexts. Moreover, how the regulatory-level effects of inherently stochastic compensatory gene networks contribute to phenotypic penetrance in single cells remains unclear. Here we combine computational analysis of existing datasets with stochastic mathematical modeling and machine learning to uncover the widespread prevalence of transcriptional adaptation in mammalian systems and the diverse single-cell manifestations of minimal compensatory gene networks. Regulon gene expression analysis of a pooled single-cell genetic perturbation dataset recapitulates important model predictions. Our integrative approach uncovers several putative hits-genes demonstrating possible transcriptional adaptation-to follow up on experimentally, and provides a formal quantitative framework to test and refine models of transcriptional adaptation.
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Affiliation(s)
- Ian A. Mellis
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Nicholas Bodkin
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeline E. Melzer
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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6
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Ghazi M, Khanna S, Subramaniam Y, Rengaraju J, Sultan F, Gupta I, Sharma K, Chandna S, Gokhale RS, Natarajan V. Sustained pigmentation causes DNA damage and invokes translesion polymerase Polκ for repair in melanocytes. Nucleic Acids Res 2023; 51:10451-10466. [PMID: 37697436 PMCID: PMC10602914 DOI: 10.1093/nar/gkad704] [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: 09/06/2022] [Revised: 08/02/2023] [Accepted: 08/14/2023] [Indexed: 09/13/2023] Open
Abstract
Melanin protects skin cells from ultraviolet radiation-induced DNA damage. However, intermediates of eumelanin are highly reactive quinones that are potentially genotoxic. In this study, we systematically investigate the effect of sustained elevation of melanogenesis and map the consequent cellular repair response of melanocytes. Pigmentation increases γH2AX foci, DNA abasic sites, causes replication stress and invokes translesion polymerase Polκ in primary human melanocytes, as well as mouse melanoma cells. Confirming the causal link, CRISPR-based genetic ablation of tyrosinase results in depigmented cells with low Polκ levels. During pigmentation, Polκ activates replication stress response and keeps a check on uncontrolled proliferation of cells harboring melanin-damaged DNA. The mutational landscape observed in human melanoma could in part explain the error-prone bypass of DNA lesions by Polκ, whose absence would lead to genome instability. Thereby, translesion polymerase Polκ is a critical response of pigmenting melanocytes to combat melanin-induced DNA alterations. Our study illuminates the dark side of melanin and identifies (eu)melanogenesis as a key missing link between tanning response and mutagenesis, mediated via the necessary evil translesion polymerase, Polκ.
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Affiliation(s)
- Madeeha Ghazi
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Shivangi Khanna
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Yogaspoorthi Subramaniam
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Jeyashri Rengaraju
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Farina Sultan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Iti Gupta
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Kanupriya Sharma
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Delhi 110054, India
| | - Sudhir Chandna
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Delhi 110054, India
| | - Rajesh S Gokhale
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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7
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Hoffman TE, Nangia V, Ill CR, Passanisi VJ, Armstrong C, Yang C, Spencer SL. Multiple cancers escape from multiple MAPK pathway inhibitors and use DNA replication stress signaling to tolerate aberrant cell cycles. Sci Signal 2023; 16:eade8744. [PMID: 37527351 DOI: 10.1126/scisignal.ade8744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
Many cancers harbor pro-proliferative mutations of the mitogen-activated protein kinase (MAPK) pathway. In BRAF-driven melanoma cells treated with BRAF inhibitors, subpopulations of cells escape drug-induced quiescence through a nongenetic manner of adaptation and resume slow proliferation. Here, we found that this phenomenon is common to many cancer types driven by EGFR, KRAS, or BRAF mutations in response to multiple, clinically approved MAPK pathway inhibitors. In 2D cultures and 3D spheroid models of various cancer cell lines, a subset of cells escaped drug-induced quiescence within 4 days to resume proliferation. These "escapee" cells exhibited DNA replication deficits, accumulated DNA lesions, and mounted a stress response that depended on the ataxia telangiectasia and RAD3-related (ATR) kinase. We further identified that components of the Fanconi anemia (FA) DNA repair pathway are recruited to sites of mitotic DNA synthesis (MiDAS) in escapee cells, enabling successful completion of cell division. Analysis of patient tumor samples and clinical data correlated disease progression with an increase in DNA replication stress response factors. Our findings suggest that many MAPK pathway-mutant cancers rapidly escape drug action and that suppressing early stress tolerance pathways may achieve more durable clinical responses to MAPK pathway inhibitors.
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Affiliation(s)
- Timothy E Hoffman
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Varuna Nangia
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Medical Scientist Training Program, University of Colorado-Anschutz Medical School, Aurora, CO 80045, USA
| | - C Ryland Ill
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Victor J Passanisi
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Claire Armstrong
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Chen Yang
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Sabrina L Spencer
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
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8
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Venkadakrishnan J, Lahane G, Dhar A, Xiao W, Bhat KM, Pandita TK, Bhat A. Implications of Translesion DNA Synthesis Polymerases on Genomic Stability and Human Health. Mol Cell Biol 2023; 43:401-425. [PMID: 37439479 PMCID: PMC10448981 DOI: 10.1080/10985549.2023.2224199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/03/2023] [Accepted: 06/01/2023] [Indexed: 07/14/2023] Open
Abstract
Replication fork arrest-induced DNA double strand breaks (DSBs) caused by lesions are effectively suppressed in cells due to the presence of a specialized mechanism, commonly referred to as DNA damage tolerance (DDT). In eukaryotic cells, DDT is facilitated through translesion DNA synthesis (TLS) carried out by a set of DNA polymerases known as TLS polymerases. Another parallel mechanism, referred to as homology-directed DDT, is error-free and involves either template switching or fork reversal. The significance of the DDT pathway is well established. Several diseases have been attributed to defects in the TLS pathway, caused either by mutations in the TLS polymerase genes or dysregulation. In the event of a replication fork encountering a DNA lesion, cells switch from high-fidelity replicative polymerases to low-fidelity TLS polymerases, which are associated with genomic instability linked with several human diseases including, cancer. The role of TLS polymerases in chemoresistance has been recognized in recent years. In addition to their roles in the DDT pathway, understanding noncanonical functions of TLS polymerases is also a key to unraveling their importance in maintaining genomic stability. Here we summarize the current understanding of TLS pathway in DDT and its implication for human health.
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Affiliation(s)
| | - Ganesh Lahane
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Hyderabad Campus, Hyderabad, India
| | - Arti Dhar
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Hyderabad Campus, Hyderabad, India
| | - Wei Xiao
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Krishna Moorthi Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA
| | - Tej K. Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, Texas, USA
| | - Audesh Bhat
- Center for Molecular Biology, Central University of Jammu, UT Jammu and Kashmir, India
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9
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Hoffman TE, Yang C, Nangia V, Ill CR, Spencer SL. Multiple cancer types rapidly escape from multiple MAPK inhibitors to generate mutagenesis-prone subpopulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533211. [PMID: 36993538 PMCID: PMC10055235 DOI: 10.1101/2023.03.17.533211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Many cancers harbor pro-proliferative mutations of the mitogen-activated protein kinase (MAPK) pathway and many targeted inhibitors now exist for clinical use, but drug resistance remains a major issue. We recently showed that BRAF-driven melanoma cells treated with BRAF inhibitors can non-genetically adapt to drug within 3-4 days to escape quiescence and resume slow proliferation. Here we show that this phenomenon is not unique to melanomas treated with BRAF inhibitors but rather is widespread across many clinical MAPK inhibitors and cancer types driven by EGFR, KRAS, and BRAF mutations. In all treatment contexts examined, a subset of cells can escape drug-induced quiescence within four days to resume proliferation. These escapee cells broadly experience aberrant DNA replication, accumulate DNA lesions, spend longer in G2-M cell cycle phases, and mount an ATR-dependent stress response. We further identify the Fanconi anemia (FA) DNA repair pathway as critical for successful mitotic completion in escapees. Long-term cultures, patient samples, and clinical data demonstrate a broad dependency on ATR- and FA-mediated stress tolerance. Together, these results highlight the pervasiveness with which MAPK-mutant cancers are able to rapidly escape drug and the importance of suppressing early stress tolerance pathways to potentially achieve more durable clinical responses to targeted MAPK pathway inhibitors.
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10
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Tarantino D, Walker C, Weekes D, Pemberton H, Davidson K, Torga G, Frankum J, Mendes-Pereira AM, Prince C, Ferro R, Brough R, Pettitt SJ, Lord CJ, Grigoriadis A, Nj Tutt A. Functional screening reveals HORMAD1-driven gene dependencies associated with translesion synthesis and replication stress tolerance. Oncogene 2022; 41:3969-3977. [PMID: 35768547 PMCID: PMC9355871 DOI: 10.1038/s41388-022-02369-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 05/21/2022] [Accepted: 05/30/2022] [Indexed: 11/09/2022]
Abstract
HORMAD1 expression is usually restricted to germline cells, but it becomes mis-expressed in epithelial cells in ~60% of triple-negative breast cancers (TNBCs), where it is associated with elevated genomic instability (1). HORMAD1 expression in TNBC is bimodal with HORMAD1-positive TNBC representing a biologically distinct disease group. Identification of HORMAD1-driven genetic dependencies may uncover novel therapies for this disease group. To study HORMAD1-driven genetic dependencies, we generated a SUM159 cell line model with doxycycline-inducible HORMAD1 that replicated genomic instability phenotypes seen in HORMAD1-positive TNBC (1). Using small interfering RNA screens, we identified candidate genes whose depletion selectively inhibited the cellular growth of HORMAD1-expressing cells. We validated five genes (ATR, BRIP1, POLH, TDP1 and XRCC1), depletion of which led to reduced cellular growth or clonogenic survival in cells expressing HORMAD1. In addition to the translesion synthesis (TLS) polymerase POLH, we identified a HORMAD1-driven dependency upon additional TLS polymerases, namely POLK, REV1, REV3L and REV7. Our data confirms that out-of-context somatic expression of HORMAD1 can lead to genomic instability and reveals that HORMAD1 expression induces dependencies upon replication stress tolerance pathways, such as translesion synthesis. Our data also suggest that HORMAD1 expression could be a patient selection biomarker for agents targeting replication stress.
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Affiliation(s)
- Dalia Tarantino
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Callum Walker
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Daniel Weekes
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Helen Pemberton
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Kathryn Davidson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Gonzalo Torga
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Jessica Frankum
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Ana M Mendes-Pereira
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Cynthia Prince
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Riccardo Ferro
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Rachel Brough
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Stephen J Pettitt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Christopher J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Anita Grigoriadis
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Andrew Nj Tutt
- Breast Cancer Now Research Unit, King's College London, London, UK.
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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11
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Nickoloff JA. Targeting Replication Stress Response Pathways to Enhance Genotoxic Chemo- and Radiotherapy. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154736. [PMID: 35897913 PMCID: PMC9330692 DOI: 10.3390/molecules27154736] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/12/2022]
Abstract
Proliferating cells regularly experience replication stress caused by spontaneous DNA damage that results from endogenous reactive oxygen species (ROS), DNA sequences that can assume secondary and tertiary structures, and collisions between opposing transcription and replication machineries. Cancer cells face additional replication stress, including oncogenic stress that results from the dysregulation of fork progression and origin firing, and from DNA damage induced by radiotherapy and most cancer chemotherapeutic agents. Cells respond to such stress by activating a complex network of sensor, signaling and effector pathways that protect genome integrity. These responses include slowing or stopping active replication forks, protecting stalled replication forks from collapse, preventing late origin replication firing, stimulating DNA repair pathways that promote the repair and restart of stalled or collapsed replication forks, and activating dormant origins to rescue adjacent stressed forks. Currently, most cancer patients are treated with genotoxic chemotherapeutics and/or ionizing radiation, and cancer cells can gain resistance to the resulting replication stress by activating pro-survival replication stress pathways. Thus, there has been substantial effort to develop small molecule inhibitors of key replication stress proteins to enhance tumor cell killing by these agents. Replication stress targets include ATR, the master kinase that regulates both normal replication and replication stress responses; the downstream signaling kinase Chk1; nucleases that process stressed replication forks (MUS81, EEPD1, Metnase); the homologous recombination catalyst RAD51; and other factors including ATM, DNA-PKcs, and PARP1. This review provides an overview of replication stress response pathways and discusses recent pre-clinical studies and clinical trials aimed at improving cancer therapy by targeting replication stress response factors.
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Affiliation(s)
- Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
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12
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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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13
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DNA Repair Genes Are Associated with Subtype Classification, Prognosis, and Immune Infiltration in Uveal Melanoma. JOURNAL OF ONCOLOGY 2022; 2022:1965451. [PMID: 35096056 PMCID: PMC8791741 DOI: 10.1155/2022/1965451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/27/2021] [Indexed: 11/18/2022]
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. DNA repair genes play a vital role in cancer development. However, there has been very little research about DNA repair genes in UM. This study aimed to evaluate the importance of DNA repair genes and established a signature for predicting prognosis and immune features of UM. In this study, we mined TCGA database through bioinformatics analysis, and the intersect was taken between DNA repair genes and prognosis related genes and yielded 52 genes. We divided 80 UM patients into C1 and C2 subtypes. GSEA results indicated that abundant cancer-promoting functions and signaling pathways were activated in C2 subtype and the proportion of SNVs was higher in C2 than in C1 which suggested a worse prognosis. We built a six DNA repair genes model including ITPA, CETN2, CCNO, POLR2J, POLD1, and POLA1 by LASSO regression to predict prognosis of UM patients and utilized the median value of risk scores as the cutoff point to differentiate high risk and low risk group. The survival analyses and the receiver operating characteristic (ROC) curves in the validation group and entire data set confirmed the accuracy of this model. We also constructed a nomogram based on age and risk scores to evaluate the relationship between risk scores and clinical outcome. The calibration curve of the overall survival (OS) indicated that the performance of this model is steady and robust. Finally, the enrichment analysis showed that there were complex regulatory mechanisms in UM patients. The immune infiltration analysis indicated that the immune infiltration in C2 in the high risk group was different from that in the low risk group. Our findings indicated that the DNA repair genes may be related to UM prognosis and provide new insight into the underlying mechanisms.
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14
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Bowman RL, Hennessey RC, Weiss TJ, Tallman DA, Crawford ER, Murphy BM, Webb A, Zhang S, La Perle KM, Burd CJ, Levine RL, Shain AH, Burd CE. UVB mutagenesis differs in Nras- and Braf-mutant mouse models of melanoma. Life Sci Alliance 2021; 4:e202101135. [PMID: 34210801 PMCID: PMC8321651 DOI: 10.26508/lsa.202101135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
BRAF-mutant melanomas are more likely than NRAS-mutant melanomas to arise in anatomical locations protected from chronic sun damage. We hypothesized that this discrepancy in tumor location is a consequence of the differential sensitivity of BRAF and NRAS-mutant melanocytes to ultraviolet light (UV)-mediated carcinogenesis. We tested this hypothesis by comparing the mutagenic consequences of a single neonatal, ultraviolet-AI (UVA; 340-400 nm) or ultraviolet-B (UVB; 280-390 nm) exposure in mouse models heterozygous for mutant Braf or homozygous for mutant Nras Tumor onset was accelerated by UVB, but not UVA, and the resulting melanomas contained recurrent mutations affecting the RING domain of MAP3K1 and Actin-binding domain of Filamin A. Melanomas from UVB-irradiated, Braf-mutant mice averaged twice as many single-nucleotide variants and five times as many dipyrimidine variants than tumors from similarly irradiated Nras-mutant mice. A mutational signature discovered in UVB-accelerated tumors mirrored COSMIC signatures associated with human skin cancer and was more prominent in Braf- than Nras-mutant murine melanomas. These data show that a single UVB exposure yields a greater burden of mutations in murine tumors driven by oncogenic Braf.
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Affiliation(s)
- Robert L Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca C Hennessey
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Tirzah J Weiss
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - David A Tallman
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Emma R Crawford
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Brandon M Murphy
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Souhui Zhang
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Krista Md La Perle
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Craig J Burd
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Hunter Shain
- Department of Dermatology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Christin E Burd
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
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15
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A catalytic-independent function of human DNA polymerase Kappa controls the stability and abundance of the Checkpoint Kinase 1. Mol Cell Biol 2021; 41:e0009021. [PMID: 34398682 DOI: 10.1128/mcb.00090-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA polymerase kappa (Pol κ) has been well documented thus far for its specialized DNA synthesis activity during translesion replication, progression of replication forks through regions difficult to replicate, restart of stalled forks and replication checkpoint efficiency. Pol κ is also required for the stabilization of stalled forks although the mechanisms are poorly understood. Here we unveiled an unexpected role for Pol κ in controlling the stability and abundance of Chk1, an important actor for the replication checkpoint and fork stabilization. We found that loss of Pol κ decreased the Chk1 protein level in the nucleus of four human cell lines. Pol κ and not the other Y-family polymerase members is required to maintain the Chk1 protein pool all along the cell cycle. We showed that Pol κ depletion affected the protein stability of Chk1 and protected it from proteasome degradation. Importantly, we also observed that the fork restart defects observed in Pol κ-depleted cells could be overcome by the re-expression of Chk1. Strikingly, this new function of Pol κ does not require its catalytic activity. We propose that Pol κ could contribute to the protection of stalled forks through Chk1 stability.
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16
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Bussey KJ, Davies PCW. Reverting to single-cell biology: The predictions of the atavism theory of cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 165:49-55. [PMID: 34371024 DOI: 10.1016/j.pbiomolbio.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
Cancer or cancer-like phenomena pervade multicellular life, implying deep evolutionary roots. Many of the hallmarks of cancer recapitulate unicellular modalities, suggesting that cancer initiation and progression represent a systematic reversion to simpler ancestral phenotypes in response to a stress or insult. This so-called atavism theory may be tested using phylostratigraphy, which can be used to assign ages to genes. Several research groups have confirmed that cancer cells tend to over-express evolutionary older genes, and rewire the architecture linking unicellular and multicellular gene networks. In addition, some of the elevated mutation rate - a well-known hallmark of cancer - is actually self-inflicted, driven by genes found to be homologs of the ancient SOS genes activated in stressed bacteria, and employed to evolve biological workarounds. These findings have obvious implications for therapy.
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Affiliation(s)
- Kimberly J Bussey
- Precision Medicine, Midwestern University, Glendale, AZ, USA; The BEYOND Center for Fundamental Concepts in Science, Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Paul C W Davies
- The BEYOND Center for Fundamental Concepts in Science, Department of Physics, Arizona State University, Tempe, AZ, USA.
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17
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Tsao WC, Buj R, Aird KM, Sidorova JM, Eckert KA. Overexpression of oncogenic H-Ras in hTERT-immortalized and SV40-transformed human cells targets replicative and specialized DNA polymerases for depletion. PLoS One 2021; 16:e0251188. [PMID: 33961649 PMCID: PMC8104423 DOI: 10.1371/journal.pone.0251188] [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: 02/09/2021] [Accepted: 04/21/2021] [Indexed: 11/26/2022] Open
Abstract
DNA polymerases play essential functions in replication fork progression and genome maintenance. DNA lesions and drug-induced replication stress result in up-regulation and re-localization of specialized DNA polymerases η and κ. Although oncogene activation significantly alters DNA replication dynamics, causing replication stress and genome instability, little is known about DNA polymerase expression and regulation in response to oncogene activation. Here, we investigated the consequences of mutant H-RASG12V overexpression on the regulation of DNA polymerases in h-TERT immortalized and SV40-transformed human cells. Focusing on DNA polymerases associated with the replication fork, we demonstrate that DNA polymerases are depleted in a temporal manner in response to H-RASG12V overexpression. The polymerases targeted for depletion, as cells display markers of senescence, include the Pol α catalytic subunit (POLA1), Pol δ catalytic and p68 subunits (POLD1 and POLD3), Pol η, and Pol κ. Both transcriptional and post-transcriptional mechanisms mediate this response. Pol η (POLH) depletion is sufficient to induce a senescence-like growth arrest in human foreskin fibroblast BJ5a cells, and is associated with decreased Pol α expression. Using an SV-40 transformed cell model, we observed cell cycle checkpoint signaling differences in cells with H-RasG12V-induced polymerase depletion, as compared to Pol η-deficient cells. Our findings contribute to our understanding of cellular events following oncogene activation and cellular transformation.
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Affiliation(s)
- Wei-chung Tsao
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Raquel Buj
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Katherine M. Aird
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
- Penn State Cancer Institute, Pennsylvania State University, Hershey, Pennsylvania, United States of America
| | - Julia M. Sidorova
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Kristin A. Eckert
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
- Penn State Cancer Institute, Pennsylvania State University, Hershey, Pennsylvania, United States of America
- * E-mail:
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18
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Russo M, Sogari A, Bardelli A. Adaptive Evolution: How Bacteria and Cancer Cells Survive Stressful Conditions and Drug Treatment. Cancer Discov 2021; 11:1886-1895. [PMID: 33952585 DOI: 10.1158/2159-8290.cd-20-1588] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cancer is characterized by loss of the regulatory mechanisms that preserve homeostasis in multicellular organisms, such as controlled proliferation, cell-cell adhesion, and tissue differentiation. The breakdown of multicellularity rules is accompanied by activation of "selfish," unicellular-like life features, which are linked to the increased adaptability to environmental changes displayed by cancer cells. Mechanisms of stress response, resembling those observed in unicellular organisms, are actively exploited by mammalian cancer cells to boost genetic diversity and increase chances of survival under unfavorable conditions, such as lack of oxygen/nutrients or exposure to drugs. Unicellular organisms under stressful conditions (e.g., antibiotic treatment) stop replicating or slowly divide and transiently increase their mutation rates to foster diversity, a process known as adaptive mutability. Analogously, tumor cells exposed to drugs enter a persister phenotype and can reduce DNA replication fidelity, which in turn fosters genetic diversity. The implications of adaptive evolution are of relevance to understand resistance to anticancer therapies.
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Affiliation(s)
- Mariangela Russo
- Department of Oncology, University of Torino, Candiolo 10060, Italy. Candiolo Cancer Institute, FPO-IRCCS, Candiolo 10060, Italy.
| | - Alberto Sogari
- Department of Oncology, University of Torino, Candiolo 10060, Italy. Candiolo Cancer Institute, FPO-IRCCS, Candiolo 10060, Italy
| | - Alberto Bardelli
- Department of Oncology, University of Torino, Candiolo 10060, Italy. Candiolo Cancer Institute, FPO-IRCCS, Candiolo 10060, Italy.
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19
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Maiorano D, El Etri J, Franchet C, Hoffmann JS. Translesion Synthesis or Repair by Specialized DNA Polymerases Limits Excessive Genomic Instability upon Replication Stress. Int J Mol Sci 2021; 22:3924. [PMID: 33920223 PMCID: PMC8069355 DOI: 10.3390/ijms22083924] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
DNA can experience "replication stress", an important source of genome instability, induced by various external or endogenous impediments that slow down or stall DNA synthesis. While genome instability is largely documented to favor both tumor formation and heterogeneity, as well as drug resistance, conversely, excessive instability appears to suppress tumorigenesis and is associated with improved prognosis. These findings support the view that karyotypic diversity, necessary to adapt to selective pressures, may be limited in tumors so as to reduce the risk of excessive instability. This review aims to highlight the contribution of specialized DNA polymerases in limiting extreme genetic instability by allowing DNA replication to occur even in the presence of DNA damage, to either avoid broken forks or favor their repair after collapse. These mechanisms and their key regulators Rad18 and Polθ not only offer diversity and evolutionary advantage by increasing mutagenic events, but also provide cancer cells with a way to escape anti-cancer therapies that target replication forks.
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Affiliation(s)
- Domenico Maiorano
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, 34396 Montpellier, France; (D.M.); (J.E.E.)
| | - Jana El Etri
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, 34396 Montpellier, France; (D.M.); (J.E.E.)
| | - Camille Franchet
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
| | - Jean-Sébastien Hoffmann
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
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20
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Zhang X, Blumenthal RM, Cheng X. A Role for N6-Methyladenine in DNA Damage Repair. Trends Biochem Sci 2020; 46:175-183. [PMID: 33077363 DOI: 10.1016/j.tibs.2020.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/15/2020] [Accepted: 09/23/2020] [Indexed: 12/23/2022]
Abstract
The leading cause of mutation due to oxidative damage is 8-oxo-2'-deoxyguanosine (8-oxoG) mispairing with adenine (Ade), which can occur in two ways. First, guanine of a G:C DNA base pair can be oxidized. If not repaired in time, DNA polymerases can mispair Ade with 8-oxoG in the template. This 8-oxoG:A can be repaired by enzymes that remove Ade opposite to template 8-oxoG, or 8-oxoG opposite to Cyt. Second, free 8-oxo-dGTP can be misincorporated by DNA polymerases into DNA opposite template Ade. However, there is no known repair activity that removes 8-oxoG opposite to template Ade. We suggest that a major role of N6-methyladenine in mammalian DNA is minimizing incorporation of 8-oxoG opposite to Ade by DNA polymerases following adduct formation.
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Affiliation(s)
- Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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21
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Abstract
In this issue of Science Signaling, Temprine et al report that up-regulation of the translesion DNA polymerase Polκ mediates resistance to BRAF pathway-targeted inhibitors and starvation in melanoma cells. These results exemplify the role that Polκ plays in cellular adaptation to stress.
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Affiliation(s)
- Joann B Sweasy
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85719, USA.,Department of Cellular and Molecular Medicine and Radiation Oncology, University of Arizona, Tucson, AZ 85721, USA.,Department of Radiation Oncology, University of Arizona, Tucson, AZ 85724, USA.
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