1
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Wang X, Deng L, Ping L, Shi Y, Wang H, Feng F, Leng X, Tang Y, Xie Y, Ying Z, Liu W, Zhu J, Song Y. Germline variants of DNA repair and immune genes in lymphoma from lymphoma-cancer families. Int J Cancer 2024; 155:93-103. [PMID: 38446987 DOI: 10.1002/ijc.34892] [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: 08/21/2023] [Revised: 11/22/2023] [Accepted: 01/23/2024] [Indexed: 03/08/2024]
Abstract
The genetic predisposition to lymphoma is not fully understood. We identified 13 lymphoma-cancer families (2011-2021), in which 27 individuals developed lymphomas and 26 individuals had cancers. Notably, male is the predominant gender in lymphoma patients, whereas female is the predominant gender in cancer patients (p = .019; OR = 4.72, 95% CI, 1.30-14.33). We collected samples from 18 lymphoma patients, and detected germline variants through exome sequencing. We found that germline protein truncating variants (PTVs) were enriched in DNA repair and immune genes. Totally, we identified 31 heterozygous germline mutations (including 12 PTVs) of 25 DNA repair genes and 19 heterozygous germline variants (including 7 PTVs) of 14 immune genes. PTVs of ATM and PNKP were found in two families, respectively. We performed whole genome sequencing of diffuse large B cell lymphomas (DLBCLs), translocations at IGH locus and activation of oncogenes (BCL6 and MYC) were verified, and homologous recombination deficiency was detected. In DLBCLs with germline PTVs of ATM, deletion and insertion in CD58 were further revealed. Thus, in lymphoma-cancer families, we identified germline defects of both DNA repair and immune genes in lymphoma patients.
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Affiliation(s)
- Xiaogan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lijuan Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lingyan Ping
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yunfei Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Haojie Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Central Laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Feier Feng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xin Leng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yahan Tang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yan Xie
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhitao Ying
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Weiping Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jun Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yuqin Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
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2
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Lin L, Hu P, Luo M, Chen X, Xiao M, Zhong Z, Peng S, Chen G, Yang G, Zhang F, Zhang Y. CircNOP14 increases the radiosensitivity of hepatocellular carcinoma via inhibition of Ku70-dependent DNA damage repair. Int J Biol Macromol 2024; 264:130541. [PMID: 38460628 DOI: 10.1016/j.ijbiomac.2024.130541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/13/2024] [Accepted: 02/27/2024] [Indexed: 03/11/2024]
Abstract
Circular RNAs (circRNAs) are profoundly affected in hepatocellular carcinoma (HCC) through various pathways. However, the role of circRNAs in the radiosensitivity of HCC cells is yet to be explored. In this study, we identified a circRNA-hsa_circ_0006737 (circNOP14) involved in the radiosensitivity of HCC. We found that circNOP14 increased the radiosensitivity of HCC cells both in vitro and in vivo. Notably, using a circRNA pulldown assay and RNA-binding protein immunoprecipitation, we identified Ku70 as a novel and robust interacting protein of circNOP14. Mechanistically, circNOP14 interacts with Ku70 and prevents its nuclear translocation, thereby increasing irradiation-induced DNA damage. Therefore, our findings may provide a predictive indicator and intervention option for 125I brachytherapy or external radiotherapy in HCC.
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Affiliation(s)
- Letao Lin
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Pan Hu
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Ma Luo
- Department of Medical Imaging, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Xi Chen
- Department of Oncology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518000, PR China
| | - Meigui Xiao
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Zhihui Zhong
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Sheng Peng
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Guanyu Chen
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Guang Yang
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Fujun Zhang
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China.
| | - Yanling Zhang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, PR China.
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3
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Hu P, Lin L, Huang T, Li Z, Xiao M, Guo H, Chen G, Liu D, Ke M, Shan H, Zhang F, Zhang Y. Circular RNA circEYA3 promotes the radiation resistance of hepatocellular carcinoma via the IGF2BP2/DTX3L axis. Cancer Cell Int 2023; 23:308. [PMID: 38042777 PMCID: PMC10693171 DOI: 10.1186/s12935-023-03168-2] [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: 07/23/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) has a high incidence and mortality rate despite various treatment options, including 125I seed implantation. However, recurrence and radiation resistance remain challenging issues. Hsa_circ_0007895 (circEYA3)-derived from exons 2-6 of EYA3-facilitates the proliferation and progression of pancreatic ductal adenocarcinoma. However, the role of circEYA3 in HCC 125I radiation resistance remains unclear. Thus, we aimed to investigate the functions and underlying molecular mechanisms of circEYA3 in HCC under 125I and X-ray irradiation conditions. METHODS CircEYA3 was identified by RNA-seq in patients with HCC before and after 125I seed implantation treatment, followed by fluorescence in situ hybridization and RNase R assays. The radiosensitivity of HCC cell lines irradiated with 125I seeds or external irradiation were evaluated using the Cell Counting Kit 8, flow cytometry, γH2A.X immunofluorescence and comet assays. RNA pull-down and RNA immunoprecipitation assays were performed to explore the interactions between circEYA3 and IGF2BP2. DTX3L mRNA was identified by RNA-seq in PLC/PRF/5 cells with overexpressed circEYA3. The corresponding in vitro results were verified using a mouse xenograft model. RESULTS CircEYA3 decreased the radiosensitivity of HCC cells both in vitro and in vivo. Notably, using a circRNA pulldown assay and RNA-binding protein immunoprecipitation, we identified IGF2BP2 as a novel and robust interacting protein of circEYA3. Mechanistically, circEYA3 binds to IGF2BP2 and enhances its ability to stabilize DTX3L mRNA, thereby specifically alleviating radiation-induced DNA damage in HCC cells. CONCLUSIONS Our findings demonstrate that circEYA3 increases the radioresistance of HCC to 125I seeds and external irradiation via the IGF2BP2/DTX3L axis. Thus, circEYA3 might be a predictive indicator and intervention option for 125I brachytherapy or external radiotherapy in HCC.
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Affiliation(s)
- Pan Hu
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Letao Lin
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Tao Huang
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Zhenyu Li
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou,, 510060, People's Republic of China
| | - Meigui Xiao
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Huanqing Guo
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Guanyu Chen
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Dengyao Liu
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Miaola Ke
- Department of Blood Transfusion, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou,, 510060, People's Republic of China
| | - Hongbo Shan
- Department of Endoscopy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, China.
| | - Fujun Zhang
- Department of Minimally Invasive Intervention, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China.
| | - Yanling Zhang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, 1023 South Shatai Road, Guangzhou, Guangdong, 510515, People's Republic of China.
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4
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Vogt A, He Y, Lees-Miller SP. How to fix DNA breaks: new insights into the mechanism of non-homologous end joining. Biochem Soc Trans 2023; 51:1789-1800. [PMID: 37787023 PMCID: PMC10657183 DOI: 10.1042/bst20220741] [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: 08/26/2023] [Revised: 08/26/2023] [Accepted: 09/22/2023] [Indexed: 10/04/2023]
Abstract
Non-homologous end joining (NHEJ) is the major pathway for the repair of ionizing radiation-induced DNA double-strand breaks (DSBs) in human cells and is essential for the generation of mature T and B cells in the adaptive immune system via the process of V(D)J recombination. Here, we review how recently determined structures shed light on how NHEJ complexes function at DNA DSBs, emphasizing how multiple structures containing the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) may function in NHEJ. Together, these studies provide an explanation for how NHEJ proteins assemble to detect and protect DSB ends, then proceed, through DNA-PKcs-dependent autophosphorylation, to a ligation-competent complex.
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Affiliation(s)
- Alex Vogt
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, U.S.A
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, U.S.A
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, U.S.A
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, U.S.A
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, U.S.A
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, U.S.A
| | - Susan P. Lees-Miller
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre and Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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5
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Tan J, Sun X, Zhao H, Guan H, Gao S, Zhou P. Double-strand DNA break repair: molecular mechanisms and therapeutic targets. MedComm (Beijing) 2023; 4:e388. [PMID: 37808268 PMCID: PMC10556206 DOI: 10.1002/mco2.388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/29/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Double-strand break (DSB), a significant DNA damage brought on by ionizing radiation, acts as an initiating signal in tumor radiotherapy, causing cancer cells death. The two primary pathways for DNA DSB repair in mammalian cells are nonhomologous end joining (NHEJ) and homologous recombination (HR), which cooperate and compete with one another to achieve effective repair. The DSB repair mechanism depends on numerous regulatory variables. DSB recognition and the recruitment of DNA repair components, for instance, depend on the MRE11-RAD50-NBS1 (MRN) complex and the Ku70/80 heterodimer/DNA-PKcs (DNA-PK) complex, whose control is crucial in determining the DSB repair pathway choice and efficiency of HR and NHEJ. In-depth elucidation on the DSB repair pathway's molecular mechanisms has greatly facilitated for creation of repair proteins or pathways-specific inhibitors to advance precise cancer therapy and boost the effectiveness of cancer radiotherapy. The architectures, roles, molecular processes, and inhibitors of significant target proteins in the DSB repair pathways are reviewed in this article. The strategy and application in cancer therapy are also discussed based on the advancement of inhibitors targeted DSB damage response and repair proteins.
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Affiliation(s)
- Jinpeng Tan
- Hengyang Medical CollegeUniversity of South ChinaHengyangHunan ProvinceChina
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
| | - Xingyao Sun
- Hengyang Medical CollegeUniversity of South ChinaHengyangHunan ProvinceChina
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
| | - Hongling Zhao
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
| | - Hua Guan
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
| | - Shanshan Gao
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
| | - Ping‐Kun Zhou
- Hengyang Medical CollegeUniversity of South ChinaHengyangHunan ProvinceChina
- Department of Radiation BiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
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6
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Kulasinghe A, Liu N, Tan CW, Monkman J, Sinclair JE, Bhuva DD, Godbolt D, Pan L, Nam A, Sadeghirad H, Sato K, Bassi GL, O'Byrne K, Hartmann C, Dos Santos Miggiolaro AFR, Marques GL, Moura LZ, Richard D, Adams M, de Noronha L, Baena CP, Suen JY, Arora R, Belz GT, Short KR, Davis MJ, Guimaraes FSF, Fraser JF. Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage. Immunology 2023; 168:403-419. [PMID: 36107637 PMCID: PMC9537957 DOI: 10.1111/imm.13577] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/12/2022] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to present with pulmonary and extra-pulmonary organ complications. In comparison with the 2009 pandemic (pH1N1), SARS-CoV-2 infection is likely to lead to more severe disease, with multi-organ effects, including cardiovascular disease. SARS-CoV-2 has been associated with acute and long-term cardiovascular disease, but the molecular changes that govern this remain unknown. In this study, we investigated the host transcriptome landscape of cardiac tissues collected at rapid autopsy from seven SARS-CoV-2, two pH1N1, and six control patients using targeted spatial transcriptomics approaches. Although SARS-CoV-2 was not detected in cardiac tissue, host transcriptomics showed upregulation of genes associated with DNA damage and repair, heat shock, and M1-like macrophage infiltration in the cardiac tissues of COVID-19 patients. The DNA damage present in the SARS-CoV-2 patient samples, were further confirmed by γ-H2Ax immunohistochemistry. In comparison, pH1N1 showed upregulation of interferon-stimulated genes, in particular interferon and complement pathways, when compared with COVID-19 patients. These data demonstrate the emergence of distinct transcriptomic profiles in cardiac tissues of SARS-CoV-2 and pH1N1 influenza infection supporting the need for a greater understanding of the effects on extra-pulmonary organs, including the cardiovascular system of COVID-19 patients, to delineate the immunopathobiology of SARS-CoV-2 infection, and long term impact on health.
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Affiliation(s)
- Arutha Kulasinghe
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Ning Liu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Chin Wee Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - James Monkman
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Jane E Sinclair
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Dharmesh D Bhuva
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - David Godbolt
- Pathology Queensland, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - Liuliu Pan
- Nanostring Technologies, Inc, Seattle, Washington, USA
| | - Andy Nam
- Nanostring Technologies, Inc, Seattle, Washington, USA
| | - Habib Sadeghirad
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Kei Sato
- Critical Care Research Group, Faculty of Medicine, University of Queensland and The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - Gianluigi Li Bassi
- Critical Care Research Group, Faculty of Medicine, University of Queensland and The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - Ken O'Byrne
- The Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Camila Hartmann
- Pontifical Catholic University of Parana, Curitiba, Brazil.,Marcelino Champagnat Hospital, Curitiba, Brazil
| | | | - Gustavo Lenci Marques
- Pontifical Catholic University of Parana, Curitiba, Brazil.,Marcelino Champagnat Hospital, Curitiba, Brazil
| | - Lidia Zytynski Moura
- Pontifical Catholic University of Parana, Curitiba, Brazil.,Marcelino Champagnat Hospital, Curitiba, Brazil
| | - Derek Richard
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Mark Adams
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | | | - Cristina Pellegrino Baena
- Pontifical Catholic University of Parana, Curitiba, Brazil.,Marcelino Champagnat Hospital, Curitiba, Brazil
| | - Jacky Y Suen
- Critical Care Research Group, Faculty of Medicine, University of Queensland and The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - Rakesh Arora
- Department of Surgery, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gabrielle T Belz
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Kirsty R Short
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | | | - John F Fraser
- Pathology Queensland, The Prince Charles Hospital, Chermside, Queensland, Australia
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7
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Molecular targets that sensitize cancer to radiation killing: From the bench to the bedside. Biomed Pharmacother 2023; 158:114126. [PMID: 36521246 DOI: 10.1016/j.biopha.2022.114126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Radiotherapy is a standard cytotoxic therapy against solid cancers. It uses ionizing radiation to kill tumor cells through damage to DNA, either directly or indirectly. Radioresistance is often associated with dysregulated DNA damage repair processes. Most radiosensitizers enhance radiation-mediated DNA damage and reduce the rate of DNA repair ultimately leading to accumulation of DNA damages, cell-cycle arrest, and cell death. Recently, agents targeting key signals in DNA damage response such as DNA repair pathways and cell-cycle have been developed. This new class of molecularly targeted radiosensitizing agents is being evaluated in preclinical and clinical studies to monitor their activity in potentiating radiation cytotoxicity of tumors and reducing normal tissue toxicity. The molecular pathways of DNA damage response are reviewed with a focus on the repair mechanisms, therapeutic targets under current clinical evaluation including ATM, ATR, CDK1, CDK4/6, CHK1, DNA-PKcs, PARP-1, Wee1, & MPS1/TTK and potential new targets (BUB1, and DNA LIG4) for radiation sensitization.
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8
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Algethami M, Kulkarni S, Sadiq MT, Tang HKC, Brownlie J, Jeyapalan JN, Mongan NP, Rakha EA, Madhusudan S. Towards Personalized Management of Ovarian Cancer. Cancer Manag Res 2022; 14:3469-3483. [PMID: 36545222 PMCID: PMC9762171 DOI: 10.2147/cmar.s366681] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022] Open
Abstract
Despite advances in surgery and chemotherapy, the overall outcomes for patients with advanced ovarian cancer remain poor. Although initial response rates to platinum-based chemotherapy is about 60-80%, most patients will have recurrence and succumb to the disease. However, a DNA repair-directed precision medicine strategy has recently generated real hope in improving survival. The clinical development of PARP inhibitors has transformed lives for many patients with BRCA germline-deficient and/or platinum-sensitive epithelial ovarian cancers. Antiangiogenic agents and intraperitoneal chemotherapy approaches may also improve outcomes in patients. Moreover, evolving immunotherapeutic opportunities could also positively impact patient outcomes. Here we review the current clinical state of PARP inhibitors and other clinically viable targeted approaches in ovarian cancer.
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Affiliation(s)
- Mashael Algethami
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Sanat Kulkarni
- Department of Medicine, City Hospital, Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, B18 7QH, UK
| | - Maaz T Sadiq
- Cancer Centre, Queen Elizabeth Hospital, University Hospitals Birmingham NHS Trust, Birmingham, B15 2GW, UK
| | - Hiu K C Tang
- Department of Oncology, Nottingham University Hospitals, Nottingham, NG51PB, UK
| | - Juliette Brownlie
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Jennie N Jeyapalan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Nigel P Mongan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Emad A Rakha
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Srinivasan Madhusudan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK,Department of Oncology, Nottingham University Hospitals, Nottingham, NG51PB, UK,Correspondence: Srinivasan Madhusudan, Nottingham Biodiscovery Institute, School of Medicine, University Park, University of Nottingham, Nottingham, NG7 3RD, UK, Tel +44(0)115 823 1850, Fax +44(0)115 823 1849, Email
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9
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Xiao H, Li F, Mladenov E, Soni A, Mladenova V, Pan B, Dueva R, Stuschke M, Timmermann B, Iliakis G. Increased Resection at DSBs in G2-Phase Is a Unique Phenotype Associated with DNA-PKcs Defects That Is Not Shared by Other Factors of c-NHEJ. Cells 2022; 11:cells11132099. [PMID: 35805183 PMCID: PMC9265841 DOI: 10.3390/cells11132099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 01/27/2023] Open
Abstract
The load of DNA double-strand breaks (DSBs) induced in the genome of higher eukaryotes by different doses of ionizing radiation (IR) is a key determinant of DSB repair pathway choice, with homologous recombination (HR) and ATR substantially gaining ground at doses below 0.5 Gy. Increased resection and HR engagement with decreasing DSB-load generate a conundrum in a classical non-homologous end-joining (c-NHEJ)-dominated cell and suggest a mechanism adaptively facilitating resection. We report that ablation of DNA-PKcs causes hyper-resection, implicating DNA-PK in the underpinning mechanism. However, hyper-resection in DNA-PKcs-deficient cells can also be an indirect consequence of their c-NHEJ defect. Here, we report that all tested DNA-PKcs mutants show hyper-resection, while mutants with defects in all other factors of c-NHEJ fail to do so. This result rules out the model of c-NHEJ versus HR competition and the passive shift from c-NHEJ to HR as the causes of the increased resection and suggests the integration of DNA-PKcs into resection regulation. We develop a model, compatible with the results of others, which integrates DNA-PKcs into resection regulation and HR for a subset of DSBs. For these DSBs, we propose that the kinase remains at the break site, rather than the commonly assumed autophosphorylation-mediated removal from DNA ends.
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Affiliation(s)
- Huaping Xiao
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Fanghua Li
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Department of Particle Therapy, University Hospital Essen, West German Proton Therapy Centre Essen (WPE), West German Cancer Center (WTZ), German Cancer Consortium (DKTK), 45147 Essen, Germany;
| | - Emil Mladenov
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Aashish Soni
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Veronika Mladenova
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Bing Pan
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Rositsa Dueva
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Institute of Physiology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Martin Stuschke
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, German Cancer Research Center (DKFZ), 45147 Essen, Germany
| | - Beate Timmermann
- Department of Particle Therapy, University Hospital Essen, West German Proton Therapy Centre Essen (WPE), West German Cancer Center (WTZ), German Cancer Consortium (DKTK), 45147 Essen, Germany;
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, German Cancer Research Center (DKFZ), 45147 Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (H.X.); (F.L.); (E.M.); (A.S.); (V.M.); (B.P.); (R.D.)
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
- Correspondence: ; Tel.: +49-201-723-4152
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10
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Chae K, Dawson C, Valentin C, Contreras B, Zapletal J, Myles KM, Adelman ZN. Engineering a self-eliminating transgene in the yellow fever mosquito, Aedes aegypti. PNAS NEXUS 2022; 1:pgac037. [PMID: 36713320 PMCID: PMC9802104 DOI: 10.1093/pnasnexus/pgac037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023]
Abstract
Promising genetics-based approaches are being developed to reduce or prevent the transmission of mosquito-vectored diseases. Less clear is how such transgenes can be removed from the environment, a concern that is particularly relevant for highly invasive gene drive transgenes. Here, we lay the groundwork for a transgene removal system based on single-strand annealing (SSA), a eukaryotic DNA repair mechanism. An SSA-based rescuer strain (kmoRG ) was engineered to have direct repeat sequences (DRs) in the Aedes aegypti kynurenine 3-monooxygenase (kmo) gene flanking the intervening transgenic cargo genes, DsRED and EGFP. Targeted induction of DNA double-strand breaks (DSBs) in the DsRED transgene successfully triggered complete elimination of the entire cargo from the kmoRG strain, restoring the wild-type kmo gene, and thereby, normal eye pigmentation. Our work establishes the framework for strategies to remove transgene sequences during the evaluation and testing of modified strains for genetics-based mosquito control.
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Affiliation(s)
- Keun Chae
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Chanell Dawson
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Collin Valentin
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Bryan Contreras
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Josef Zapletal
- Department of Industrial and Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Kevin M Myles
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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11
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Pini V, Mariot V, Dumonceaux J, Counsell J, O'Neill HC, Farmer S, Conti F, Muntoni F. Transiently expressed CRISPR/Cas9 induces wild-type dystrophin in vitro in DMD patient myoblasts carrying duplications. Sci Rep 2022; 12:3756. [PMID: 35260651 PMCID: PMC8904532 DOI: 10.1038/s41598-022-07671-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/09/2022] [Indexed: 01/14/2023] Open
Abstract
Among the mutations arising in the DMD gene and causing Duchenne Muscular Dystrophy (DMD), 10–15% are multi-exon duplications. There are no current therapeutic approaches with the ability to excise large multi-exon duplications, leaving this patient cohort without mutation-specific treatment. Using CRISPR/Cas9 could provide a valid alternative to achieve targeted excision of genomic duplications of any size. Here we show that the expression of a single CRISPR/Cas9 nuclease targeting a genomic region within a DMD duplication can restore the production of wild-type dystrophin in vitro. We assessed the extent of dystrophin repair following both constitutive and transient nuclease expression by either transducing DMD patient-derived myoblasts with integrating lentiviral vectors or electroporating them with CRISPR/Cas9 expressing plasmids. Comparing genomic, transcript and protein data, we observed that both continuous and transient nuclease expression resulted in approximately 50% dystrophin protein restoration in treated myoblasts. Our data demonstrate that a high transient expression profile of Cas9 circumvents its requirement of continuous expression within the cell for targeting DMD duplications. This proof-of-concept study therefore helps progress towards a clinically relevant gene editing strategy for in vivo dystrophin restoration, by highlighting important considerations for optimizing future therapeutic approaches.
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Affiliation(s)
- Veronica Pini
- Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neuroscience Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK.
| | - Virginie Mariot
- Translational Myology Laboratory, Molecular Neurosciences Section, Developmental Neuroscience Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Julie Dumonceaux
- Translational Myology Laboratory, Molecular Neurosciences Section, Developmental Neuroscience Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - John Counsell
- Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neuroscience Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Helen C O'Neill
- Genome Editing and Reproductive Genetics Group, Institute for Women's Health, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK
| | - Sarah Farmer
- Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neuroscience Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Francesco Conti
- Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neuroscience Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neuroscience Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK. .,NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK.
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12
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Niewolik D, Schwarz K. Physical ARTEMIS:DNA-PKcs interaction is necessary for V(D)J recombination. Nucleic Acids Res 2022; 50:2096-2110. [PMID: 35150269 PMCID: PMC8887466 DOI: 10.1093/nar/gkac071] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/12/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
The nuclease ARTEMIS and the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) are involved in the repair of physiological and pathogenic DNA double strand breaks. Both proteins are indispensable for the hairpin-opening activity in V(D)J recombination and therefore essential for the adaptive immune response. ARTEMIS and DNA-PKcs interact, however experimental evidence for in vivo significance is missing. We demonstrate that mutations abolishing this protein-protein interaction affect nuclease function. In DNA-PKcs, mutation L3062R impairs the physical interaction with ARTEMIS and was previously identified as pathogenic variant, resulting in radiosensitive severe combined immunodeficiency. In ARTEMIS, specific mutations in two conserved regions affect interaction with DNA-PKcs. In combination they impair V(D)J recombination activity, independent of ARTEMIS autoinhibitory self-interaction between the ARTEMIS C-terminus and the N-terminal nuclease domain. We describe small fragments from both proteins, capable of interaction with the corresponding full-length partner proteins: In DNA-PKcs 42 amino acids out of FAT region 2 (PKcs3041-3082) can mediate interaction with ARTEMIS. In the nuclease we have defined 26 amino acids (ARM378-403) as minimal DNA-PKcs interacting fragment. The exact mapping of the ARTEMIS:DNA-PKcs interaction may pave the way for the design of specific inhibitors targeting the repair of DNA double strand breaks.
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Affiliation(s)
- Doris Niewolik
- Institute for Transfusion Medicine, University of Ulm, Ulm 89081, Germany
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University of Ulm, Ulm 89081, Germany.,Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg-Hessen, Ulm 89081, Germany
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13
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Cheng Z, Cheng D, Li J, Guo L, Zhang W, Zhang C, Liu Y, Huang Y, Xu K. Polymorphisms Within DNA Double-Strand Breaks Repair-Related Genes Contribute to Structural Chromosome Abnormality in Recurrent Pregnancy Loss. Front Genet 2022; 12:787718. [PMID: 35003222 PMCID: PMC8733605 DOI: 10.3389/fgene.2021.787718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/06/2021] [Indexed: 12/05/2022] Open
Abstract
Background: Structural chromosome abnormality (SCA) is an important cause of human diseases, including recurrent pregnancy loss (RPL). DNA double-strand breaks (DSBs) repair-related genes play critical roles in SCA. The present study aims to investigate the potential contribution of DSBs repair-related gene polymorphisms to SCA. Methods: Fifty-four affected RPL individuals with SCA, 88 affected RPL individuals without SCA, and 84 controls were analyzed. Targeted whole-exome sequencing (WES) was used for screening single nucleotide polymorphisms in six DSBs repair-related genes (EP300, XRCC6, LIG4, XRCC4, PRKDC, and DCLRE1C), and validation was performed by Sanger sequencing. Finally, we detected the frequency of radiation-induced chromosome translocations in no SCA samples with significant polymorphisms by fluorescence in situ hybridization (FISH). Results: A total of 35 polymorphisms have been identified and confirmed. Frequencies of EP300 rs20551, XRCC6 rs132788, and LIG4 rs1805388 were significantly different between SCA RPL and no SCA RPL (p = 0.030, 0.031, and 0.040 respectively). Frequencies of those three gene polymorphisms between SCA RPL and controls also were significantly different (p = 0.017, 0.028, and 0.029 respectively). Moreover, the frequency of the G allele at rs20551 locus, the T allele at rs132788 locus and the A allele at rs1805388 locus was significantly higher in SCA RPL than no SCA RPL (OR = 3.227, p = 0.005; OR = 1.978, p = 0.008 and OR = 1.769, p = 0.036 respectively) and controls (OR = 7.130, p = 0.000; OR = 2.157, p = 0.004; OR = 2.397, p = 0.003 respectively). Additionally, the frequency of radiation-induced translocation in no SCA samples with rs20551, rs132788 or rs1805388 was significantly higher compared with the wild type samples (p = 0.015, 0.012, and 0.007 respectively). Conclusion: Our results suggest that rs20551, rs132788, and rs1805388 might be associated with the risk of SCA. Larger scales of genetic variations studies and functional experiments are necessary to further confirm these findings.
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Affiliation(s)
- Zhenbo Cheng
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Dehua Cheng
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Jiancheng Li
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Lihuang Guo
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Wei Zhang
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Conghui Zhang
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yangxu Liu
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yue Huang
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Keqian Xu
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
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14
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Chinnam NB, Syed A, Burnett KH, Hura GL, Tainer JA, Tsutakawa SE. Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights. Methods Mol Biol 2022; 2444:43-68. [PMID: 35290631 PMCID: PMC9020468 DOI: 10.1007/978-1-0716-2063-2_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Structures provide a critical breakthrough step for biological analyses, and small angle X-ray scattering (SAXS) is a powerful structural technique to study dynamic DNA repair proteins. As toxic and mutagenic repair intermediates need to be prevented from inadvertently harming the cell, DNA repair proteins often chaperone these intermediates through dynamic conformations, coordinated assemblies, and allosteric regulation. By measuring structural conformations in solution for both proteins, DNA, RNA, and their complexes, SAXS provides insight into initial DNA damage recognition, mechanisms for validation of their substrate, and pathway regulation. Here, we describe exemplary SAXS analyses of a DNA damage response protein spanning from what can be derived directly from the data to obtaining super resolution through the use of SAXS selection of atomic models. We outline strategies and tactics for practical SAXS data collection and analysis. Making these structural experiments in reach of any basic and clinical researchers who have protein, SAXS data can readily be collected at government-funded synchrotrons, typically at no cost for academic researchers. In addition to discussing how SAXS complements and enhances cryo-electron microscopy, X-ray crystallography, NMR, and computational modeling, we furthermore discuss taking advantage of recent advances in protein structure prediction in combination with SAXS analysis.
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Affiliation(s)
- Naga Babu Chinnam
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Kathryn H Burnett
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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15
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Poláková E, Albanaz ATS, Zakharova A, Novozhilova TS, Gerasimov ES, Yurchenko V. Ku80 is involved in telomere maintenance but dispensable for genomic stability in Leishmania mexicana. PLoS Negl Trop Dis 2021; 15:e0010041. [PMID: 34965251 PMCID: PMC8716037 DOI: 10.1371/journal.pntd.0010041] [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: 07/13/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Telomeres are indispensable for genome stability maintenance. They are maintained by the telomere-associated protein complex, which include Ku proteins and a telomerase among others. Here, we investigated a role of Ku80 in Leishmania mexicana. Leishmania is a genus of parasitic protists of the family Trypanosomatidae causing a vector-born disease called leishmaniasis. METHODOLOGY/PRINCIPAL FINDINGS We used the previously established CRISPR/Cas9 system to mediate ablation of Ku80- and Ku70-encoding genes in L. mexicana. Complete knock-outs of both genes were confirmed by Southern blotting, whole-genome Illumina sequencing, and RT-qPCR. Resulting telomeric phenotypes were subsequently investigated using Southern blotting detection of terminal restriction fragments. The genome integrity in the Ku80- deficient cells was further investigated by whole-genome sequencing. Our work revealed that telomeres in the ΔKu80 L. mexicana are elongated compared to those of the wild type. This is a surprising finding considering that in another model trypanosomatid, Trypanosoma brucei, they are shortened upon ablation of the same gene. A telomere elongation phenotype has been documented in other species and associated with a presence of telomerase-independent alternative telomere lengthening pathway. Our results also showed that Ku80 appears to be not involved in genome stability maintenance in L. mexicana. CONCLUSION/SIGNIFICANCE Ablation of the Ku proteins in L. mexicana triggers telomere elongation, but does not have an adverse impact on genome integrity.
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Affiliation(s)
- Ester Poláková
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Amanda T. S. Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | | | - Evgeny S. Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
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16
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Unfried JP, Marín-Baquero M, Rivera-Calzada Á, Razquin N, Martín-Cuevas EM, de Bragança S, Aicart-Ramos C, McCoy C, Prats-Mari L, Arribas-Bosacoma R, Lee L, Caruso S, Zucman-Rossi J, Sangro B, Williams G, Moreno-Herrero F, Llorca O, Lees-Miller SP, Fortes P. Long Noncoding RNA NIHCOLE Promotes Ligation Efficiency of DNA Double-Strand Breaks in Hepatocellular Carcinoma. Cancer Res 2021; 81:4910-4925. [PMID: 34321241 PMCID: PMC8488005 DOI: 10.1158/0008-5472.can-21-0463] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/25/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022]
Abstract
Long noncoding RNAs (lncRNA) are emerging as key players in cancer as parts of poorly understood molecular mechanisms. Here, we investigated lncRNAs that play a role in hepatocellular carcinoma (HCC) and identified NIHCOLE, a novel lncRNA induced in HCC with oncogenic potential and a role in the ligation efficiency of DNA double-stranded breaks (DSB). NIHCOLE expression was associated with poor prognosis and survival of HCC patients. Depletion of NIHCOLE from HCC cells led to impaired proliferation and increased apoptosis. NIHCOLE deficiency led to accumulation of DNA damage due to a specific decrease in the activity of the nonhomologous end-joining (NHEJ) pathway of DSB repair. DNA damage induction in NIHCOLE-depleted cells further decreased HCC cell growth. NIHCOLE was associated with DSB markers and recruited several molecules of the Ku70/Ku80 heterodimer. Further, NIHCOLE putative structural domains supported stable multimeric complexes formed by several NHEJ factors including Ku70/80, APLF, XRCC4, and DNA ligase IV. NHEJ reconstitution assays showed that NIHCOLE promoted the ligation efficiency of blunt-ended DSBs. Collectively, these data show that NIHCOLE serves as a scaffold and facilitator of NHEJ machinery and confers an advantage to HCC cells, which could be exploited as a targetable vulnerability. SIGNIFICANCE: This study characterizes the role of lncRNA NIHCOLE in DNA repair and cellular fitness in HCC, thus implicating it as a therapeutic target.See related commentary by Barcena-Varela and Lujambio, p. 4899.
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MESH Headings
- Biomarkers, Tumor
- Carcinoma, Hepatocellular/diagnosis
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/mortality
- Cell Line, Tumor
- DNA Breaks, Double-Stranded
- DNA End-Joining Repair
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- High-Throughput Nucleotide Sequencing
- Humans
- Liver Neoplasms/diagnosis
- Liver Neoplasms/genetics
- Liver Neoplasms/mortality
- Models, Biological
- Nucleic Acid Conformation
- Nucleotide Motifs
- Prognosis
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
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Affiliation(s)
- Juan P Unfried
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain.
| | - Mikel Marín-Baquero
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Ángel Rivera-Calzada
- Structural Biology Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Nerea Razquin
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Eva M Martín-Cuevas
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Sara de Bragança
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Christopher McCoy
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Laura Prats-Mari
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Raquel Arribas-Bosacoma
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Linda Lee
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, Functional Genomics of Solid Tumors laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, Paris, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, Functional Genomics of Solid Tumors laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, Paris, France
| | - Bruno Sangro
- University of Navarra Clinic (CUN), Liver Unit, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Madrid, Spain
| | - Gareth Williams
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Oscar Llorca
- Structural Biology Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Puri Fortes
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain.
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Madrid, Spain
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17
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Targeting the Interplay between HDACs and DNA Damage Repair for Myeloma Therapy. Int J Mol Sci 2021; 22:ijms221910406. [PMID: 34638744 PMCID: PMC8508842 DOI: 10.3390/ijms221910406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
Multiple myeloma (MM) is a malignancy of terminally differentiated plasma cells, and accounts for 10% of all hematologic malignancies and 1% of all cancers. MM is characterized by genomic instability which results from DNA damage with certain genomic rearrangements being prognostic factors for the disease and patients’ clinical response. Following genotoxic stress, the evolutionary conserved DNA damage response (DDR) is activated and, in turn, coordinates DNA repair with cell-cycle events. However, the process of carcinogenesis cannot be attributed only to the genetic alterations, but also involves epigenetic processes. Regulation of expression and activity of key players in DNA repair and checkpoint proteins are essential and mediated partly by posttranslational modifications (PTM), such as acetylation. Crosstalk between different PTMs is important for regulation of DNA repair pathways. Acetylation, which is mediated by acetyltransferases (HAT) and histone deacetylases (HDAC), not only affects gene expression through its modulation of histone tails but also has recently been implicated in regulating non-histone proteins. Currently, several HDAC inhibitors (HDACi) have been developed both in pre-clinical and clinical studies, with some of them exhibiting significant anti-MM activities. Due to reversibility of epigenetic changes during the evolutionary process of myeloma genesis, the potency of epigenetic therapies seems to be of great importance. The aim of the present paper is the summary of all data on the role of HDACi in DDR, the interference with each DNA repair mechanism and the therapeutic implications of HDACi in MM.
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Joshi JS, Vora HH, Ghosh NR, Tankshali RN, Jetly DH, Trivedi TI. Nonhomologous end joining repair pathway molecules as predictive biomarkers for patients with oral squamous cell carcinoma. J Cancer Res Ther 2021; 17:1031-1038. [PMID: 34528560 DOI: 10.4103/jcrt.jcrt_582_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Purpose Nonhomologous end-joining (NHEJ) is critical for the repair of either pathologic double-strand breaks (DSBs) and/or for the repair of physiologic DSBs created during radiotherapy to kill the tumor cell. Therefore, patients with higher expression of NHEJ repair proteins might develop resistance to ionizing radiation, allowing the disease to recur. As cancer of the oral cavity is a serious health problem globally, the present study aimed to examine the expression of Ku70/80, X-ray repair cross-complementing protein 4 (XRCC4) and DNA ligase IV-core molecules of the NHEJ pathway in patients with oral cancer. Materials and Methods Protein expression of Ku70/80, XRCC4, and DNA ligase IV were studied by Immunohistochemistry and mRNA expression of Ku70 and Ku80 were studied using reverse transcription polymerase chain reaction. Data were analyzed statistically using SPSS. Results A univariate survival analysis revealed an association of Ku70 mRNA with shorter overall survival (OS). While protein expression of XRCC4 showed an association with reduced relapse-free survival and shorter OS. Multivariate survival analysis demonstrated that XRCC4 and DNA ligase IV are independent prognosticators for predicting adverse disease outcomes. Conclusion Strong expression of repair proteins - XRCC4 and DNA ligase IV is associated with unfavorable disease outcome in patients with oral squamous cell carcinoma.
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Affiliation(s)
- Jigna S Joshi
- Stem Cell Biology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Hemangini H Vora
- Immunohematology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Nandita R Ghosh
- Tumor Biology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Rajen N Tankshali
- Department of Surgical Oncology, Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Dhaval H Jetly
- Department of Onco-Pathology, Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Trupti I Trivedi
- Clinical Carcinogenesis Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
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VAV2 is required for DNA repair and implicated in cancer radiotherapy resistance. Signal Transduct Target Ther 2021; 6:322. [PMID: 34462423 PMCID: PMC8405816 DOI: 10.1038/s41392-021-00735-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 07/19/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023] Open
Abstract
Radiotherapy remains the mainstay for treatment of various types of human cancer; however, the clinical efficacy is often limited by radioresistance, in which the underlying mechanism is largely unknown. Here, using esophageal squamous cell carcinoma (ESCC) as a model, we demonstrate that guanine nucleotide exchange factor 2 (VAV2), which is overexpressed in most human cancers, plays an important role in primary and secondary radioresistance. We have discovered for the first time that VAV2 is required for the Ku70/Ku80 complex formation and participates in non-homologous end joining repair of DNA damages caused by ionizing radiation. We show that VAV2 overexpression substantially upregulates signal transducer and activator of transcription 1 (STAT1) and the STAT1 inhibitor Fludarabine can significantly promote the sensitivity of radioresistant patient-derived ESCC xenografts in vivo in mice to radiotherapy. These results shed new light on the mechanism of cancer radioresistance, which may be important for improving clinical radiotherapy.
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20
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Rashid I, Hammel M, Sverzhinsky A, Tsai MS, Pascal JM, Tainer JA, Tomkinson AE. Direct interaction of DNA repair protein tyrosyl DNA phosphodiesterase 1 and the DNA ligase III catalytic domain is regulated by phosphorylation of its flexible N-terminus. J Biol Chem 2021; 297:100921. [PMID: 34181949 PMCID: PMC8318918 DOI: 10.1016/j.jbc.2021.100921] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/10/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Tyrosyl DNA phosphodiesterase 1 (TDP1) and DNA Ligase IIIα (LigIIIα) are key enzymes in single-strand break (SSB) repair. TDP1 removes 3′-tyrosine residues remaining after degradation of DNA topoisomerase (TOP) 1 cleavage complexes trapped by either DNA lesions or TOP1 inhibitors. It is not known how TDP1 is linked to subsequent processing and LigIIIα-catalyzed joining of the SSB. Here we define a direct interaction between the TDP1 catalytic domain and the LigIII DNA-binding domain (DBD) regulated by conformational changes in the unstructured TDP1 N-terminal region induced by phosphorylation and/or alterations in amino acid sequence. Full-length and N-terminally truncated TDP1 are more effective at correcting SSB repair defects in TDP1 null cells compared with full-length TDP1 with amino acid substitutions of an N-terminal serine residue phosphorylated in response to DNA damage. TDP1 forms a stable complex with LigIII170–755, as well as full-length LigIIIα alone or in complex with the DNA repair scaffold protein XRCC1. Small-angle X-ray scattering and negative stain electron microscopy combined with mapping of the interacting regions identified a TDP1/LigIIIα compact dimer of heterodimers in which the two LigIII catalytic cores are positioned in the center, whereas the two TDP1 molecules are located at the edges of the core complex flanked by highly flexible regions that can interact with other repair proteins and SSBs. As TDP1and LigIIIα together repair adducts caused by TOP1 cancer chemotherapy inhibitors, the defined interaction architecture and regulation of this enzyme complex provide insights into a key repair pathway in nonmalignant and cancer cells.
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Affiliation(s)
- Ishtiaque Rashid
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, USA
| | - Michal Hammel
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Miaw-Sheue Tsai
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, USA.
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21
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Hammel M, Tainer JA. X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology. Protein Sci 2021; 30:1735-1756. [PMID: 34056803 PMCID: PMC8376411 DOI: 10.1002/pro.4133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022]
Abstract
Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIVBRCT–Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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22
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Murashko MM, Stasevich EM, Schwartz AM, Kuprash DV, Uvarova AN, Demin DE. The Role of RNA in DNA Breaks, Repair and Chromosomal Rearrangements. Biomolecules 2021; 11:biom11040550. [PMID: 33918762 PMCID: PMC8069526 DOI: 10.3390/biom11040550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 12/28/2022] Open
Abstract
Incorrect reparation of DNA double-strand breaks (DSB) leading to chromosomal rearrangements is one of oncogenesis's primary causes. Recently published data elucidate the key role of various types of RNA in DSB formation, recognition and repair. With growing interest in RNA biology, increasing RNAs are classified as crucial at the different stages of the main pathways of DSB repair in eukaryotic cells: nonhomologous end joining (NHEJ) and homology-directed repair (HDR). Gene mutations or variation in expression levels of such RNAs can lead to local DNA repair defects, increasing the chromosome aberration frequency. Moreover, it was demonstrated that some RNAs could stimulate long-range chromosomal rearrangements. In this review, we discuss recent evidence demonstrating the role of various RNAs in DSB formation and repair. We also consider how RNA may mediate certain chromosomal rearrangements in a sequence-specific manner.
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Affiliation(s)
- Matvey Mikhailovich Murashko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Ekaterina Mikhailovna Stasevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Anton Markovich Schwartz
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
- Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, 141701 Moscow, Russia
| | - Dmitriy Vladimirovich Kuprash
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Aksinya Nicolaevna Uvarova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Denis Eriksonovich Demin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
- Correspondence:
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23
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Cheng C, Pei X, Li SW, Yang J, Li C, Tang J, Hu K, Huang G, Min WP, Sang Y. CRISPR/Cas9 library screening uncovered methylated PKP2 as a critical driver of lung cancer radioresistance by stabilizing β-catenin. Oncogene 2021; 40:2842-2857. [PMID: 33742119 DOI: 10.1038/s41388-021-01692-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 01/31/2023]
Abstract
Radiation resistance is a major cause of lung cancer treatment failure. Armadillo (ARM) superfamily proteins participate in various fundamental cellular processes; however, whether ARM proteins regulate radiation resistance is not fully understood. Here, we used an unbiased CRISPR/Cas9 library screen and identified plakophilin 2 (PKP2), a member of the ARM superfamily of proteins, as a critical driver of radiation resistance in lung cancer. The PKP2 level was significantly higher after radiotherapy than before radiotherapy, and high PKP2 expression after radiotherapy predicted poor overall survival (OS) and postprogression survival (PPS). Mechanistically, mass spectrometry analysis identified that PKP2 was methylated at the arginine site and interacted with protein arginine methyltransferase 1 (PRMT1). Methylation of PKP2 by PRMT1 stabilized β-catenin by recruiting USP7, further inducing LIG4, a key DNA ligase in nonhomologous end-joining (NHEJ) repair. Concomitantly, PKP2-induced radioresistance depended on facilitating LIG4-mediated NHEJ repair in lung cancer. More strikingly, after exposure to irradiation, treatment with the PRMT1 inhibitor C-7280948 abolished PKP2-induced radioresistance, and C-7280948 is a potential radiosensitizer in lung cancer. In summary, our results demonstrate that targeting the PRMT1/PKP2/β-catenin/LIG4 pathway is an effective approach to overcome radiation resistance in lung cancer.
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Affiliation(s)
- Chun Cheng
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaofeng Pei
- Department of Thoracic Oncology, The Cancer Center of the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Si-Wei Li
- Department of Oncology, Tongji Huangzhou Hospital of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jun Yang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chenxi Li
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianjun Tang
- Department of Respiratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Guofu Huang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei-Ping Min
- Department of Surgery, Pathology and Oncology, University of Western Ontario, London, ON, Canada
| | - Yi Sang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University, Nanchang, China.
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Structural insights into the role of DNA-PK as a master regulator in NHEJ. GENOME INSTABILITY & DISEASE 2021; 2:195-210. [PMID: 34723130 PMCID: PMC8549938 DOI: 10.1007/s42764-021-00047-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 12/26/2022]
Abstract
DNA-dependent protein kinase catalytic subunit DNA-PKcs/PRKDC is the largest serine/threonine protein kinase of the phosphatidyl inositol 3-kinase-like protein kinase (PIKK) family and is the most highly expressed PIKK in human cells. With its DNA-binding partner Ku70/80, DNA-PKcs is required for regulated and efficient repair of ionizing radiation-induced DNA double-strand breaks via the non-homologous end joining (NHEJ) pathway. Loss of DNA-PKcs or other NHEJ factors leads to radiation sensitivity and unrepaired DNA double-strand breaks (DSBs), as well as defects in V(D)J recombination and immune defects. In this review, we highlight the contributions of the late Dr. Carl W. Anderson to the discovery and early characterization of DNA-PK. We furthermore build upon his foundational work to provide recent insights into the structure of NHEJ synaptic complexes, an evolutionarily conserved and functionally important YRPD motif, and the role of DNA-PKcs and its phosphorylation in NHEJ. The combined results identify DNA-PKcs as a master regulator that is activated by its detection of two double-strand DNA ends for a cascade of phosphorylation events that provide specificity and efficiency in assembling the synaptic complex for NHEJ.
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25
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Bhat MA, Bhat MA, Kumar V, Wani IA, Bashir H, Shah AA, Rahman S, Jan AT. The era of editing plant genomes using CRISPR/Cas: A critical appraisal. J Biotechnol 2020; 324:34-60. [DOI: 10.1016/j.jbiotec.2020.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
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26
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Shi T, Dansen TB. Reactive Oxygen Species Induced p53 Activation: DNA Damage, Redox Signaling, or Both? Antioxid Redox Signal 2020; 33:839-859. [PMID: 32151151 DOI: 10.1089/ars.2020.8074] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Significance: The p53 tumor suppressor has been dubbed the "guardian of genome" because of its various roles in the response to DNA damage such as DNA damage repair, cell cycle arrest, senescence, and apoptosis, all of which are in place to prevent mutations from being passed on down the lineage. Recent Advances: Reactive oxygen species (ROS), for instance hydrogen peroxide derived from mitochondrial respiration, have long been regarded mainly as a major source of cellular damage to DNA and other macromolecules. Critical Issues: More recently, ROS have been shown to also play important physiological roles as second messengers in so-called redox signaling. It is, therefore, not clear whether the observed activation of p53 by ROS is mediated through the DNA damage response, redox signaling, or both. In this review, we will discuss the similarities and differences between p53 activation in response to DNA damage and redox signaling in terms of upstream signaling and downstream transcriptional program activation. Future Directions: Understanding whether and how DNA damage and redox signaling-dependent p53 activation can be dissected could be useful to develop anti-cancer therapeutic p53-reactivation strategies that do not depend on the induction of DNA damage and the resulting additional mutational load.
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Affiliation(s)
- Tao Shi
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tobias B Dansen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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27
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Hu K, Li Y, Wu W, Xie L, Yan H, Cai Y, Chen D, Jiang Q, Lin L, Chen Z, Liao J, Zhang Y, Koeffler HP, Yin D, Song E. ATM-Dependent Recruitment of BRD7 is required for Transcriptional Repression and DNA Repair at DNA Breaks Flanking Transcriptional Active Regions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000157. [PMID: 33101843 PMCID: PMC7578904 DOI: 10.1002/advs.202000157] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 08/01/2020] [Indexed: 06/11/2023]
Abstract
Repair of DNA double-strand breaks (DSBs) is essential for genome integrity, and is accompanied by transcriptional repression at the DSB regions. However, the mechanisms how DNA repair induces transcriptional inhibition remain elusive. Here, it is identified that BRD7 participates in DNA damage response (DDR) and is recruited to the damaged chromatin via ATM signaling. Mechanistically, BRD7 joins the polycomb repressive complex 2 (PRC2), the nucleosome remodeling and histone deacetylation (NuRD) complex at the damaged DNA and recruits E3 ubiquitin ligase RNF168 to the DSBs. Furthermore, ATM-mediated BRD7 phosphorylation is required for recruitment of the PRC2 complex, NuRD complex, DSB sensor complex MRE11-RAD50-NBS1 (MRN), and RNF168 to the active transcription sites at DSBs, resulting in transcriptional repression and DNA repair. Moreover, BRD7 deficiency sensitizes cancer cells to PARP inhibition. Collectively, BRD7 is crucial for DNA repair and DDR-mediated transcription repression, which may serve as a therapeutic target. The findings identify the missing link between DNA repair and transcription regulation that maintains genome integrity.
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Affiliation(s)
- Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Yu Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Wenjing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Department of Breast OncologySun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Limin Xie
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Haiyan Yan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Yuexin Cai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Dong Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Qiongchao Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Department of UltrasoundSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Lehang Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Zhen Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Jian‐You Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - H. Phillip Koeffler
- Division of Hematology/OncologyCedars‐Sinai Medical CenterUniversity of California Los Angeles School of MedicineLos AngelesCA90048USA
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Department of Breast OncologySun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
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Hammel M, Rosenberg DJ, Bierma J, Hura GL, Thapar R, Lees-Miller SP, Tainer JA. Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 163:74-86. [PMID: 32966823 DOI: 10.1016/j.pbiomolbio.2020.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/19/2020] [Accepted: 09/17/2020] [Indexed: 12/27/2022]
Abstract
Assembly of KU and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) at DNA double strand breaks (DSBs) forms DNA-PK holoenzyme as a critical initiating step for non-homologous end joining (NHEJ) repair of DSBs produced by radiation and chemotherapies. Advanced cryo-electron microscopy (cryo-EM) imaging together with breakthrough macromolecular X-ray crystal (MX) structures of KU and DNA-PKcs recently enabled visualization of the ∼600 kDa DNA-PK assembly at near atomic resolution. These important static structures provide the foundation for definition and interpretation of functional movements crucial to mechanistic understanding that can be tested through solution state structure analysis. We herein therefore leverage Cryo-EM and MX structures for the interpretation of synchrotron small-angle X-ray scattering (SAXS) data on DNA-PK conformations in solution to inform the structural mechanism for NHEJ initiation. SAXS, which measures thermodynamic solution-state conformational states and assemblies outside of cryo- and solid-state conditions, unveils the inherent flexibility of KU, DNA-PKcs and DNA-PK. The combined structural measurements reveal mobility of KU80 C-terminal region (KU80CTR), motion/plasticity of HEAT (DNA-PKcs Huntingtin, Elongation Factor 3, PP2 A, and TOR1) regions, allosteric switching upon DNA-PKcs autophosphorylation, and dimeric arrangements of DNA-PK assembly. Importantly, the results uncover displacement of the N-terminal HEAT domain during autophosphorylation as suitable for a regulated release mechanism of DNA-PKcs from DNA-PK to control unproductive access to toxic and mutagenic DNA repair intermediates. These integrated analyses show that the marriage of SAXS with cryo-EM leverages the strengths of both techniques to enable assessment of functional conformations and flexibility defining atomic-resolution molecular mechanisms for DSB repair.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Daniel J Rosenberg
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Graduate Group in Biophysics, University of California, Berkeley, CA, 94720, USA
| | - Jan Bierma
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Gregory L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Roopa Thapar
- Department of Cancer Biology, Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, T2N 4N1, Canada
| | - John A Tainer
- Department of Cancer Biology, Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Starcher CL, Pay SL, Singh N, Yeh IJ, Bhandare SB, Su X, Huang X, Bey EA, Motea EA, Boothman DA. Targeting Base Excision Repair in Cancer: NQO1-Bioactivatable Drugs Improve Tumor Selectivity and Reduce Treatment Toxicity Through Radiosensitization of Human Cancer. Front Oncol 2020; 10:1575. [PMID: 32974194 PMCID: PMC7468503 DOI: 10.3389/fonc.2020.01575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/21/2020] [Indexed: 01/23/2023] Open
Abstract
Ionizing radiation (IR) creates lethal DNA damage that can effectively kill tumor cells. However, the high dose required for a therapeutic outcome also damages healthy tissue. Thus, a therapeutic strategy with predictive biomarkers to enhance the beneficial effects of IR allowing a dose reduction without losing efficacy is highly desirable. NAD(P)H:quinone oxidoreductase 1 (NQO1) is overexpressed in the majority of recalcitrant solid tumors in comparison with normal tissue. Studies have shown that NQO1 can bioactivate certain quinone molecules (e.g., ortho-naphthoquinone and β-lapachone) to induce a futile redox cycle leading to the formation of oxidative DNA damage, hyperactivation of poly(ADP-ribose) polymerase 1 (PARP1), and catastrophic depletion of NAD+ and ATP, which culminates in cellular lethality via NAD+-Keresis. However, NQO1-bioactivatable drugs induce methemoglobinemia and hemolytic anemia at high doses. To circumvent this, NQO1-bioactivatable agents have been shown to synergize with PARP1 inhibitors, pyrimidine radiosensitizers, and IR. This therapeutic strategy allows for a reduction in the dose of the combined agents to decrease unwanted side effects by increasing tumor selectivity. In this review, we discuss the mechanisms of radiosensitization between NQO1-bioactivatable drugs and IR with a focus on the involvement of base excision repair (BER). This combination therapeutic strategy presents a unique tumor-selective and minimally toxic approach for targeting solid tumors that overexpress NQO1.
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Affiliation(s)
- Colton L Starcher
- Department of Biochemistry and Molecular Biology, IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - S Louise Pay
- Department of Biochemistry and Molecular Biology, IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Naveen Singh
- Department of Biochemistry and Molecular Biology, IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - I-Ju Yeh
- Department of Biochemistry and Molecular Biology, IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Snehal B Bhandare
- Department of Biochemistry and Molecular Biology, IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Xiaolin Su
- Department of Biochemistry and Molecular Biology, IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Xiumei Huang
- Department of Radiation Oncology, IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Erik A Bey
- Department of Biochemistry and Molecular Biology, IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Edward A Motea
- Department of Biochemistry and Molecular Biology, IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - David A Boothman
- Department of Biochemistry and Molecular Biology, IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
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DNA damage response signaling pathways and targets for radiotherapy sensitization in cancer. Signal Transduct Target Ther 2020; 5:60. [PMID: 32355263 PMCID: PMC7192953 DOI: 10.1038/s41392-020-0150-x] [Citation(s) in RCA: 458] [Impact Index Per Article: 114.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/20/2020] [Accepted: 03/16/2020] [Indexed: 12/19/2022] Open
Abstract
Radiotherapy is one of the most common countermeasures for treating a wide range of tumors. However, the radioresistance of cancer cells is still a major limitation for radiotherapy applications. Efforts are continuously ongoing to explore sensitizing targets and develop radiosensitizers for improving the outcomes of radiotherapy. DNA double-strand breaks are the most lethal lesions induced by ionizing radiation and can trigger a series of cellular DNA damage responses (DDRs), including those helping cells recover from radiation injuries, such as the activation of DNA damage sensing and early transduction pathways, cell cycle arrest, and DNA repair. Obviously, these protective DDRs confer tumor radioresistance. Targeting DDR signaling pathways has become an attractive strategy for overcoming tumor radioresistance, and some important advances and breakthroughs have already been achieved in recent years. On the basis of comprehensively reviewing the DDR signal pathways, we provide an update on the novel and promising druggable targets emerging from DDR pathways that can be exploited for radiosensitization. We further discuss recent advances identified from preclinical studies, current clinical trials, and clinical application of chemical inhibitors targeting key DDR proteins, including DNA-PKcs (DNA-dependent protein kinase, catalytic subunit), ATM/ATR (ataxia–telangiectasia mutated and Rad3-related), the MRN (MRE11-RAD50-NBS1) complex, the PARP (poly[ADP-ribose] polymerase) family, MDC1, Wee1, LIG4 (ligase IV), CDK1, BRCA1 (BRCA1 C terminal), CHK1, and HIF-1 (hypoxia-inducible factor-1). Challenges for ionizing radiation-induced signal transduction and targeted therapy are also discussed based on recent achievements in the biological field of radiotherapy.
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Kurihara T, Kouyama-Suzuki E, Satoga M, Li X, Badawi M, Thiha, Baig DN, Yanagawa T, Uemura T, Mori T, Tabuchi K. DNA repair protein RAD51 enhances the CRISPR/Cas9-mediated knock-in efficiency in brain neurons. Biochem Biophys Res Commun 2020; 524:621-628. [PMID: 32029273 DOI: 10.1016/j.bbrc.2020.01.132] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 10/25/2022]
Abstract
Gene knock-in using the CRISPR/Cas9 system can be achieved in a specific population of neurons in the mouse brain, by using in utero electroporation to introduce DNA fragments into neural progenitor cells. Using this strategy, we previously knocked-in the EGFP coding sequence into the N-terminal region of the β-actin gene specifically in the pyramidal neurons in layer 2/3 of the somatosensory cortex. However, the knock-in efficiency was less than 2% of the transfected neurons. In this study, we sought to improve the knock-in efficiency using this system. First, we varied the length of the homology arms of the β-actin donor template DNA, and found that the knock-in efficiency was increased to ∼14% by extending the length of the 5' and 3' homology arms to 1.6 kb and 2.0 kb, respectively. We then tested the effect of the DNA repair protein RAD51 and the knock-in efficiency was increased up to 2.5-fold when co-transfecting with two different β-actin and a camk2a targeting EGFP knock-in modules. The RAD51 overexpression did not alter the migration of developing neurons, density or morphology of the dendritic spines compared to those in neurons not transfected with RAD51. RAD51 expression will be useful for increasing the knock-in efficiency in neurons in vivo by CRISPR/Cas9-mediated homology directed repair (HDR).
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Affiliation(s)
- Taiga Kurihara
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano, 390-8621, Japan
| | - Emi Kouyama-Suzuki
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano, 390-8621, Japan
| | - Michiru Satoga
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano, 390-8621, Japan
| | - Xue Li
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano, 390-8621, Japan
| | - Moataz Badawi
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano, 390-8621, Japan
| | - Thiha
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano, 390-8621, Japan
| | - Deeba Noreen Baig
- School of Life Sciences Forman Christian College (A Chartared University), Lahore, 54600, Pakistan
| | - Toru Yanagawa
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Takeshi Uemura
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano, 390-8621, Japan; Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Nagano, 390-8621, Japan
| | - Takuma Mori
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano, 390-8621, Japan; Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Nagano, 390-8621, Japan
| | - Katsuhiko Tabuchi
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano, 390-8621, Japan; Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Nagano, 390-8621, Japan.
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Lorat Y, Fleckenstein J, Görlinger P, Rübe C, Rübe CE. Assessment of DNA damage by 53PB1 and pKu70 detection in peripheral blood lymphocytes by immunofluorescence and high-resolution transmission electron microscopy. Strahlenther Onkol 2020; 196:821-833. [PMID: 32006067 PMCID: PMC7449954 DOI: 10.1007/s00066-020-01576-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/07/2020] [Indexed: 11/29/2022]
Abstract
Purpose 53BP1 foci detection in peripheral blood lymphocytes (PBLs) by immunofluorescence microscopy (IFM) is a sensitive and quantifiable DNA double-strand break (DSB) marker. In addition, high-resolution transmission electron microscopy (TEM) with immunogold labeling of 53BP1 and DSB-bound phosphorylated Ku70 (pKu70) can be used to determine the progression of the DNA repair process. To establish this TEM method in the PBLs of patients with cancer, we analyzed and characterized whether different modes of irradiation influence the formation of DSBs, and whether accompanying chemotherapy influences DSB formation. Methods We obtained 86 blood samples before and 0.1, 0.5, and 24 h after irradiation from patients (n = 9) with head and neck or rectal cancers receiving radiotherapy (RT; n = 4) or radiochemotherapy (RCT; n = 5). 53BP1 foci were quantified by IFM. In addition, TEM was used to quantify gold-labelled pKu70 dimers and 53BP1 clusters within euchromatin and heterochromatin of PBLs. Results IFM analyses showed that during radiation therapy, persistent 53BP1 foci in PBLs accumulated with increasing numbers of administered RT fractions. This 53BP1 foci accumulation was not influenced by the irradiation technique applied (3D conformal radiotherapy versus intensity-modulated radiotherapy), dose intensity per fraction, number of irradiation fields, or isodose volume. However, more 53BP1 foci were detected in PBLs of patients treated with accompanying chemotherapy. TEM analyses showed that DSBs, indicated by pKu70, were present for longer periods in PBLs of RCT patients than in PBLs of RT only patients. Moreover, not every residual 53BP1 focus was equivalent to a remaining DSB, since pKu70 was not present at every damage site. Persistent 53BP1 clusters, visualized by TEM, without colocalizing pKu70 likely indicate chromatin alterations after repair completion or, possibly, defective repair. Conclusion IFM 53BP1 foci analyses alone are not adequate to determine individual repair capacity after irradiation of PBLs, as a DSB may be indicated by a 53BP1 focus but not every 53BP1 focus represents a DSB. Electronic supplementary material The online version of this article (10.1007/s00066-020-01576-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yvonne Lorat
- Department of Radiotherapy and Radiation Oncology, Medical Center, Saarland University, Homburg/Saar, Germany.
| | - Jochen Fleckenstein
- Department of Radiotherapy and Radiation Oncology, Medical Center, Saarland University, Homburg/Saar, Germany
| | - Patric Görlinger
- Department of Radiotherapy and Radiation Oncology, Medical Center, Saarland University, Homburg/Saar, Germany.,Department of Anesthesiology, DRK Hospitals Berlin Westend, Berlin, Germany
| | - Christian Rübe
- Department of Radiotherapy and Radiation Oncology, Medical Center, Saarland University, Homburg/Saar, Germany
| | - Claudia E Rübe
- Department of Radiotherapy and Radiation Oncology, Medical Center, Saarland University, Homburg/Saar, Germany
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Riccio AA, Schellenberg MJ, Williams RS. Molecular mechanisms of topoisomerase 2 DNA-protein crosslink resolution. Cell Mol Life Sci 2020; 77:81-91. [PMID: 31728578 PMCID: PMC6960353 DOI: 10.1007/s00018-019-03367-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022]
Abstract
The compaction of DNA and the continuous action of DNA transactions, including transcription and DNA replication, create complex DNA topologies that require Type IIA Topoisomerases, which resolve DNA topological strain and control genome dynamics. The human TOP2 enzymes catalyze their reactions via formation of a reversible covalent enzyme DNA-protein crosslink, the TOP2 cleavage complex (TOP2cc). Spurious interactions of TOP2 with DNA damage, environmental toxicants and chemotherapeutic "poisons" perturbs the TOP2 reaction cycle, leading to an accumulation of DNA-protein crosslinks, and ultimately, genomic instability and cell death. Emerging evidence shows that TOP2-DNA protein crosslink (DPC) repair entails multiple strand break repair activities, such as removal of the poisoned TOP2 protein and rejoining of the DNA ends through homologous recombination (HR) or non-homologous end joining (NHEJ). Herein, we discuss the molecular mechanisms of TOP2-DPC resolution, with specific emphasis on the recently uncovered ZATTZnf451-licensed TDP2-catalyzed TOP2-DPC reversal mechanism.
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Affiliation(s)
- Amanda A Riccio
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA
| | - Matthew J Schellenberg
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA
| | - R Scott Williams
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA.
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34
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Tiwari V, Wilson DM. DNA Damage and Associated DNA Repair Defects in Disease and Premature Aging. Am J Hum Genet 2019; 105:237-257. [PMID: 31374202 PMCID: PMC6693886 DOI: 10.1016/j.ajhg.2019.06.005] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/05/2019] [Indexed: 12/14/2022] Open
Abstract
Genetic information is constantly being attacked by intrinsic and extrinsic damaging agents, such as reactive oxygen species, atmospheric radiation, environmental chemicals, and chemotherapeutics. If DNA modifications persist, they can adversely affect the polymerization of DNA or RNA, leading to replication fork collapse or transcription arrest, or can serve as mutagenic templates during nucleic acid synthesis reactions. To combat the deleterious consequences of DNA damage, organisms have developed complex repair networks that remove chemical modifications or aberrant base arrangements and restore the genome to its original state. Not surprisingly, inherited or sporadic defects in DNA repair mechanisms can give rise to cellular outcomes that underlie disease and aging, such as transformation, apoptosis, and senescence. In the review here, we discuss several genetic disorders linked to DNA repair defects, attempting to draw correlations between the nature of the accumulating DNA damage and the pathological endpoints, namely cancer, neurological disease, and premature aging.
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Affiliation(s)
- Vinod Tiwari
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA.
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA.
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35
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Zhu LS, Wang DQ, Cui K, Liu D, Zhu LQ. Emerging Perspectives on DNA Double-strand Breaks in Neurodegenerative Diseases. Curr Neuropharmacol 2019; 17:1146-1157. [PMID: 31362659 PMCID: PMC7057204 DOI: 10.2174/1570159x17666190726115623] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/03/2019] [Accepted: 07/01/2019] [Indexed: 11/22/2022] Open
Abstract
DNA double-strand breaks (DSBs) are common events that were recognized as one of the most toxic lesions in eu-karyotic cells. DSBs are widely involved in many physiological processes such as V(D)J recombination, meiotic recombina-tion, DNA replication and transcription. Deregulation of DSBs has been reported in multiple diseases in human beings, such as the neurodegenerative diseases, with which the underlying mechanisms are needed to be illustrated. Here, we reviewed the recent insights into the dysfunction of DSB formation and repair, contributing to the pathogenesis of neurodegenerative dis-orders including Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), Huntington’s disease (HD) and ataxia tel-angiectasia (A-T).
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Affiliation(s)
- Ling-Shuang Zhu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China.,Department of Pathophysiology, Key Lab of Neurological Disorder of Education, Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ding-Qi Wang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China.,Department of Pathophysiology, Key Lab of Neurological Disorder of Education, Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ke Cui
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China.,Department of Pathophysiology, Key Lab of Neurological Disorder of Education, Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Dan Liu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education, Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.,Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ling-Qiang Zhu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China.,Department of Pathophysiology, Key Lab of Neurological Disorder of Education, Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
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Nenarokova A, Záhonová K, Krasilnikova M, Gahura O, McCulloch R, Zíková A, Yurchenko V, Lukeš J. Causes and Effects of Loss of Classical Nonhomologous End Joining Pathway in Parasitic Eukaryotes. mBio 2019; 10:e01541-19. [PMID: 31311886 PMCID: PMC6635534 DOI: 10.1128/mbio.01541-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 01/22/2023] Open
Abstract
We report frequent losses of components of the classical nonhomologous end joining pathway (C-NHEJ), one of the main eukaryotic tools for end joining repair of DNA double-strand breaks, in several lineages of parasitic protists. Moreover, we have identified a single lineage among trypanosomatid flagellates that has lost Ku70 and Ku80, the core C-NHEJ components, and accumulated numerous insertions in many protein-coding genes. We propose a correlation between these two phenomena and discuss the possible impact of the C-NHEJ loss on genome evolution and transition to the parasitic lifestyle.IMPORTANCE Parasites tend to evolve small and compact genomes, generally endowed with a high mutation rate, compared with those of their free-living relatives. However, the mechanisms by which they achieve these features, independently in unrelated lineages, remain largely unknown. We argue that the loss of the classical nonhomologous end joining pathway components may be one of the crucial steps responsible for characteristic features of parasite genomes.
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Affiliation(s)
- Anna Nenarokova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Marija Krasilnikova
- Wellcome Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Richard McCulloch
- Wellcome Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vyacheslav Yurchenko
- Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow, Russia
- Life Science Research Centre and Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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Satheesh V, Zhang H, Wang X, Lei M. Precise editing of plant genomes - Prospects and challenges. Semin Cell Dev Biol 2019; 96:115-123. [PMID: 31002868 DOI: 10.1016/j.semcdb.2019.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 12/26/2022]
Abstract
The past decade has witnessed unprecedented development in genome engineering, a process that enables targeted modification of genomes. The identification of sequence-specific nucleases such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the CRISPR/Cas system, in particular, has led to precise and efficient introduction of genetic variations into genomes of various organisms. Since the CRISPR/Cas system is highly versatile, cost-effective and much superior to ZFNs and TALENs, its widespread adoption by the research community has been inevitable. In plants, a number of studies have shown that CRISPR/Cas could be a potential tool in basic research where insertion, deletion and/or substitution in the genetic sequence could help answer fundamental questions about plant processes, and in applied research these technologies could help build or reverse-engineer plant systems to make them more useful. In this review article, we summarize technologies for precise editing of genomes with a special focus on the CRISPR/Cas system, highlight the latest developments in the CRISPR/Cas system and discuss the challenges and prospects in using the system for plant biology research.
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Affiliation(s)
- Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hui Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xianting Wang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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38
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Plugged into the Ku-DNA hub: The NHEJ network. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:62-76. [PMID: 30851288 DOI: 10.1016/j.pbiomolbio.2019.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022]
Abstract
In vertebrates, double-strand breaks in DNA are primarily repaired by Non-Homologous End-Joining (NHEJ). The ring-shaped Ku heterodimer rapidly senses and threads onto broken DNA ends forming a recruiting hub. Through protein-protein contacts eventually reinforced by protein-DNA interactions, the Ku-DNA hub attracts a series of specialized proteins with scaffolding and/or enzymatic properties. To shed light on these dynamic interplays, we review here current knowledge on proteins directly interacting with Ku and on the contact points involved, with a particular accent on the different classes of Ku-binding motifs identified in several Ku partners. An integrated structural model of the core NHEJ network at the synapsis step is proposed.
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39
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Cimini S, Gualtieri C, Macovei A, Balestrazzi A, De Gara L, Locato V. Redox Balance-DDR-miRNA Triangle: Relevance in Genome Stability and Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:989. [PMID: 31428113 PMCID: PMC6688120 DOI: 10.3389/fpls.2019.00989] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/15/2019] [Indexed: 05/05/2023]
Abstract
Plants are continuously faced with complex environmental conditions which can affect the oxidative metabolism and photosynthetic efficiency, thus leading to the over-production of reactive oxygen species (ROS). Over a certain threshold, ROS can damage DNA. DNA damage, unless repaired, can affect genome stability, thus interfering with cell survival and severely reducing crop productivity. A complex network of pathways involved in DNA damage response (DDR) needs to be activated in order to maintain genome integrity. The expression of specific genes belonging to these pathways can be used as indicators of oxidative DNA damage and effective DNA repair in plants subjected to stress conditions. Managing ROS levels by modulating their production and scavenging systems shifts the role of these compounds from toxic molecules to key messengers involved in plant tolerance acquisition. Oxidative and anti-oxidative signals normally move among the different cell compartments, including the nucleus, cytosol, and organelles. Nuclei are dynamically equipped with different redox systems, such as glutathione (GSH), thiol reductases, and redox regulated transcription factors (TFs). The nuclear redox network participates in the regulation of the DNA metabolism, in terms of transcriptional events, replication, and repair mechanisms. This mainly occurs through redox-dependent regulatory mechanisms comprising redox buffering and post-translational modifications, such as the thiol-disulphide switch, glutathionylation, and S-nitrosylation. The regulatory role of microRNAs (miRNAs) is also emerging for the maintenance of genome stability and the modulation of antioxidative machinery under adverse environmental conditions. In fact, redox systems and DDR pathways can be controlled at a post-transcriptional level by miRNAs. This review reports on the interconnections between the DDR pathways and redox balancing systems. It presents a new dynamic picture by taking into account the shared regulatory mechanism mediated by miRNAs in plant defense responses to stress.
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Affiliation(s)
- Sara Cimini
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
| | - Carla Gualtieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Laura De Gara
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
| | - Vittoria Locato
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
- *Correspondence: Vittoria Locato,
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40
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Yan J, Xie Y, Zhang Q, Gan L, Wang F, Li H, Si J, Zhang H. Dynamic recognition and repair of DNA complex damage. J Cell Physiol 2018; 234:13014-13020. [PMID: 30537094 DOI: 10.1002/jcp.27971] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/19/2018] [Indexed: 11/11/2022]
Abstract
Irradiation (IR) can be used to treat cancer by inducing complex and irreparable DNA damage in the cancer cells, which may lead to their apoptotic death. However, little is known about the molecular mechanism of this DNA damage. Here, the non-small-cell lung cancer cell line A549 was treated with either X-ray or carbon ion combined with bleomycin (BLM). The cell survival rate, frequency of double-strand breaks (DSBs), dynamic changes in γH2AX, and p53 binding protein 1 (53BP1), and protein expression of Ku70, Rad51, and XRCC1 were determined by the clone formation assay, agarose gel electrophoresis, immunofluorescence, and western blot analysis. The results showed that the most obvious complex DSBs occurred in the carbon IR + BLM group. The number of γH2AX and 53BP1 foci in the 0.5 hr X-ray IR + BLM group was the highest (p < 0.001) among all the groups. γH2AX foci were detected in the nucleus at 0.5, 1, 2, and 4 hr, but were distributed throughout the cell at 6 hr after IR in the carbon ion IR + BLM group. The expression of Ku70 increased and XRCC1 decreased at 2 and 6 hr after IR. Our data indicate that a DNA damage frequency of 13.4/Mbp is caused by clustered DNA damage and further show a correlation between γH2AX, 53BP1, and XRCC1 levels and the extent of DNA damage. The results of this study provide insights into DNA damage recognition and a rationale for the clinical use of radiotherapy.
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Affiliation(s)
- Junfang Yan
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China.,Graduate School of University of Chinese Academy of Sciences, Beijing, China
| | - Yi Xie
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
| | - Qianjing Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China.,Graduate School of University of Chinese Academy of Sciences, Beijing, China
| | - Lu Gan
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China.,Graduate School of University of Chinese Academy of Sciences, Beijing, China
| | - Fang Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China.,Graduate School of University of Chinese Academy of Sciences, Beijing, China
| | - Hongyan Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
| | - Jing Si
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
| | - Hong Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
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Corbeski I, Dolinar K, Wienk H, Boelens R, van Ingen H. DNA repair factor APLF acts as a H2A-H2B histone chaperone through binding its DNA interaction surface. Nucleic Acids Res 2018; 46:7138-7152. [PMID: 29905837 PMCID: PMC6101569 DOI: 10.1093/nar/gky507] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 05/02/2018] [Accepted: 05/22/2018] [Indexed: 01/23/2023] Open
Abstract
Genome replication, transcription and repair require the assembly/disassembly of the nucleosome. Histone chaperones are regulators of this process by preventing formation of non-nucleosomal histone-DNA complexes. Aprataxin and polynucleotide kinase like factor (APLF) is a non-homologous end-joining (NHEJ) DNA repair factor that possesses histone chaperone activity in its acidic domain (APLFAD). Here, we studied the molecular basis of this activity using biochemical and structural methods. We find that APLFAD is intrinsically disordered and binds histone complexes (H3-H4)2 and H2A-H2B specifically and with high affinity. APLFAD prevents unspecific complex formation between H2A-H2B and DNA in a chaperone assay, establishing for the first time its specific histone chaperone function for H2A-H2B. On the basis of a series of nuclear magnetic resonance studies, supported by mutational analysis, we show that the APLFAD histone binding domain uses two aromatic side chains to anchor to the α1-α2 patches on both H2A and H2B, thereby covering most of their DNA-interaction surface. An additional binding site on both APLFAD and H2A-H2B may be involved in the handoff between APLF and DNA or other chaperones. Together, our data support the view that APLF provides not only a scaffold but also generic histone chaperone activity for the NHEJ-complex.
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Affiliation(s)
- Ivan Corbeski
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Klemen Dolinar
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Group for Nano- and Biotechnological applications, Department of Fundamentals of Electrical Engineering, Mathematics and Physics, University of Ljubljana, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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42
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Campillo-Marcos I, Lazo PA. Implication of the VRK1 chromatin kinase in the signaling responses to DNA damage: a therapeutic target? Cell Mol Life Sci 2018; 75:2375-2388. [PMID: 29679095 PMCID: PMC5986855 DOI: 10.1007/s00018-018-2811-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/14/2018] [Accepted: 04/03/2018] [Indexed: 12/19/2022]
Abstract
DNA damage causes a local distortion of chromatin that triggers the sequential processes that participate in specific DNA repair mechanisms. This initiation of the repair response requires the involvement of a protein whose activity can be regulated by histones. Kinases are candidates to regulate and coordinate the connection between a locally altered chromatin and the response initiating signals that lead to identification of the type of lesion and the sequential steps required in specific DNA damage responses (DDR). This initiating kinase must be located in chromatin, and be activated independently of the type of DNA damage. We review the contribution of the Ser-Thr vaccinia-related kinase 1 (VRK1) chromatin kinase as a new player in the signaling of DNA damage responses, at chromatin and cellular levels, and its potential as a new therapeutic target in oncology. VRK1 is involved in the regulation of histone modifications, such as histone phosphorylation and acetylation, and in the formation of γH2AX, NBS1 and 53BP1 foci induced in DDR. Induction of DNA damage by chemotherapy or radiation is a mainstay of cancer treatment. Therefore, novel treatments can be targeted to proteins implicated in the regulation of DDR, rather than by directly causing DNA damage.
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Affiliation(s)
- Ignacio Campillo-Marcos
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Pedro A Lazo
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, 37007, Salamanca, Spain.
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
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Syed A, Tainer JA. The MRE11-RAD50-NBS1 Complex Conducts the Orchestration of Damage Signaling and Outcomes to Stress in DNA Replication and Repair. Annu Rev Biochem 2018; 87:263-294. [PMID: 29709199 PMCID: PMC6076887 DOI: 10.1146/annurev-biochem-062917-012415] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genomic instability in disease and its fidelity in health depend on the DNA damage response (DDR), regulated in part from the complex of meiotic recombination 11 homolog 1 (MRE11), ATP-binding cassette-ATPase (RAD50), and phosphopeptide-binding Nijmegen breakage syndrome protein 1 (NBS1). The MRE11-RAD50-NBS1 (MRN) complex forms a multifunctional DDR machine. Within its network assemblies, MRN is the core conductor for the initial and sustained responses to DNA double-strand breaks, stalled replication forks, dysfunctional telomeres, and viral DNA infection. MRN can interfere with cancer therapy and is an attractive target for precision medicine. Its conformations change the paradigm whereby kinases initiate damage sensing. Delineated results reveal kinase activation, posttranslational targeting, functional scaffolding, conformations storing binding energy and enabling access, interactions with hub proteins such as replication protein A (RPA), and distinct networks at DNA breaks and forks. MRN biochemistry provides prototypic insights into how it initiates, implements, and regulates multifunctional responses to genomic stress.
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Affiliation(s)
- Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; ,
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; ,
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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44
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Ramaekers VT, Segers K, Sequeira JM, Koenig M, Van Maldergem L, Bours V, Kornak U, Quadros EV. Genetic assessment and folate receptor autoantibodies in infantile-onset cerebral folate deficiency (CFD) syndrome. Mol Genet Metab 2018; 124:87-93. [PMID: 29661558 DOI: 10.1016/j.ymgme.2018.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Cerebral folate deficiency (CFD) syndromes are defined as neuro-psychiatric conditions with low CSF folate and attributed to different causes such as autoantibodies against the folate receptor-alpha (FR) protein that can block folate transport across the choroid plexus, FOLR1 gene mutations or mitochondrial disorders. High-dose folinic acid treatment restores many neurologic deficits. STUDY AIMS AND METHODS Among 36 patients from 33 families the infantile-onset CFD syndrome was diagnosed based on typical clinical features and low CSF folate. All parents were healthy. Three families had 2 affected siblings, while parents from 4 families were first cousins. We analysed serum FR autoantibodies and the FOLR1 and FOLR2 genes. Among three consanguineous families homozygosity mapping attempted to identify a monogenetic cause. Whole exome sequencing (WES) was performed in the fourth consanguineous family, where two siblings also suffered from polyneuropathy as an atypical finding. RESULTS Boys (72%) outnumbered girls (28%). Most patients (89%) had serum FR autoantibodies fluctuating over 5-6 weeks. Two children had a genetic FOLR1 variant without pathological significance. Homozygosity mapping failed to detect a single autosomal recessive gene. WES revealed an autosomal recessive polynucleotide kinase 3´phosphatase (PNKP) gene abnormality in the siblings with polyneuropathy. DISCUSSION Infantile-onset CFD was characterized by serum FR autoantibodies as its predominant pathology whereas pathogenic FOLR1 gene mutations were absent. Homozygosity mapping excluded autosomal recessive inheritance of any single responsible gene. WES in one consanguineous family identified a PNKP gene abnormality that explained the polyneuropathy and also its contribution to the infantile CFD syndrome because the PNKP gene plays a dual role in both neurodevelopment and immune-regulatory function. Further research for candidate genes predisposing to FRα-autoimmunity is suggested to include X-chromosomal and non-coding DNA regions.
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Affiliation(s)
- V Th Ramaekers
- Center of Autism and Department of Genetics, University Hospital Liège (CHU), Belgium.
| | - K Segers
- Center of Autism and Department of Genetics, University Hospital Liège (CHU), Belgium
| | - J M Sequeira
- Department of Medicine, SUNY-Downstate Medical Center, Brooklyn, New York, USA
| | - M Koenig
- EA7402 Institut Universitaire de Recherche Clinique, Montpellier, France
| | - L Van Maldergem
- Center Human Genetics, Université de Franche-Comté, Besançon, France
| | - V Bours
- Center of Autism and Department of Genetics, University Hospital Liège (CHU), Belgium
| | - U Kornak
- Institut für Humangenetik, Charité-University Berlin, Berlin, Germany
| | - E V Quadros
- Department of Medicine, SUNY-Downstate Medical Center, Brooklyn, New York, USA
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45
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Isobe SY, Nagao K, Nozaki N, Kimura H, Obuse C. Inhibition of RIF1 by SCAI Allows BRCA1-Mediated Repair. Cell Rep 2018; 20:297-307. [PMID: 28700933 DOI: 10.1016/j.celrep.2017.06.056] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 04/24/2017] [Accepted: 06/21/2017] [Indexed: 12/19/2022] Open
Abstract
DNA double-strand breaks (DSBs) are repaired by either the homology-directed repair (HDR) or the non-homologous end-joining (NHEJ) pathway. RIF1 (RAP1-interacting factor homolog) was recently shown to stimulate NHEJ through an interaction with 53BP1 (p53-binding protein 1) phosphorylated at S/TQ sites, but the molecular mechanism underlying pathway choice remains unclear. Here, we show that SCAI (suppressor of cancer cell invasion) binds to 53BP1 phosphorylated at S/TP sites and facilitates HDR. Upon DNA damage, RIF1 immediately accumulates at damage sites and then gradually dissociates from 53BP1 and is subsequently replaced with SCAI. Depletion of SCAI reduces both the accumulation of HDR factors, including BRCA1 (breast cancer susceptibility gene 1), at damage sites and the efficiency of HDR, as detected by a reporter assay system. These data suggest that SCAI inhibits RIF1 function to allow BRCA1-mediated repair, which possibly includes alt-NHEJ and resection-dependent NHEJ in G1, as well as HDR in S/G2.
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Affiliation(s)
- Shin-Ya Isobe
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo, Hokkaido 001-0021, Japan; Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Koji Nagao
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo, Hokkaido 001-0021, Japan; Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Naohito Nozaki
- MAB Institute, Inc., 2070-11 Oosegi, Iida, Nagano 395-0157, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Chikashi Obuse
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo, Hokkaido 001-0021, Japan; Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
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46
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Wieczorek A, Fornalewicz K, Mocarski Ł, Łyżeń R, Węgrzyn G. Double silencing of relevant genes suggests the existence of the direct link between DNA replication/repair and central carbon metabolism in human fibroblasts. Gene 2018; 650:1-6. [PMID: 29407228 DOI: 10.1016/j.gene.2018.01.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 01/17/2018] [Accepted: 01/19/2018] [Indexed: 01/15/2023]
Abstract
Genetic evidence for a link between DNA replication and glycolysis has been demonstrated a decade ago in Bacillus subtilis, where temperature-sensitive mutations in genes coding for replication proteins could be suppressed by mutations in genes of glycolytic enzymes. Then, a strong influence of dysfunctions of particular enzymes from the central carbon metabolism (CCM) on DNA replication and repair in Escherichia coli was reported. Therefore, we asked if such a link occurs only in bacteria or it is a more general phenomenon. Here, we demonstrate that effects of silencing (provoked by siRNA) of expression of genes coding for proteins involved in DNA replication and repair (primase, DNA polymerase ι, ligase IV, and topoisomerase IIIβ) on these processes (less efficient entry into the S phase of the cell cycle and decreased level of DNA synthesis) could be suppressed by silencing of specific genes of enzymes from CMM. Silencing of other pairs of replication/repair and CMM genes resulted in enhancement of the negative effects of lower expression levels of replication/repair genes. We suggest that these results may be proposed as a genetic evidence for the link between DNA replication/repair and CMM in human cells, indicating that it is a common biological phenomenon, occurring from bacteria to humans.
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Affiliation(s)
- Aneta Wieczorek
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Karolina Fornalewicz
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Łukasz Mocarski
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Robert Łyżeń
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
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47
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Khodaverdian VY, Hanscom T, Yu AM, Yu TL, Mak V, Brown AJ, Roberts SA, McVey M. Secondary structure forming sequences drive SD-MMEJ repair of DNA double-strand breaks. Nucleic Acids Res 2018; 45:12848-12861. [PMID: 29121353 PMCID: PMC5728401 DOI: 10.1093/nar/gkx1056] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/18/2017] [Indexed: 12/29/2022] Open
Abstract
Alternative end-joining (alt-EJ) repair of DNA double-strand breaks is associated with deletions, chromosome translocations, and genome instability. Alt-EJ frequently uses annealing of microhomologous sequences to tether broken ends. When accessible pre-existing microhomologies do not exist, we have postulated that new microhomologies can be created via limited DNA synthesis at secondary-structure forming sequences. This model, called synthesis-dependent microhomology-mediated end joining (SD-MMEJ), predicts that differences between DNA sequences near double-strand breaks should alter repair outcomes in predictable ways. To test this hypothesis, we injected plasmids with sequence variations flanking an I-SceI endonuclease recognition site into I-SceI expressing Drosophila embryos and used Illumina amplicon sequencing to compare repair junctions. As predicted by the model, we found that small changes in sequences near the I-SceI site had major impacts on the spectrum of repair junctions. Bioinformatic analyses suggest that these repair differences arise from transiently forming loops and hairpins within 30 nucleotides of the break. We also obtained evidence for ‘trans SD-MMEJ,’ involving at least two consecutive rounds of microhomology annealing and synthesis across the break site. These results highlight the importance of sequence context for alt-EJ repair and have important implications for genome editing and genome evolution.
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Affiliation(s)
- Varandt Y Khodaverdian
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Terrence Hanscom
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Amy Marie Yu
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Taylor L Yu
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Victoria Mak
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Alexander J Brown
- School of Molecular Biosciences, Washington State University, P100 Dairy Road, Pullman, WA 99164, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, P100 Dairy Road, Pullman, WA 99164, USA
| | - Mitch McVey
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
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Abstract
Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure. Here, we describe protocols for modeling atomic structures based on SAXS profiles. The first protocol is for comparing solution and crystal structures including modeling of missing regions and determination of the oligomeric state. The second protocol performs multi-state modeling by finding a set of conformations and their weights that fit the SAXS profile starting from a single-input structure. The third protocol is for protein-protein docking based on the SAXS profile of the complex. We describe the underlying software, followed by demonstrating their application on interleukin 33 (IL33) with its primary receptor ST2 and DNA ligase IV-XRCC4 complex.
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Affiliation(s)
- Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Schuler N, Palm J, Schmitz S, Lorat Y, Rübe CE. Increasing genomic instability during cancer therapy in a patient with Li-Fraumeni syndrome. Clin Transl Radiat Oncol 2017; 7:71-78. [PMID: 29594232 PMCID: PMC5862648 DOI: 10.1016/j.ctro.2017.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/05/2017] [Accepted: 10/07/2017] [Indexed: 11/28/2022] Open
Abstract
Tumor suppressor p53 plays a central role in maintaining genomic stability by promoting cell-cycle checkpoints and apoptosis after genotoxic insults. Here, we show that a patient with Li-Fraumeni syndrome receiving craniospinal irradiation including large volumes of bone marrow developed progressive genomic instability of the hematopoietic system.
Background Li-Fraumeni syndrome (LFS) is a cancer predisposition disorder characterized by germline mutations of the p53 tumor-suppressor gene. In response to DNA damage, p53 stimulates protective cellular processes including cell-cycle arrest and apoptosis to prevent aberrant cell proliferation. Current cancer therapies involve agents that damage DNA, which also affect non-cancerous hematopoietic stem/progenitor cells. Here, we report on a child with LFS who developed genomic instability during craniospinal irradiation for metastatic choroid plexus carcinoma (CPC). Case presentation This previously healthy 4-year-old boy presented with parieto-temporal brain tumor, diagnosed as CPC grade-3. Screening for cancer-predisposing syndrome revealed heterozygous p53 germline mutation, leading to LFS diagnosis. After tumour resection and systemic chemotherapy, entire craniospinal axis was irradiated due to leptomeningeal seeding, resulting in disease stabilization for nearly 12 months. Blood lymphocytes of LFS patient (p53-deficient) and age-matched tumor-children (p53-proficient) were collected before, during and after craniospinal irradiation and compared with asymptomatic carriers for identical p53 mutation, not exposed to DNA-damaging treatment. In p53-deficient lymphocytes of LFS patient radiation-induced DNA damage failed to induce cell-cycle arrest or apoptosis. Although DNA repair capacity was not impaired, p53-deficient blood lymphocytes of LFS patient showed significant accumulation of 53BP1-foci during and even several months after irradiation, reflecting persistent DNA damage. Electron microscopy revealed DNA abnormalities ranging from simple unrepaired lesions to chromosomal abnormalities. Metaphase spreads of p53-deficient lymphocytes explored by mFISH revealed high amounts of complex chromosomal aberrations after craniospinal irradiation. Conclusions Tumor suppressor p53 plays a central role in maintaining genomic stability by promoting cell-cycle checkpoints and apoptosis. Here, we demonstrate that a patient with LFS receiving craniospinal irradiation including large volumes of bone marrow developed progressive genomic instability of the hematopoietic system. During DNA-damaging radiotherapy, genome-stabilizing mechanisms in proliferating stem/progenitor cells are perturbed by p53 deficiency, increasing the risk of cancer initiation and progression.
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Affiliation(s)
- Nadine Schuler
- Department of Radiation Oncology, Saarland University, D-66421 Homburg/Saar, Germany
| | - Jan Palm
- Department of Radiation Oncology, Saarland University, D-66421 Homburg/Saar, Germany
| | - Sabine Schmitz
- Department of Safety and Radiation Protection, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Yvonne Lorat
- Department of Radiation Oncology, Saarland University, D-66421 Homburg/Saar, Germany
| | - Claudia E Rübe
- Department of Radiation Oncology, Saarland University, D-66421 Homburg/Saar, Germany
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50
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Zhuang L, Liu F, Peng P, Xiong H, Qiu H, Fu X, Xiao Z, Huang X. Effect of Ku80 on the radiosensitization of cisplatin in the cervical carcinoma cell line HeLa. Oncol Lett 2017; 15:147-154. [PMID: 29375707 PMCID: PMC5766065 DOI: 10.3892/ol.2017.7304] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 09/15/2017] [Indexed: 11/06/2022] Open
Abstract
Cisplatin chemotherapy in combination with radiotherapy is the primary therapeutic strategy for the treatment of cervical cancer; however, the underlying molecular mechanism for cisplatin radiosensitization remains unknown. The aim of the present study was to investigate the effect of Ku80, a DNA double-strand break (DSB) repair protein, on cisplatin radiosensitization in cervical cancer. The pre-established Ku80 suppression cervical cancer cell line HeLa/Ku80-siRNA and the normal HeLa cell line underwent 6 MV X-ray irradiation (6 Gy) individually or in combination with 5 µg/ml cisplatin treatment. Alterations in apoptosis, the cell cycle and γH2AX expression were detected. Following irradiation individually and combined with cisplatin, compared with normal HeLa cells, HeLa/Ku80-siRNAexhibited an increased rate of apoptosis (P<0.05). It was identified that the earlier cisplatin was administered following irradiation, the higher the rate of apoptosis. Cell cycle analysis indicated that, following irradiation combined with cisplatin, the cells were arrested in G1 and S phase rather than in G2/M phase following irradiation alone. Microscopic imaging of immunofluorescence staining and western blotting identified that HeLa/Ku80-siRNA cells exhibited more γH2AX foci remaining following treatment with irradiation and cisplatin, particularly in the group treated with 6 Gy irradiation for 1 h together with 23 h of exposure to cisplatin. Irradiation in combination with cisplatin promoted the apoptosis of HeLa cells in association with the inhibition of Ku80, and it was identified that the earlier cisplatin was administered following irradiation, the more apoptosis was induced. This maybe because irradiation combined with cisplatin is able to arrest cells in G1 and S phase to rapidly repair damaged DNA, and the lack of Ku80 induces the inability to repair DSB, resulting in increased apoptosis. The results of the present study suggest that Ku80 may be a potent molecular target in cisplatin radiosensitization.
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Affiliation(s)
- Liang Zhuang
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Fei Liu
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Ping Peng
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Huihua Xiong
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Hong Qiu
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xiugen Fu
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Zhiping Xiao
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xiaoyuan Huang
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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