51
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Velichko AK, Ovsyannikova N, Petrova NV, Luzhin AV, Vorobjeva M, Gavrikov AS, Mishin AS, Kireev II, Razin SV, Kantidze OL. Treacle and TOPBP1 control replication stress response in the nucleolus. J Cell Biol 2021; 220:212262. [PMID: 34100862 PMCID: PMC8190600 DOI: 10.1083/jcb.202008085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 04/26/2021] [Accepted: 05/18/2021] [Indexed: 12/22/2022] Open
Abstract
Replication stress is one of the main sources of genome instability. Although the replication stress response in eukaryotic cells has been extensively studied, almost nothing is known about the replication stress response in nucleoli. Here, we demonstrate that initial replication stress-response factors, such as RPA, TOPBP1, and ATR, are recruited inside the nucleolus in response to drug-induced replication stress. The role of TOPBP1 goes beyond the typical replication stress response; it interacts with the low-complexity nucleolar protein Treacle (also referred to as TCOF1) and forms large Treacle-TOPBP1 foci inside the nucleolus. In response to replication stress, Treacle and TOPBP1 facilitate ATR signaling at stalled replication forks, reinforce ATR-mediated checkpoint activation inside the nucleolus, and promote the recruitment of downstream replication stress response proteins inside the nucleolus without forming nucleolar caps. Characterization of the Treacle-TOPBP1 interaction mode leads us to propose that these factors can form a molecular platform for efficient stress response in the nucleolus.
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Affiliation(s)
- Artem K Velichko
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Natalia Ovsyannikova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Artem V Luzhin
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Maria Vorobjeva
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, Russia
| | - Igor I Kireev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology, and Perinatology, Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Omar L Kantidze
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
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52
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Gaillard S, Charasson V, Ribeyre C, Salifou K, Pillaire MJ, Hoffmann JS, Constantinou A, Trouche D, Vandromme M. KDM5A and KDM5B histone-demethylases contribute to HU-induced replication stress response and tolerance. Biol Open 2021; 10:268370. [PMID: 34184733 PMCID: PMC8181900 DOI: 10.1242/bio.057729] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/20/2021] [Indexed: 12/25/2022] Open
Abstract
KDM5A and KDM5B histone-demethylases are overexpressed in many cancers and have been involved in drug tolerance. Here, we describe that KDM5A, together with KDM5B, contribute to replication stress (RS) response and tolerance. First, they positively regulate RRM2, the regulatory subunit of ribonucleotide reductase. Second, they are required for optimal levels of activated Chk1, a major player of the intra-S phase checkpoint that protects cells from RS. We also found that KDM5A is enriched at ongoing replication forks and associates with both PCNA and Chk1. Because RRM2 is a major determinant of replication stress tolerance, we developed cells resistant to HU, and show that KDM5A/B proteins are required for both RRM2 overexpression and tolerance to HU. Altogether, our results indicate that KDM5A/B are major players of RS management. They also show that drugs targeting the enzymatic activity of KDM5 proteins may not affect all cancer-related consequences of KDM5A/B overexpression.
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Affiliation(s)
- Solenne Gaillard
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Virginie Charasson
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Cyril Ribeyre
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Kader Salifou
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Marie-Jeanne Pillaire
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037 Toulouse, France
| | - Jean-Sebastien Hoffmann
- Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 avenue Irène-Joliot-Curie, 31059 Toulouse cedex, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Didier Trouche
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Marie Vandromme
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
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53
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Hanaki S, Habara M, Shimada M. UV-induced activation of ATR is mediated by UHRF2. Genes Cells 2021; 26:447-454. [PMID: 33848395 DOI: 10.1111/gtc.12851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/09/2021] [Accepted: 04/09/2021] [Indexed: 11/27/2022]
Abstract
UHRF1 (Ubiquitin-like with PHD and ring finger domains 1) regulates DNA methylation and histone modifications and plays a key role in cell proliferation and the DNA damage response. However, the function of UHRF2, a paralog of UHRF1, in the DNA damage response remains largely unknown. Here, we show that UHRF2 is essential for maintaining cell viability after UV irradiation, as well as for the proliferation of cancer cells. UHRF2 was found to physically interact with ATR in a DNA damage-dependent manner through UHRF2's TTD domain. In addition, phosphorylation of threonine at position 1989, which is required for UV-induced activation of ATR, was impaired in cells depleted of UHRF2, suggesting that UHRF2 is essential in ATR activation. In conclusion, these results suggest a new regulatory mechanism of ATR activation mediated by UHRF2.
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Affiliation(s)
- Shunsuke Hanaki
- Department of Veterinary Biochemistry, Yamaguchi University, Yamaguchi City, Japan
| | - Makoto Habara
- Department of Veterinary Biochemistry, Yamaguchi University, Yamaguchi City, Japan
| | - Midori Shimada
- Department of Veterinary Biochemistry, Yamaguchi University, Yamaguchi City, Japan
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54
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Ma S, Cao C, Che S, Wang Y, Su D, Liu S, Gong W, Liu L, Sun J, Zhao J, Wang Q, Song N, Ge T, Guo Q, Tian S, Chen CD, Zhang T, Wang J, Ding X, Yang F, Ying G, Yang J, Zhang K, Zhu Y, Yao Z, Yang N, Shi L. PHF8-promoted TOPBP1 demethylation drives ATR activation and preserves genome stability. SCIENCE ADVANCES 2021; 7:7/19/eabf7684. [PMID: 33952527 PMCID: PMC8099190 DOI: 10.1126/sciadv.abf7684] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
Abstract
The checkpoint kinase ATR [ATM (ataxia-telangiectasia mutated) and rad3-related] is a master regulator of DNA damage response. Yet, how ATR activity is regulated remains to be investigated. We report here that histone demethylase PHF8 (plant homeodomain finger protein 8) plays a key role in ATR activation and replication stress response. Mechanistically, PHF8 interacts with and demethylates TOPBP1 (DNA topoisomerase 2-binding protein 1), an essential allosteric activator of ATR, under unperturbed conditions, but replication stress results in PHF8 phosphorylation and dissociation from TOPBP1. Consequently, hypomethylated TOPBP1 facilitates RAD9 (RADiation sensitive 9) binding and chromatin loading of the TOPBP1-RAD9 complex to fully activate ATR and thus safeguard the genome and protect cells against replication stress. Our study uncovers a demethylation and phosphorylation code that controls the assembly of TOPBP1-scaffolded protein complex, and provides molecular insight into non-histone methylation switch in ATR activation.
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Affiliation(s)
- Shuai Ma
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Cheng Cao
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Shiyou Che
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353 Tianjin, China
| | - Yuejiao Wang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Dongxue Su
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Shuai Liu
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Wenchen Gong
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Ling Liu
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353 Tianjin, China
| | - Jiao Zhao
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Qian Wang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Nan Song
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Tong Ge
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Qiushi Guo
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Shanshan Tian
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Tao Zhang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Ju Wang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Xiang Ding
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuquan Yang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoguang Ying
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Jie Yang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Kai Zhang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Yi Zhu
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Zhi Yao
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China.
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353 Tianjin, China.
| | - Lei Shi
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China.
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55
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Ho K, Luo H, Zhu W, Tang Y. Critical role of SMG7 in activation of the ATR-CHK1 axis in response to genotoxic stress. Sci Rep 2021; 11:7502. [PMID: 33820915 PMCID: PMC8021557 DOI: 10.1038/s41598-021-86957-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/15/2021] [Indexed: 11/30/2022] Open
Abstract
CHK1 is a crucial DNA damage checkpoint kinase and its activation, which requires ATR and RAD17, leads to inhibition of DNA replication and cell cycle progression. Recently, we reported that SMG7 stabilizes and activates p53 to induce G1 arrest upon DNA damage; here we show that SMG7 plays a critical role in the activation of the ATR-CHK1 axis. Following genotoxic stress, SMG7-null cells exhibit deficient ATR signaling, indicated by the attenuated phosphorylation of CHK1 and RPA32, and importantly, unhindered DNA replication and fork progression. Through its 14-3-3 domain, SMG7 interacts directly with the Ser635-phosphorylated RAD17 and promotes chromatin retention of the 9-1-1 complex by the RAD17-RFC, an essential step to CHK1 activation. Furthermore, through maintenance of CHK1 activity, SMG7 controls G2-M transition and facilitates orderly cell cycle progression during recovery from replication stress. Taken together, our data reveals SMG7 as an indispensable signaling component in the ATR-CHK1 pathway during genotoxic stress response.
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Affiliation(s)
- Kathleen Ho
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, 47 New Scotland Ave, Albany, NY, 12208, USA
| | - Hongwei Luo
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, 47 New Scotland Ave, Albany, NY, 12208, USA
| | - Wei Zhu
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, 47 New Scotland Ave, Albany, NY, 12208, USA
- Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Yi Tang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, 47 New Scotland Ave, Albany, NY, 12208, USA.
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56
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Frattini C, Promonet A, Alghoul E, Vidal-Eychenie S, Lamarque M, Blanchard MP, Urbach S, Basbous J, Constantinou A. TopBP1 assembles nuclear condensates to switch on ATR signaling. Mol Cell 2021; 81:1231-1245.e8. [PMID: 33503405 DOI: 10.1016/j.molcel.2020.12.049] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/01/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022]
Abstract
ATR checkpoint signaling is crucial for cellular responses to DNA replication impediments. Using an optogenetic platform, we show that TopBP1, the main activator of ATR, self-assembles extensively to yield micrometer-sized condensates. These opto-TopBP1 condensates are functional entities organized in tightly packed clusters of spherical nano-particles. TopBP1 condensates are reversible, occasionally fuse, and co-localize with TopBP1 partner proteins. We provide evidence that TopBP1 condensation is a molecular switch that amplifies ATR activity to phosphorylate checkpoint kinase 1 (Chk1) and slow down replication forks. Single amino acid substitutions of key residues in the intrinsically disordered ATR activation domain disrupt TopBP1 condensation and consequently ATR/Chk1 signaling. In physiologic salt concentration and pH, purified TopBP1 undergoes liquid-liquid phase separation in vitro. We propose that the actuation mechanism of ATR signaling is the assembly of TopBP1 condensates driven by highly regulated multivalent and cooperative interactions.
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Affiliation(s)
- Camilla Frattini
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Alexy Promonet
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Emile Alghoul
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | | | - Marie Lamarque
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | | | - Serge Urbach
- Institut de Génomique Fonctionnelle, CNRS INSERM, Université de Montpellier, Montpellier, France
| | - Jihane Basbous
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
| | - Angelos Constantinou
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
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57
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Chen YJ, Roumeliotis TI, Chang YH, Chen CT, Han CL, Lin MH, Chen HW, Chang GC, Chang YL, Wu CT, Lin MW, Hsieh MS, Wang YT, Chen YR, Jonassen I, Ghavidel FZ, Lin ZS, Lin KT, Chen CW, Sheu PY, Hung CT, Huang KC, Yang HC, Lin PY, Yen TC, Lin YW, Wang JH, Raghav L, Lin CY, Chen YS, Wu PS, Lai CT, Weng SH, Su KY, Chang WH, Tsai PY, Robles AI, Rodriguez H, Hsiao YJ, Chang WH, Sung TY, Chen JS, Yu SL, Choudhary JS, Chen HY, Yang PC, Chen YJ. Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression. Cell 2021; 182:226-244.e17. [PMID: 32649875 DOI: 10.1016/j.cell.2020.06.012] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/13/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022]
Abstract
Lung cancer in East Asia is characterized by a high percentage of never-smokers, early onset and predominant EGFR mutations. To illuminate the molecular phenotype of this demographically distinct disease, we performed a deep comprehensive proteogenomic study on a prospectively collected cohort in Taiwan, representing early stage, predominantly female, non-smoking lung adenocarcinoma. Integrated genomic, proteomic, and phosphoproteomic analysis delineated the demographically distinct molecular attributes and hallmarks of tumor progression. Mutational signature analysis revealed age- and gender-related mutagenesis mechanisms, characterized by high prevalence of APOBEC mutational signature in younger females and over-representation of environmental carcinogen-like mutational signatures in older females. A proteomics-informed classification distinguished the clinical characteristics of early stage patients with EGFR mutations. Furthermore, integrated protein network analysis revealed the cellular remodeling underpinning clinical trajectories and nominated candidate biomarkers for patient stratification and therapeutic intervention. This multi-omic molecular architecture may help develop strategies for management of early stage never-smoker lung adenocarcinoma.
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Affiliation(s)
- Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Theodoros I Roumeliotis
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, UK
| | - Ya-Hsuan Chang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Ching-Tai Chen
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
| | - Miao-Hsia Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Huei-Wen Chen
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Gee-Chen Chang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yih-Leong Chang
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chen-Tu Wu
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Mong-Wei Lin
- Division of Thoracic Surgery, Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Min-Shu Hsieh
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Tai Wang
- National Applied Research Laboratories, National Center for High-performance Computing, Hsinchu, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Inge Jonassen
- Computational Biology Unit (CBU), Informatics Department, University of Bergen, Bergen, Norway
| | | | - Ze-Shiang Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Kuen-Tyng Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ching-Wen Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Yuan Sheu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chen-Ting Hung
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | | | - Hao-Chin Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ta-Chi Yen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yi-Wei Lin
- Division of Thoracic Surgery, Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Jen-Hung Wang
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Lovely Raghav
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan; Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Bioinformatics Program, Taiwan International Graduate Program, Hsinchu, Taiwan
| | - Chien-Yu Lin
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Yan-Si Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Pei-Shan Wu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chi-Ting Lai
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Hung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Pang-Yan Tsai
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yi-Jing Hsiao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Hsin Chang
- Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica, Taipei, Taiwan.
| | - Jin-Shing Chen
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan.
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Jyoti S Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, UK.
| | - Hsuan-Yu Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan; Ph.D. Program in Microbial Genomics, National Chung Hsing University, Taichung, Taiwan.
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University, Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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58
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Feng H, Lu J, Song X, Thongkum A, Zhang F, Lou L, Reizes O, Almasan A, Gong Z. CK2 kinase-mediated PHF8 phosphorylation controls TopBP1 stability to regulate DNA replication. Nucleic Acids Res 2020; 48:10940-10952. [PMID: 33010150 PMCID: PMC7641741 DOI: 10.1093/nar/gkaa756] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 11/12/2022] Open
Abstract
ATR functions as a master regulator of the DNA-damage response. ATR activation requires the ATR activator, topoisomerase IIβ-binding protein 1 (TopBP1). However, the underlying mechanism of TopBP1 regulation and how its regulation affects DNA replication remain unknown. Here, we report a specific interaction between TopBP1 and the histone demethylase PHF8. The TopBP1/PHF8 interaction is mediated by the BRCT 7+8 domain of TopBP1 and phosphorylation of PHF8 at Ser854. This interaction is cell-cycle regulated and phosphorylation-dependent. PHF8 is phosphorylated by CK2, which regulates binding of PHF8 to TopBP1. Importantly, PHF8 regulates TopBP1 protein level by preventing its ubiquitination and degradation mediated by the E3 ligase UBR5. Interestingly, PHF8pS854 is likely to contribute to regulation of TopBP1 stability and DNA replication checkpoint. Further, both TopBP1 and PHF8 are required for efficient replication fork restart. Together, these data identify PHF8 as a TopBP1-binding protein and provide mechanistic insight into how PHF8 regulates TopBP1 stability to maintain DNA replication.
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Affiliation(s)
- Haihua Feng
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Jingchen Lu
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA.,Department of Medical Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaotian Song
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Angkana Thongkum
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Fan Zhang
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Lihong Lou
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Ofer Reizes
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Alexandru Almasan
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Zihua Gong
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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59
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Rainey MD, Bennett D, O’Dea R, Zanchetta ME, Voisin M, Seoighe C, Santocanale C. ATR Restrains DNA Synthesis and Mitotic Catastrophe in Response to CDC7 Inhibition. Cell Rep 2020; 32:108096. [DOI: 10.1016/j.celrep.2020.108096] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/19/2020] [Accepted: 08/10/2020] [Indexed: 12/31/2022] Open
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60
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Memisoglu G, Lanz MC, Eapen VV, Jordan JM, Lee K, Smolka MB, Haber JE. Mec1 ATR Autophosphorylation and Ddc2 ATRIP Phosphorylation Regulates DNA Damage Checkpoint Signaling. Cell Rep 2020; 28:1090-1102.e3. [PMID: 31340146 DOI: 10.1016/j.celrep.2019.06.068] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 02/21/2019] [Accepted: 06/18/2019] [Indexed: 11/26/2022] Open
Abstract
In budding yeast, a single DNA double-strand break (DSB) triggers the activation of Mec1ATR-dependent DNA damage checkpoint. After about 12 h, cells turn off the checkpoint signaling and adapt despite the persistence of the DSB. We report that the adaptation involves the autophosphorylation of Mec1 at site S1964. A non-phosphorylatable mec1-S1964A mutant causes cells to arrest permanently in response to a single DSB without affecting the initial kinase activity of Mec1. Autophosphorylation of S1964 is dependent on Ddc1Rad9 and Dpb11TopBP1, and it correlates with the timing of adaptation. We also report that Mec1's binding partner, Ddc2ATRIP, is an inherently stable protein that is degraded specifically upon DNA damage. Ddc2 is regulated extensively through phosphorylation, which, in turn, regulates the localization of the Mec1-Ddc2 complex to DNA lesions. Taken together, these results suggest that checkpoint response is regulated through the autophosphorylation of Mec1 kinase and through the changes in Ddc2 abundance and phosphorylation.
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Affiliation(s)
- Gonen Memisoglu
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Michael C Lanz
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Vinay V Eapen
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jacqueline M Jordan
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Kihoon Lee
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA; Seegene, Inc., Ogeum-ro, Songpa-gu, Seoul 05548, Korea
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA.
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61
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Lam FC, Kong YW, Huang Q, Vu Han TL, Maffa AD, Kasper EM, Yaffe MB. BRD4 prevents the accumulation of R-loops and protects against transcription-replication collision events and DNA damage. Nat Commun 2020; 11:4083. [PMID: 32796829 PMCID: PMC7428008 DOI: 10.1038/s41467-020-17503-y] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
Proper chromatin function and maintenance of genomic stability depends on spatiotemporal coordination between the transcription and replication machinery. Loss of this coordination can lead to DNA damage from increased transcription-replication collision events. We report that deregulated transcription following BRD4 loss in cancer cells leads to the accumulation of RNA:DNA hybrids (R-loops) and collisions with the replication machinery causing replication stress and DNA damage. Whole genome BRD4 and γH2AX ChIP-Seq with R-loop IP qPCR reveals that BRD4 inhibition leads to accumulation of R-loops and DNA damage at a subset of known BDR4, JMJD6, and CHD4 co-regulated genes. Interference with BRD4 function causes transcriptional downregulation of the DNA damage response protein TopBP1, resulting in failure to activate the ATR-Chk1 pathway despite increased replication stress, leading to apoptotic cell death in S-phase and mitotic catastrophe. These findings demonstrate that inhibition of BRD4 induces transcription-replication conflicts, DNA damage, and cell death in oncogenic cells.
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Affiliation(s)
- Fred C Lam
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA.
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA.
- Faculty of Health Sciences, Division of Neurosurgery, Hamilton General Hospital, McMaster University, 237 Barton St E, Hamilton, ON, L8L 2X2, Canada.
| | - Yi Wen Kong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA
| | - Qiuying Huang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA
| | - Tu-Lan Vu Han
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA
| | - Amanda D Maffa
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA
| | - Ekkehard M Kasper
- Faculty of Health Sciences, Division of Neurosurgery, Hamilton General Hospital, McMaster University, 237 Barton St E, Hamilton, ON, L8L 2X2, Canada
| | - Michael B Yaffe
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA.
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA.
- Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Beth Israel Deaconess Medical Center, Department of Surgery, Harvard Medical School, Boston, MA, 02215, USA.
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62
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Ito SS, Nakagawa Y, Matsubayashi M, Sakaguchi YM, Kobashigawa S, Matsui TK, Nanaura H, Nakanishi M, Kitayoshi F, Kikuchi S, Kajihara A, Tamaki S, Sugie K, Kashino G, Takahashi A, Hasegawa M, Mori E, Kirita T. Inhibition of the ATR kinase enhances 5-FU sensitivity independently of nonhomologous end-joining and homologous recombination repair pathways. J Biol Chem 2020; 295:12946-12961. [PMID: 32675286 DOI: 10.1074/jbc.ra120.013726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/13/2020] [Indexed: 10/23/2022] Open
Abstract
The anticancer agent 5-fluorouracil (5-FU) is cytotoxic and often used to treat various cancers. 5-FU is thought to inhibit the enzyme thymidylate synthase, which plays a role in nucleotide synthesis and has been found to induce single- and double-strand DNA breaks. ATR Ser/Thr kinase (ATR) is a principal kinase in the DNA damage response and is activated in response to UV- and chemotherapeutic drug-induced DNA replication stress, but its role in cellular responses to 5-FU is unclear. In this study, we examined the effect of ATR inhibition on 5-FU sensitivity of mammalian cells. Using immunoblotting, we found that 5-FU treatment dose-dependently induced the phosphorylation of ATR at the autophosphorylation site Thr-1989 and thereby activated its kinase. Administration of 5-FU with a specific ATR inhibitor remarkably decreased cell survival, compared with 5-FU treatment combined with other major DNA repair kinase inhibitors. Of note, the ATR inhibition enhanced induction of DNA double-strand breaks and apoptosis in 5-FU-treated cells. Using gene expression analysis, we found that 5-FU induced the activation of the intra-S cell-cycle checkpoint. Cells lacking BRCA2 were sensitive to 5-FU in the presence of ATR inhibitor. Moreover, ATR inhibition enhanced the efficacy of the 5-FU treatment, independently of the nonhomologous end-joining and homologous recombination repair pathways. These findings suggest that ATR could be a potential therapeutic target in 5-FU-based chemotherapy.
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Affiliation(s)
- Soichiro S Ito
- Department of Oral and Maxillofacial Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Yosuke Nakagawa
- Department of Oral and Maxillofacial Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Masaya Matsubayashi
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Nara, Japan
| | - Yoshihiko M Sakaguchi
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Nara, Japan
| | - Shinko Kobashigawa
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Nara, Japan
| | - Takeshi K Matsui
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Nara, Japan; Department of Neurology, Nara Medical University, Kashihara, Nara, Japan
| | - Hitoki Nanaura
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Nara, Japan; Department of Neurology, Nara Medical University, Kashihara, Nara, Japan
| | - Mari Nakanishi
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Nara, Japan
| | - Fumika Kitayoshi
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Nara, Japan
| | - Sotaro Kikuchi
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Nara, Japan
| | - Atsuhisa Kajihara
- Department of Oral and Maxillofacial Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Shigehiro Tamaki
- Department of Oral and Maxillofacial Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Kazuma Sugie
- Department of Neurology, Nara Medical University, Kashihara, Nara, Japan
| | - Genro Kashino
- Radioisotope Research Center, Nara Medical University, Kashihara, Nara, Japan
| | | | - Masatoshi Hasegawa
- Department of Radiation Oncology, Nara Medical University, Kashihara, Nara, Japan
| | - Eiichiro Mori
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Nara, Japan.
| | - Tadaaki Kirita
- Department of Oral and Maxillofacial Surgery, Nara Medical University, Kashihara, Nara, Japan.
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63
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Zheng T, Zhou H, Li X, Peng D, Yang Y, Zeng Y, Liu H, Ren J, Zhao Y. RBMX is required for activation of ATR on repetitive DNAs to maintain genome stability. Cell Death Differ 2020; 27:3162-3176. [PMID: 32494026 DOI: 10.1038/s41418-020-0570-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 01/11/2023] Open
Abstract
ATR is a master regulator of cell response to replication stress. Adequate activation of ATR is essential for preventing genome aberrance induced by replication defect. However, the mechanism underlying ATR activation is not fully understood. Here, we identify that RBMX is an ssDNA binding protein that orchestrates a novel pathway to activate ATR. Using super-resolution STORM, we observe that RBMX and RPA bind to adjacent but nonoverlapping sites on ssDNA in response to replication stress. RBMX then binds to and facilitates positioning of TopBP1, which activates nearby ATR associated with RPA. In addition, ATR activation by ssDNA-RBMX-TopBP1 is independent of ssDNA-dsDNA junction and 9-1-1 complex. ChIP-seq analysis reveals that RBMX/RPA are highly enriched on repetitive DNAs, which are considered as fragile sites with high replication stress. RBMX depletion leads to defective localization of TopBP1 to replication stressed sites and inadequate activation of ATR. Furthermore, cells with deficient RBMX demonstrate replication defect, leading to formation of micronuclei and a high rate of sister-chromatin exchange, indicative of genome instability. Together, the results identify a new ssDNA-RBMX-TopBP1 pathway that is specifically required for activation of ATR on repetitive DNAs. Therefore, RBMX is a key factor to ensure genome stability during replication.
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Affiliation(s)
- Tian Zheng
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Haoxian Zhou
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaocui Li
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Di Peng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Yiding Yang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yanru Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Haiying Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jian Ren
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China. .,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China.
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64
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Lee JW, Ratnakumar K, Hung KF, Rokunohe D, Kawasumi M. Deciphering UV-induced DNA Damage Responses to Prevent and Treat Skin Cancer. Photochem Photobiol 2020; 96:478-499. [PMID: 32119110 DOI: 10.1111/php.13245] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/11/2020] [Indexed: 12/11/2022]
Abstract
Ultraviolet (UV) radiation is among the most prevalent environmental factors that influence human health and disease. Even 1 h of UV irradiation extensively damages the genome. To cope with resulting deleterious DNA lesions, cells activate a multitude of DNA damage response pathways, including DNA repair. Strikingly, UV-induced DNA damage formation and repair are affected by chromatin state. When cells enter S phase with these lesions, a distinct mutation signature is created via error-prone translesion synthesis. Chronic UV exposure leads to high mutation burden in skin and consequently the development of skin cancer, the most common cancer in the United States. Intriguingly, UV-induced oxidative stress has opposing effects on carcinogenesis. Elucidating the molecular mechanisms of UV-induced DNA damage responses will be useful for preventing and treating skin cancer with greater precision. Excitingly, recent studies have uncovered substantial depth of novel findings regarding the molecular and cellular consequences of UV irradiation. In this review, we will discuss updated mechanisms of UV-induced DNA damage responses including the ATR pathway, which maintains genome integrity following UV irradiation. We will also present current strategies for preventing and treating nonmelanoma skin cancer, including ATR pathway inhibition for prevention and photodynamic therapy for treatment.
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Affiliation(s)
- Jihoon W Lee
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
| | - Kajan Ratnakumar
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
| | - Kai-Feng Hung
- Division of Translational Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Dentistry, National Yang-Ming University, Taipei, Taiwan
| | - Daiki Rokunohe
- Department of Dermatology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Masaoki Kawasumi
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
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65
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Wang H, Cao Q, Zhao Q, Arfan M, Liu W. Mechanisms used by DNA MMR system to cope with Cadmium-induced DNA damage in plants. CHEMOSPHERE 2020; 246:125614. [PMID: 31883478 DOI: 10.1016/j.chemosphere.2019.125614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 05/27/2023]
Abstract
Cadmium (Cd) is found widely in soil and is severely toxic for plants, causing oxidative damage in plant cells because of its heavy metal characteristics. The DNA damage response (DDR) is triggered in plants to cope with the Cd stress. The DNA mismatch repair (MMR) system known for its mismatch repair function determines DDR, as mispairs are easily generated by a translesional synthesis under Cd-induced genomic instability. Cd-induced mismatches are recognized by three heterodimeric complexes including MutSα (MSH2/MSH6), MutSβ (MSH2/MSH3), and MutSγ (MSH2/MSH7). MutLα (MLH1/PMS1), PCNA/RFC, EXO1, DNA polymerase δ and DNA ligase participate in mismatch repair in turn. Meanwhile, ATR is preferentially activated by MSH2 to trigger DDR including the regulation of the cell cycle, endoreduplication, cell death, and recruitment of other DNA repair, which enhances plant tolerance to Cd. However, plants with deficient MutS will bypass MMR-mediated DDR and release the multiple-effect MLH1 from requisition of the MMR system, which leads to weak tolerance to Cd in plants. In this review, we systematically illustrate how the plant DNA MMR system works in a Cd-induced DDR, and how MMR genes regulate plant tolerance to Cd. Additionally, we also reviewed multiple epigenetic regulation systems acting on MMR genes under stress.
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Affiliation(s)
- Hetong Wang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Shenyang, 110044, PR China.
| | - Qijiang Cao
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Shenyang, 110044, PR China.
| | - Qiang Zhao
- Agricultural College, Shenyang Agricultural University, Shenyang, 110866, PR China.
| | - Muhammad Arfan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China.
| | - Wan Liu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China.
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66
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Makinwa Y, Musich PR, Zou Y. Phosphorylation-Dependent Pin1 Isomerization of ATR: Its Role in Regulating ATR's Anti-apoptotic Function at Mitochondria, and the Implications in Cancer. Front Cell Dev Biol 2020; 8:281. [PMID: 32426354 PMCID: PMC7203486 DOI: 10.3389/fcell.2020.00281] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/31/2020] [Indexed: 12/11/2022] Open
Abstract
Peptidyl-prolyl isomerization is an important post-translational modification of protein because proline is the only amino acid that can stably exist as cis and trans, while other amino acids are in the trans conformation in protein backbones. This makes prolyl isomerization a unique mechanism for cells to control many cellular processes. Isomerization is a rate-limiting process that requires a peptidyl-prolyl cis/trans isomerase (PPIase) to overcome the energy barrier between cis and trans isomeric forms. Pin1, a key PPIase in the cell, recognizes a phosphorylated Ser/Thr-Pro motif to catalyze peptidyl-prolyl isomerization in proteins. The significance of the phosphorylation-dependent Pin1 activity was recently highlighted for isomerization of ATR (ataxia telangiectasia- and Rad3-related). ATR, a PIKK protein kinase, plays a crucial role in DNA damage responses (DDR) by phosphorylating hundreds of proteins. ATR can form cis or trans isomers in the cytoplasm depending on Pin1 which isomerizes cis-ATR to trans-ATR. Trans-ATR functions primarily in the nucleus. The cis-ATR, containing an exposed BH3 domain, is anti-apoptotic at mitochondria by binding to tBid, preventing activation of pro-apoptotic Bax. Given the roles of apoptosis in many human diseases, particularly cancer, we propose that cytoplasmic cis-ATR enables cells to evade apoptosis, thus addicting cancer cells to cis-ATR formation for survival. But in normal DDR, a predominance of trans-ATR in the nucleus coordinates with a minimal level of cytoplasmic cis-ATR to promote DNA repair while preventing cell death; however, cells can die when DNA repair fails. Therefore, a delicate balance/equilibrium of the levels of cis- and trans-ATR is required to ensure the cellular homeostasis. In this review, we make a case that this anti-apoptotic role of cis-ATR supports oncogenesis, while Pin1 that drives the formation of trans-ATR suppresses tumor growth. We offer a potential, novel target that can be specifically targeted in cancer cells, without killing normal cells, to significantly reduce the adverse effects usually seen in cancer treatment. We also raise important issues regarding the roles of phosphorylation-dependent Pin1 isomerization of ATR in diseases and propose areas of future studies that would shed more understanding on this important cellular mechanism.
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Affiliation(s)
- Yetunde Makinwa
- Department of Cancer Biology, University of Toledo College of Medicine, Toledo, OH, United States
| | - Phillip R Musich
- Department of Biomedical Sciences, JH Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Yue Zou
- Department of Cancer Biology, University of Toledo College of Medicine, Toledo, OH, United States.,Department of Biomedical Sciences, JH Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
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67
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Abe Y, Hirano H, Shoji H, Tada A, Isoyama J, Kakudo A, Gunji D, Honda K, Boku N, Adachi J, Tomonaga T. Comprehensive characterization of the phosphoproteome of gastric cancer from endoscopic biopsy specimens. Theranostics 2020; 10:2115-2129. [PMID: 32089736 PMCID: PMC7019165 DOI: 10.7150/thno.37623] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 12/09/2019] [Indexed: 12/26/2022] Open
Abstract
Rationale: Cancer phosphoproteomics can provide insights regarding kinases that can be targeted for therapeutic applications. Monitoring the phosphoproteomics in cancer is expected to play a key role in optimizing treatments with kinase inhibitors. Clinical phosphoproteomics in surgical tissues and patient-derived models has been studied intensively. However, the reported data may not accurately reflect the phosphosignaling status in patients due to the effect of ischemia occurring during surgery or changes in the characteristics of cancer cells when establishing the models. In contrast, endoscopic biopsies have an advantage for clinical phosphoproteomics because they can be rapidly cryo-preserved. We aimed to develop a highly sensitive method for phosphoproteomics in endoscopic biopsies of gastric cancer. Methods: Three tumor biopsies and three normal gastric biopsies were obtained by endoscopy at one time, and subjected to our optimized phosphoproteomics. Phosphopeptides were enriched with an immobilized metal affinity chromatography, and labeled with Tandem Mass Tag reagent. Quantified phosphosites were compared between the pairs of tumor/normal biopsies within same patient. Cancer-specific activated pathways and kinases were identified by pathway enrichment analysis and kinase-substrate enrichment analysis. Results: Our protocol enabled the identification of more than 10,000 class 1 phosphosites from endoscopic biopsies. A comparison between samples from cancer tissue and normal mucosa demonstrated differences in the phosphosignaling, including biomarkers of response to DNA damage. Finally, cancer-specific activation of DNA damage response signaling was validated by additional phosphoproteomics of other patients and western blotting of gastric cancer/normal cells. Conclusion: In summary, our pioneering approach will facilitate more accurate clinical phosphoproteomics in endoscopic biopsies, which can be applied to monitor the activities of therapeutic kinases and, ultimately, can be a useful tool to precision medicine.
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68
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Sun Y, McCorvie TJ, Yates LA, Zhang X. Structural basis of homologous recombination. Cell Mol Life Sci 2020; 77:3-18. [PMID: 31748913 PMCID: PMC6957567 DOI: 10.1007/s00018-019-03365-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/10/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022]
Abstract
Homologous recombination (HR) is a pathway to faithfully repair DNA double-strand breaks (DSBs). At the core of this pathway is a DNA recombinase, which, as a nucleoprotein filament on ssDNA, pairs with homologous DNA as a template to repair the damaged site. In eukaryotes Rad51 is the recombinase capable of carrying out essential steps including strand invasion, homology search on the sister chromatid and strand exchange. Importantly, a tightly regulated process involving many protein factors has evolved to ensure proper localisation of this DNA repair machinery and its correct timing within the cell cycle. Dysregulation of any of the proteins involved can result in unchecked DNA damage, leading to uncontrolled cell division and cancer. Indeed, many are tumour suppressors and are key targets in the development of new cancer therapies. Over the past 40 years, our structural and mechanistic understanding of homologous recombination has steadily increased with notable recent advancements due to the advances in single particle cryo electron microscopy. These have resulted in higher resolution structural models of the signalling proteins ATM (ataxia telangiectasia mutated), and ATR (ataxia telangiectasia and Rad3-related protein), along with various structures of Rad51. However, structural information of the other major players involved, such as BRCA1 (breast cancer type 1 susceptibility protein) and BRCA2 (breast cancer type 2 susceptibility protein), has been limited to crystal structures of isolated domains and low-resolution electron microscopy reconstructions of the full-length proteins. Here we summarise the current structural understanding of homologous recombination, focusing on key proteins in recruitment and signalling events as well as the mediators for the Rad51 recombinase.
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Affiliation(s)
- Yueru Sun
- Section of Structural Biology, Department of Infectious Diseases, Imperial College, London, SW7 2AZ, UK
| | - Thomas J McCorvie
- Section of Structural Biology, Department of Infectious Diseases, Imperial College, London, SW7 2AZ, UK
| | - Luke A Yates
- Section of Structural Biology, Department of Infectious Diseases, Imperial College, London, SW7 2AZ, UK
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Infectious Diseases, Imperial College, London, SW7 2AZ, UK.
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69
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Chauhan N, Wagh V, Joshi P, Jariyal H. ATM and ATR checkpoint kinase pathways: A concise review. ADVANCES IN HUMAN BIOLOGY 2020. [DOI: 10.4103/aihb.aihb_78_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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70
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β-HPV 8E6 Attenuates ATM and ATR Signaling in Response to UV Damage. Pathogens 2019; 8:pathogens8040267. [PMID: 31779191 PMCID: PMC6963835 DOI: 10.3390/pathogens8040267] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/13/2019] [Accepted: 11/22/2019] [Indexed: 12/12/2022] Open
Abstract
Given the high prevalence of cutaneous genus beta human papillomavirus (β-HPV) infections, it is important to understand how they manipulate their host cells. This is particularly true for cellular responses to UV damage, since our skin is continually exposed to UV. The E6 protein from β-genus HPV (β-HPV E6) decreases the abundance of two essential UV-repair kinases (ATM and ATR). Although β-HPV E6 reduces their availability, the impact on downstream signaling events is unclear. We demonstrate that β-HPV E6 decreases ATM and ATR activation. This inhibition extended to XPA, an ATR target necessary for UV repair, lowering both its phosphorylation and accumulation. β-HPV E6 also hindered POLη accumulation and foci formation, critical steps in translesion synthesis. ATM’s phosphorylation of BRCA1 is also attenuated by β-HPV E6. While there was a striking decrease in phosphorylation of direct ATM/ATR targets, events further down the cascade were not reduced. In summary, despite being incomplete, β-HPV 8E6’s hindrance of ATM/ATR has functional consequences.
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71
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Hutcherson RJ, Kemp MG. ATR kinase inhibition sensitizes quiescent human cells to the lethal effects of cisplatin but increases mutagenesis. Mutat Res 2019; 816-818:111678. [PMID: 31557599 PMCID: PMC6905468 DOI: 10.1016/j.mrfmmm.2019.111678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/19/2019] [Accepted: 09/15/2019] [Indexed: 12/25/2022]
Abstract
The ATR protein kinase is known to protect cells from DNA damage induced during the replicative phase of the cell cycle. Small molecule ATR kinase inhibitors have therefore been developed to improve the effectiveness of DNA damage-based chemotherapy regimens aimed at killing rapidly proliferating tumor cells. However, whether ATR functions in a similar manner in non-replicating cells has not been examined and is important considering the fact that most cells in the body, including cancer stem cells in solid tumors, normally reside in either a quiescent or differentiated non-replicating state. Using cultured human cell lines maintained in a quiescent or slowly growing state in vitro, ATR was found to be activated following treatment with the common anti-cancer drug cisplatin in a manner dependent on the nucleotide excision repair (NER) system. Moreover, treatment with the ATR kinase inhibitors VE-821 and AZD6738 enhanced quiescent cell killing and apoptotic signaling induced by cisplatin. However, ATR kinase inhibition in quiescent cells treated with a low concentration of cisplatin also elevated the level of mutagenesis at the hypoxanthine phosphoribosyltransferase locus and resulted in increased levels of PCNA mono-ubiquitination. These results suggest that the excision gaps generated by NER may require a greater utilization of potentially mutagenic translesion synthesis polymerases in the absence of ATR kinase function. Thus, though ATR kinase inhibitors can aid in the killing of cisplatin-treated quiescent cells, such treatments may also result in a greater reliance on alternative mutagenic DNA polymerases to complete the repair of cisplatin-DNA adducts.
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Affiliation(s)
- Rebekah J Hutcherson
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, United States
| | - Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, United States.
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72
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Shaj K, Hutcherson RJ, Kemp MG. ATR Kinase Activity Limits Mutagenesis and Promotes the Clonogenic Survival of Quiescent Human Keratinocytes Exposed to UVB Radiation. Photochem Photobiol 2019; 96:105-112. [PMID: 31554014 DOI: 10.1111/php.13164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/04/2019] [Indexed: 01/03/2023]
Abstract
The ATR protein kinase has well-described roles in maintaining genomic integrity during the DNA synthesis phase of the cell cycle. However, ATR function in cells that are not actively replicating DNA remains largely unexplored. Using HaCaT and telomerase-immortalized human keratinocytes maintained in a confluent, nonreplicating state in vitro, ATR was found to be robustly activated in response to UVB radiation in a manner dependent on the nucleotide excision repair factor and DNA translocase XPB. Inhibition of ATR kinase activity under these conditions negatively impacted acute cell survival and cytotoxicity and severely inhibited the ability of UVB-irradiated HaCaT keratinocytes to proliferate upon stimulation with growth factors. Furthermore, ATR kinase inhibition in quiescent HaCaT keratinocytes potentiated UVB mutagenesis at the hypoxanthine phosphoribosyltransferase locus. Though ATR inhibition did not impact the rate of removal of cyclobutane pyrimidine dimers from genomic DNA, elevated levels of PCNA mono-ubiquitination and chromatin-associated PCNA and RPA indicate that excision gap-filling synthesis was altered in the absence of ATR signaling. These results indicate that the ATR kinase plays important roles in preventing mutagenesis and in promoting the proliferative potential of quiescent keratinocytes exposed to UVB radiation.
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Affiliation(s)
- Kavya Shaj
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, OH
| | - Rebekah J Hutcherson
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, OH
| | - Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, OH
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73
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Wengner AM, Siemeister G, Lücking U, Lefranc J, Wortmann L, Lienau P, Bader B, Bömer U, Moosmayer D, Eberspächer U, Golfier S, Schatz CA, Baumgart SJ, Haendler B, Lejeune P, Schlicker A, von Nussbaum F, Brands M, Ziegelbauer K, Mumberg D. The Novel ATR Inhibitor BAY 1895344 Is Efficacious as Monotherapy and Combined with DNA Damage-Inducing or Repair-Compromising Therapies in Preclinical Cancer Models. Mol Cancer Ther 2019; 19:26-38. [PMID: 31582533 DOI: 10.1158/1535-7163.mct-19-0019] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 07/05/2019] [Accepted: 09/27/2019] [Indexed: 11/16/2022]
Abstract
The DNA damage response (DDR) secures the integrity of the genome of eukaryotic cells. DDR deficiencies can promote tumorigenesis but concurrently may increase dependence on alternative repair pathways. The ataxia telangiectasia and Rad3-related (ATR) kinase plays a central role in the DDR by activating essential signaling pathways of DNA damage repair. Here, we studied the effect of the novel selective ATR kinase inhibitor BAY 1895344 on tumor cell growth and viability. Potent antiproliferative activity was demonstrated in a broad spectrum of human tumor cell lines. BAY 1895344 exhibited strong monotherapy efficacy in cancer xenograft models that carry DNA damage repair deficiencies. The combination of BAY 1895344 with DNA damage-inducing chemotherapy or external beam radiotherapy (EBRT) showed synergistic antitumor activity. Combination treatment with BAY 1895344 and DDR inhibitors achieved strong synergistic antiproliferative activity in vitro, and combined inhibition of ATR and PARP signaling using olaparib demonstrated synergistic antitumor activity in vivo Furthermore, the combination of BAY 1895344 with the novel, nonsteroidal androgen receptor antagonist darolutamide resulted in significantly improved antitumor efficacy compared with respective single-agent treatments in hormone-dependent prostate cancer, and addition of EBRT resulted in even further enhanced antitumor efficacy. Thus, the ATR inhibitor BAY 1895344 may provide new therapeutic options for the treatment of cancers with certain DDR deficiencies in monotherapy and in combination with DNA damage-inducing or DNA repair-compromising cancer therapies by improving their efficacy.
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Affiliation(s)
- Antje M Wengner
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany.
| | | | - Ulrich Lücking
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Julien Lefranc
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Lars Wortmann
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Philip Lienau
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Benjamin Bader
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Ulf Bömer
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Dieter Moosmayer
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Uwe Eberspächer
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Sven Golfier
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | | | - Simon J Baumgart
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Bernard Haendler
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Pascale Lejeune
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Andreas Schlicker
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | | | - Michael Brands
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Karl Ziegelbauer
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
| | - Dominik Mumberg
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany
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74
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Landsverk HB, Sandquist LE, Sridhara SC, Rødland GE, Sabino JC, de Almeida SF, Grallert B, Trinkle-Mulcahy L, Syljuåsen RG. Regulation of ATR activity via the RNA polymerase II associated factors CDC73 and PNUTS-PP1. Nucleic Acids Res 2019; 47:1797-1813. [PMID: 30541148 PMCID: PMC6393312 DOI: 10.1093/nar/gky1233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/23/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
Ataxia telangiectasia mutated and Rad3-related (ATR) kinase is a key factor activated by DNA damage and replication stress. An alternative pathway for ATR activation has been proposed to occur via stalled RNA polymerase II (RNAPII). However, how RNAPII might signal to activate ATR remains unknown. Here, we show that ATR signaling is increased after depletion of the RNAPII phosphatase PNUTS-PP1, which dephosphorylates RNAPII in its carboxy-terminal domain (CTD). High ATR signaling was observed in the absence and presence of ionizing radiation, replication stress and even in G1, but did not correlate with DNA damage or RPA chromatin loading. R-loops were enhanced, but overexpression of EGFP-RNaseH1 only slightly reduced ATR signaling after PNUTS depletion. However, CDC73, which interacted with RNAPII in a phospho-CTD dependent manner, was required for the high ATR signaling, R-loop formation and for activation of the endogenous G2 checkpoint after depletion of PNUTS. In addition, ATR, RNAPII and CDC73 co-immunoprecipitated. Our results suggest a novel pathway involving RNAPII, CDC73 and PNUTS-PP1 in ATR signaling and give new insight into the diverse functions of ATR.
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Affiliation(s)
- Helga B Landsverk
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Lise E Sandquist
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sreerama C Sridhara
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Gro Elise Rødland
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - João C Sabino
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Sérgio F de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Beata Grallert
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Randi G Syljuåsen
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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75
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Wang P, Guan D, Zhang XP, Liu F, Wang W. Modeling the regulation of p53 activation by HIF-1 upon hypoxia. FEBS Lett 2019; 593:2596-2611. [PMID: 31282018 DOI: 10.1002/1873-3468.13525] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/27/2019] [Accepted: 06/27/2019] [Indexed: 12/19/2022]
Abstract
As a famous tumor suppressor, p53 is also activated under hypoxic conditions. Hypoxia-inducuble factor 1, HIF-1, is involved in the activation of p53 upon hypoxia. However, how p53 is modulated by the HIF-1 pathway to decide cell fate is less understood. In this work, we developed a network model including p53 and HIF-1 pathways to clarify the mechanism of cell fate decision in response to hypoxia. We found that HIF-1α and p53 are activated under different conditions. Under moderate hypoxia, HIF-1α is activated to induce glycolysis or angiogenesis, and promotes partial accumulation of p53 by inducing PNUTS. Under severe hypoxia, p53 rises to high levels due to ATR-dependent stabilization and promotes Mdm2-dependent HIF-1α degradation. As a result, fully activated p53 triggers apoptosis. Of note, competition for p300 between HIF-1α and p53 plays a key role in regulating their transcriptional activities. This work may advance the understanding of the mechanism for p53 regulation by HIF-1 in the hypoxic response.
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Affiliation(s)
- Ping Wang
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, China
| | - Di Guan
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, China
| | - Xiao-Peng Zhang
- Kuang Yaming Honors School, Nanjing University, China.,Institute for Brain Sciences, Nanjing University, China
| | - Feng Liu
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, China.,Institute for Brain Sciences, Nanjing University, China
| | - Wei Wang
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, China.,Institute for Brain Sciences, Nanjing University, China
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76
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Lin YF, Shih HY, Shang ZF, Kuo CT, Guo J, Du C, Lee H, Chen BPC. PIDD mediates the association of DNA-PKcs and ATR at stalled replication forks to facilitate the ATR signaling pathway. Nucleic Acids Res 2019; 46:1847-1859. [PMID: 29309644 PMCID: PMC5829747 DOI: 10.1093/nar/gkx1298] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022] Open
Abstract
The DNA-dependent protein kinase (DNA-PK), consisting of the DNA binding Ku70/80 heterodimer and the catalytic subunit DNA-PKcs, has been well characterized in the non-homologous end-joining mechanism for DNA double strand break (DSB) repair and radiation resistance. Besides playing a role in DSB repair, DNA-PKcs is required for the cellular response to replication stress and participates in the ATR-Chk1 signaling pathway. However, the mechanism through which DNA-PKcs is recruited to stalled replication forks is still unclear. Here, we report that the apoptosis mediator p53-induced protein with a death domain (PIDD) is required to promote DNA-PKcs activity in response to replication stress. PIDD is known to interact with PCNA upon UV-induced replication stress. Our results demonstrate that PIDD is required to recruit DNA-PKcs to stalled replication forks through direct binding to DNA-PKcs at the N’ terminal region. Disruption of the interaction between DNA-PKcs and PIDD not only compromises the ATR association and regulation of DNA-PKcs, but also the ATR signaling pathway, intra-S-phase checkpoint and cellular resistance to replication stress. Taken together, our results indicate that PIDD, but not the Ku heterodimer, mediates the DNA-PKcs activity at stalled replication forks and facilitates the ATR signaling pathway in the cellular response to replication stress.
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Affiliation(s)
- Yu-Fen Lin
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Hung-Ying Shih
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Zeng-Fu Shang
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Ching-Te Kuo
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.,Department of Life Science, National Taiwan University, Taipei 10617, Taiwan, Republic of China
| | - Jiaming Guo
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.,Department of Radiation Medicine, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, People's Republic of China
| | - Chunying Du
- Department of Cancer and Cell Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Hsinyu Lee
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan, Republic of China
| | - Benjamin P C Chen
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
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77
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Fragkos M, Barra V, Egger T, Bordignon B, Lemacon D, Naim V, Coquelle A. Dicer prevents genome instability in response to replication stress. Oncotarget 2019; 10:4407-4423. [PMID: 31320994 PMCID: PMC6633883 DOI: 10.18632/oncotarget.27034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/05/2019] [Indexed: 11/25/2022] Open
Abstract
Dicer, an endoribonuclease best-known for its role in microRNA biogenesis and RNA interference pathway, has been shown to play a role in the DNA damage response and repair of double-stranded DNA breaks (DSBs) in mammalian cells. However, it remains unknown whether Dicer is also important to preserve genome integrity upon replication stress. To address this question, we focused our study on common fragile sites (CFSs), which are susceptible to breakage after replication stress. We show that inhibition of the Dicer pathway leads to an increase in CFS expression upon induction of replication stress and to an accumulation of 53BP1 nuclear bodies, indicating transmission of replication-associated damage. We also show that in absence of a functional Dicer or Drosha, the assembly into nuclear foci of the Fanconi anemia (FA) protein FANCD2 and of the replication and checkpoint factor TopBP1 in response to replication stress is impaired, and the activation of the S-phase checkpoint is defective. Based on these results, we propose that Dicer pre-vents genomic instability after replication stress, by allowing the proper recruitment to stalled forks of proteins that are necessary to maintain replication fork stability and activate the S-phase checkpoint, thus limiting cells from proceeding into mitosis with under-replicated DNA.
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Affiliation(s)
- Michalis Fragkos
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France.,Laboratory of Genetic Instability and Oncogenesis, UMR 8200 CNRS, University Paris-Sud, Gustave Roussy, Villejuif, France.,These authors contributed equally to this work
| | - Viviana Barra
- Laboratory of Genetic Instability and Oncogenesis, UMR 8200 CNRS, University Paris-Sud, Gustave Roussy, Villejuif, France.,These authors contributed equally to this work
| | - Tom Egger
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Benoit Bordignon
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Delphine Lemacon
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France.,Present address: Department of Biochemistry and Molecular Biology, Doisy Research Center, St. Louis, MO, USA
| | - Valeria Naim
- Laboratory of Genetic Instability and Oncogenesis, UMR 8200 CNRS, University Paris-Sud, Gustave Roussy, Villejuif, France.,These authors contributed equally to this work
| | - Arnaud Coquelle
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
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78
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Mladenov E, Fan X, Dueva R, Soni A, Iliakis G. Radiation-dose-dependent functional synergisms between ATM, ATR and DNA-PKcs in checkpoint control and resection in G 2-phase. Sci Rep 2019; 9:8255. [PMID: 31164689 PMCID: PMC6547644 DOI: 10.1038/s41598-019-44771-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/23/2019] [Indexed: 12/31/2022] Open
Abstract
Using data generated with cells exposed to ionizing-radiation (IR) in G2-phase of the cell cycle, we describe dose-dependent interactions between ATM, ATR and DNA-PKcs revealing unknown mechanistic underpinnings for two key facets of the DNA damage response: DSB end-resection and G2-checkpoint activation. At low IR-doses that induce low DSB-numbers in the genome, ATM and ATR regulate epistatically the G2-checkpoint, with ATR at the output-node, interfacing with the cell-cycle predominantly through Chk1. Strikingly, at low IR-doses, ATM and ATR epistatically regulate also resection, and inhibition of either activity fully suppresses resection. At high IR-doses that induce high DSB-numbers in the genome, the tight ATM/ATR coupling relaxes and independent outputs to G2-checkpoint and resection occur. Consequently, both kinases must be inhibited to fully suppress checkpoint activation and resection. DNA-PKcs integrates to the ATM/ATR module by regulating resection at all IR-doses, with defects in DNA-PKcs causing hyper-resection and G2-checkpoint hyper-activation. Notably, hyper-resection is absent from other c-NHEJ mutants. Thus, DNA-PKcs specifically regulates resection and adjusts the activation of the ATM/ATR module. We propose that selected DSBs are shepherd by DNA-PKcs from c-NHEJ to resection-dependent pathways for processing under the regulatory supervision of the ATM/ATR module.
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Affiliation(s)
- Emil Mladenov
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Xiaoxiang Fan
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Rositsa Dueva
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Aashish Soni
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany.
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79
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Ge C, Vilfranc CL, Che L, Pandita RK, Hambarde S, Andreassen PR, Niu L, Olowokure O, Shah S, Waltz SE, Zou L, Wang J, Pandita TK, Du C. The BRUCE-ATR Signaling Axis Is Required for Accurate DNA Replication and Suppression of Liver Cancer Development. Hepatology 2019; 69:2608-2622. [PMID: 30693543 PMCID: PMC6541504 DOI: 10.1002/hep.30529] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/23/2019] [Indexed: 01/10/2023]
Abstract
Replication fork stability during DNA replication is vital for maintenance of genomic stability and suppression of cancer development in mammals. ATR (ataxia-telangiectasia mutated [ATM] and RAD3-related) is a master regulatory kinase that activates the replication stress response to overcome replication barriers. Although many downstream effectors of ATR have been established, the upstream regulators of ATR and the effect of such regulation on liver cancer remain unclear. The ubiquitin conjugase BRUCE (BIR Repeat containing Ubiquitin-Conjugating Enzyme) is a guardian of chromosome integrity and activator of ATM signaling, which promotes DNA double-strand break repair through homologous recombination. Here we demonstrate the functions for BRUCE in ATR activation in vitro and liver tumor suppression in vivo. BRUCE is recruited to induced DNA damage sites. Depletion of BRUCE inhibited multiple ATR-dependent signaling events during replication stress, including activation of ATR itself, phosphorylation of its downstream targets CHK1 and RPA, and the mono-ubiquitination of FANCD2. Consequently, BRUCE deficiency resulted in stalled DNA replication forks and increased firing of new replication origins. The in vivo impact of BRUCE loss on liver tumorigenesis was determined using the hepatocellular carcinoma model induced by genotoxin diethylnitrosamine. Liver-specific knockout of murine Bruce impaired ATR activation and exacerbated inflammation, fibrosis and hepatocellular carcinoma, which exhibited a trabecular architecture, closely resembling human hepatocellular carcinoma (HCC). In humans, the clinical relevance of BRUCE down-regulation in liver disease was found in hepatitis, cirrhosis, and HCC specimens, and deleterious somatic mutations of the Bruce gene was found in human hepatocellular carcinoma in the Cancer Genome Atlas database. Conclusion: These findings establish a BRUCE-ATR signaling axis in accurate DNA replication and suppression of liver cancer in mice and humans and provides a clinically relevant HCC mouse model.
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Affiliation(s)
- Chunmin Ge
- Department of Cancer and Cell Biology, University of Cincinnati, Cincinnati, Ohio 45267
| | | | - Lixiao Che
- Department of Cancer and Cell Biology, University of Cincinnati, Cincinnati, Ohio 45267
| | - Raj K. Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston Texas 77030
| | - Shashank Hambarde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston Texas 77030
| | - Paul R. Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children Hospital Medical Center, Cincinnati, Ohio 45229
| | - Liang Niu
- Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio 45267
| | - Olugbenga Olowokure
- Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio 45267
| | - Shimul Shah
- University of Cincinnati College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267
| | - Susan E. Waltz
- Department of Cancer and Cell Biology, University of Cincinnati, Cincinnati, Ohio 45267
| | - Lee Zou
- Department of Pathology, Massachusetts General Hospital Cancer Center; Harvard Medical School, Charlestown, MA 02129
| | - Jiang Wang
- Department of Pathology, University of Cincinnati, Cincinnati, Ohio 45267
| | - Tej K. Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston Texas 77030
| | - Chunying Du
- Department of Cancer and Cell Biology, University of Cincinnati, Cincinnati, Ohio 45267,Corresponding author: Chunying Du, Ph.D. Phone: (513) 558-4803,
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80
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Tang M, Li Z, Zhang C, Lu X, Tu B, Cao Z, Li Y, Chen Y, Jiang L, Wang H, Wang L, Wang J, Liu B, Xu X, Wang H, Zhu WG. SIRT7-mediated ATM deacetylation is essential for its deactivation and DNA damage repair. SCIENCE ADVANCES 2019; 5:eaav1118. [PMID: 30944854 PMCID: PMC6436926 DOI: 10.1126/sciadv.aav1118] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 02/04/2019] [Indexed: 06/09/2023]
Abstract
The activation of ataxia-telangiectasia mutated (ATM) upon DNA damage involves a cascade of reactions, including acetylation by TIP60 and autophosphorylation. However, how ATM is progressively deactivated after completing DNA damage repair remains obscure. Here, we report that sirtuin 7 (SIRT7)-mediated deacetylation is essential for dephosphorylation and deactivation of ATM. We show that SIRT7, a class III histone deacetylase, interacts with and deacetylates ATM in vitro and in vivo. In response to DNA damage, SIRT7 is mobilized onto chromatin and deacetylates ATM during the late stages of DNA damage response, when ATM is being gradually deactivated. Deacetylation of ATM by SIRT7 is prerequisite for its dephosphorylation by its phosphatase WIP1. Consequently, depletion of SIRT7 or acetylation-mimic mutation of ATM induces persistent ATM phosphorylation and activation, thus leading to impaired DNA damage repair. Together, our findings reveal a previously unidentified role of SIRT7 in regulating ATM activity and DNA damage repair.
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Affiliation(s)
- Ming Tang
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518060, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhiming Li
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518060, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function
| | - Chaohua Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function
| | - Xiaopeng Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518060, China
| | - Bo Tu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function
| | - Ziyang Cao
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518060, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function
| | - Yinglu Li
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518060, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function
| | - Yongcan Chen
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518060, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China
| | - Lu Jiang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function
| | - Hui Wang
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518060, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function
| | - Lina Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function
| | - Jiadong Wang
- Peking University-Tsinghua University Center for Life Sciences, Beijing 100871, China
| | - Baohua Liu
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518060, China
| | - Xingzhi Xu
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518060, China
| | - Haiying Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518060, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China
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81
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Kinase-dead ATR differs from ATR loss by limiting the dynamic exchange of ATR and RPA. Nat Commun 2018; 9:5351. [PMID: 30559436 PMCID: PMC6297235 DOI: 10.1038/s41467-018-07798-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022] Open
Abstract
ATR kinase is activated by RPA-coated single-stranded DNA (ssDNA) to orchestrate DNA damage responses. Here we show that ATR inhibition differs from ATR loss. Mouse model expressing kinase-dead ATR (Atr+/KD), but not loss of ATR (Atr+/−), displays ssDNA-dependent defects at the non-homologous region of X-Y chromosomes during male meiosis leading to sterility, and at telomeres, rDNA, and fragile sites during mitosis leading to lymphocytopenia. Mechanistically, we find that ATR kinase activity is necessary for the rapid exchange of ATR at DNA-damage-sites, which in turn promotes CHK1-phosphorylation. ATR-KD, but not loss of ATR, traps a subset of ATR and RPA on chromatin, where RPA is hyper-phosphorylated by ATM/DNA-PKcs and prevents downstream repair. Consequently, Atr+/KD cells have shorter inter-origin distances and are vulnerable to induced fork collapses, genome instability and mitotic catastrophe. These results reveal mechanistic differences between ATR inhibition and ATR loss, with implications for ATR signaling and cancer therapy. ATR kinase is a key regulator of chromosome integrity. Here the authors by analysing the phenotype of a mouse model expressing a kinase-dead ATR, reveal the effect of ATR inhibition compared to ATR loss and its consequences for meiosis, DNA replication, checkpoint activation and genome instability .
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82
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Byrne BM, Oakley GG. Replication protein A, the laxative that keeps DNA regular: The importance of RPA phosphorylation in maintaining genome stability. Semin Cell Dev Biol 2018; 86:112-120. [PMID: 29665433 DOI: 10.1016/j.semcdb.2018.04.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/30/2018] [Accepted: 04/06/2018] [Indexed: 11/25/2022]
Abstract
The eukaryotic ssDNA-binding protein, Replication protein A (RPA), was first discovered almost three decades ago. Since then, much progress has been made to elucidate the critical roles for RPA in DNA metabolic pathways that help promote genomic stability. The canonical RPA heterotrimer (RPA1-3) is an essential coordinator of DNA metabolism that interacts with ssDNA and numerous protein partners to coordinate its roles in DNA replication, repair, recombination and telomere maintenance. An alternative form of RPA, termed aRPA, is formed by a complex of RPA4 with RPA1 and RPA3. aRPA is expressed differentially in cells compared to canonical RPA and has been shown to inhibit canonical RPA function while allowing for regular maintenance of cell viability. Interestingly, while aRPA is defective in DNA replication and cell cycle progression, it was shown to play a supporting role in nucleotide excision repair and recombination. The binding domains of canonical RPA interact with a growing number of partners involved in numerous genome maintenance processes. The protein interactions of the RPA-ssDNA complex are not only governed by competition between the binding proteins but also by post-translation modifications such as phosphorylation. Phosphorylation of RPA2 is an important post-translational modification of the RPA complex, and is essential for directing context-specific functions of the RPA complex in the DNA damage response. Due to the importance of RPA in cellular metabolism, it was identified as an appealing target for chemotherapeutic drug development that could be used in future cancer treatment regimens.
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Affiliation(s)
- Brendan M Byrne
- University of Nebraska Medical Center Department of Oral Biology, Lincoln NE, USA.
| | - Gregory G Oakley
- University of Nebraska Medical Center Department of Oral Biology, Lincoln NE, USA; Eppley Cancer Center, Omaha NE, USA.
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83
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Yates M, Maréchal A. Ubiquitylation at the Fork: Making and Breaking Chains to Complete DNA Replication. Int J Mol Sci 2018; 19:E2909. [PMID: 30257459 PMCID: PMC6213728 DOI: 10.3390/ijms19102909] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
The complete and accurate replication of the genome is a crucial aspect of cell proliferation that is often perturbed during oncogenesis. Replication stress arising from a variety of obstacles to replication fork progression and processivity is an important contributor to genome destabilization. Accordingly, cells mount a complex response to this stress that allows the stabilization and restart of stalled replication forks and enables the full duplication of the genetic material. This response articulates itself on three important platforms, Replication Protein A/RPA-coated single-stranded DNA, the DNA polymerase processivity clamp PCNA and the FANCD2/I Fanconi Anemia complex. On these platforms, the recruitment, activation and release of a variety of genome maintenance factors is regulated by post-translational modifications including mono- and poly-ubiquitylation. Here, we review recent insights into the control of replication fork stability and restart by the ubiquitin system during replication stress with a particular focus on human cells. We highlight the roles of E3 ubiquitin ligases, ubiquitin readers and deubiquitylases that provide the required flexibility at stalled forks to select the optimal restart pathways and rescue genome stability during stressful conditions.
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Affiliation(s)
- Maïlyn Yates
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
| | - Alexandre Maréchal
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
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84
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Chen MY, Hsu WC, Hsu SC, Yang YS, Chuang TH, Lin WJ, Tan TH, Su YW. PP4 deficiency leads to DNA replication stress that impairs immunoglobulin class switch efficiency. Cell Death Differ 2018; 26:1221-1234. [PMID: 30237510 PMCID: PMC6748143 DOI: 10.1038/s41418-018-0199-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 07/30/2018] [Accepted: 08/27/2018] [Indexed: 01/02/2023] Open
Abstract
The serine/threonine phosphatase PP4 has been implicated in DNA damage repair and cell cycle regulation through its dephosphorylation of specific substrates. We previously showed that PP4 is required for mouse B cell development, germinal center (GC) formation and immunoglobulin (Ig) class switch recombination (CSR). Here, we investigate the mechanisms underlying this requirement and demonstrate that murine PP4-deficient B lymphocytes have a defect in cell proliferation. Strikingly, the DNA damage response pathway that involves ATM/p53 and is linked to cell cycle arrest and impaired cell survival is strongly induced in these mutant B cells. In response to LPS + IL-4, stimuli that trigger IgG1 production, these PP4-deficient B cells show inefficient phosphorylation of ATR, leading to reduced retention of γH2AX-NBS1 complexes at sites of DNA damage, and compromised switching to IgG1. However, beyond the cell proliferation phase, conditional deletion of PP4 under the control of AID/cre completely restores normal IgG1 production in mutant B cell cultures. In vivo, co-deletion of PP4 and p53 by AID/cre partially rescues switching to IgG1 in B cells of mice immunized with TNP-KLH. Our findings establish that PP4 is indispensable for preventing DNA replication stress that could interfere with CSR, thereby promoting antibody switching during the humoral immune response.
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Affiliation(s)
- Ming-Yu Chen
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan
| | - Wei-Chan Hsu
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan
| | - Shu-Ching Hsu
- National Institute of Infectious Diseases and Vaccinology, NHRI, Zhunan, Miaoli County, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medical Research and Development, Chang Bing Show Chwan Memorial Hospital, Chang Hua, Taiwan
| | - Yu-Shao Yang
- National Institute of Infectious Diseases and Vaccinology, NHRI, Zhunan, Miaoli County, Taiwan
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan
| | - Wen-Jye Lin
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan
| | - Tse-Hua Tan
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Yu-Wen Su
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan.
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85
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LIM Protein Ajuba associates with the RPA complex through direct cell cycle-dependent interaction with the RPA70 subunit. Sci Rep 2018; 8:9536. [PMID: 29934626 PMCID: PMC6015067 DOI: 10.1038/s41598-018-27919-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/13/2018] [Indexed: 12/04/2022] Open
Abstract
DNA damage response pathways are essential for genome stability and cell survival. Specifically, the ATR kinase is activated by DNA replication stress. An early event in this activation is the recruitment and phosphorylation of RPA, a single stranded DNA binding complex composed of three subunits, RPA70, RPA32 and RPA14. We have previously shown that the LIM protein Ajuba associates with RPA, and that depletion of Ajuba leads to potent activation of ATR. In this study, we provide evidence that the Ajuba-RPA interaction occurs through direct protein contact with RPA70, and that their association is cell cycle-regulated and is reduced upon DNA replication stress. We propose a model in which Ajuba negatively regulates the ATR pathway by directly interacting with RPA70, thereby preventing inappropriate ATR activation. Our results provide a framework to further our understanding of the mechanism of ATR regulation in human cells in the context of cellular transformation.
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86
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Rauch A, Carlstedt A, Emmerich C, Mustafa AHM, Göder A, Knauer SK, Linnebacher M, Heinzel T, Krämer OH. Survivin antagonizes chemotherapy-induced cell death of colorectal cancer cells. Oncotarget 2018; 9:27835-27850. [PMID: 29963241 PMCID: PMC6021236 DOI: 10.18632/oncotarget.25600] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 05/08/2018] [Indexed: 02/06/2023] Open
Abstract
Irinotecan (CPT-11) and oxaliplatin (L-OHP) are among the most frequently used drugs against colorectal tumors. Therefore, it is important to define the molecular mechanisms that these agents modulate in colon cancer cells. Here we demonstrate that CPT-11 stalls such cells in the G2/M phase of the cell cycle, induces an accumulation of the tumor suppressor p53, the replicative stress/DNA damage marker γH2AX, phosphorylation of the checkpoint kinases ATM and ATR, and an ATR-dependent accumulation of the pro-survival molecule survivin. L-OHP reduces the number of cells in S-phase, stalls cell cycle progression, transiently triggers an accumulation of low levels of γH2AX and phosphorylated checkpoint kinases, and L-OHP suppresses survivin expression at the mRNA and protein levels. Compared to CPT-11, L-OHP is a stronger inducer of caspases and p53-dependent apoptosis. Overexpression and RNAi against survivin reveal that this factor critically antagonizes caspase-dependent apoptosis in cells treated with CPT-11 and L-OHP. We additionally show that L-OHP suppresses survivin through p53 and its downstream target p21, which stalls cell cycle progression as a cyclin-dependent kinase inhibitor (CDKi). These data shed new light on the regulation of survivin by two clinically significant drugs and its biological and predictive relevance in drug-exposed cancer cells.
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Affiliation(s)
- Anke Rauch
- Center for Molecular Biomedicine, Institute of Biochemistry and Biophysics, Department of Biochemistry, Friedrich Schiller University Jena, 07745 Jena, Germany
| | - Annemarie Carlstedt
- Center for Molecular Biomedicine, Institute of Biochemistry and Biophysics, Department of Biochemistry, Friedrich Schiller University Jena, 07745 Jena, Germany.,Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Claudia Emmerich
- Center for Molecular Biomedicine, Institute of Biochemistry and Biophysics, Department of Biochemistry, Friedrich Schiller University Jena, 07745 Jena, Germany
| | - Al-Hassan M Mustafa
- Department of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Anja Göder
- Department of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Shirley K Knauer
- Department of Molecular Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45141 Essen, Germany
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, University of Rostock, 18057 Rostock, Germany
| | - Thorsten Heinzel
- Center for Molecular Biomedicine, Institute of Biochemistry and Biophysics, Department of Biochemistry, Friedrich Schiller University Jena, 07745 Jena, Germany
| | - Oliver H Krämer
- Department of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
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87
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Limpose KL, Trego KS, Li Z, Leung SW, Sarker AH, Shah JA, Ramalingam SS, Werner EM, Dynan WS, Cooper PK, Corbett AH, Doetsch PW. Overexpression of the base excision repair NTHL1 glycosylase causes genomic instability and early cellular hallmarks of cancer. Nucleic Acids Res 2018; 46:4515-4532. [PMID: 29522130 PMCID: PMC5961185 DOI: 10.1093/nar/gky162] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 02/18/2018] [Accepted: 02/21/2018] [Indexed: 12/22/2022] Open
Abstract
Base excision repair (BER), which is initiated by DNA N-glycosylase proteins, is the frontline for repairing potentially mutagenic DNA base damage. The NTHL1 glycosylase, which excises DNA base damage caused by reactive oxygen species, is thought to be a tumor suppressor. However, in addition to NTHL1 loss-of-function mutations, our analysis of cancer genomic datasets reveals that NTHL1 frequently undergoes amplification or upregulation in some cancers. Whether NTHL1 overexpression could contribute to cancer phenotypes has not yet been explored. To address the functional consequences of NTHL1 overexpression, we employed transient overexpression. Both NTHL1 and a catalytically-dead NTHL1 (CATmut) induce DNA damage and genomic instability in non-transformed human bronchial epithelial cells (HBEC) when overexpressed. Strikingly, overexpression of either NTHL1 or CATmut causes replication stress signaling and a decrease in homologous recombination (HR). HBEC cells that overexpress NTHL1 or CATmut acquire the ability to grow in soft agar and exhibit loss of contact inhibition, suggesting that a mechanism independent of NTHL1 catalytic activity contributes to acquisition of cancer-related cellular phenotypes. We provide evidence that NTHL1 interacts with the multifunctional DNA repair protein XPG suggesting that interference with HR is a possible mechanism that contributes to acquisition of early cellular hallmarks of cancer.
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Affiliation(s)
- Kristin L Limpose
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA 30322, USA
| | - Kelly S Trego
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zhentian Li
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Sara W Leung
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Altaf H Sarker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jason A Shah
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Suresh S Ramalingam
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Erica M Werner
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - William S Dynan
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Priscilla K Cooper
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Paul W Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
- Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC 27709, USA
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88
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Li Z, Liu B, Jin W, Wu X, Zhou M, Liu VZ, Goel A, Shen Z, Zheng L, Shen B. hDNA2 nuclease/helicase promotes centromeric DNA replication and genome stability. EMBO J 2018; 37:embj.201796729. [PMID: 29773570 PMCID: PMC6043852 DOI: 10.15252/embj.201796729] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/16/2018] [Accepted: 04/25/2018] [Indexed: 11/18/2022] Open
Abstract
DNA2 is a nuclease/helicase that is involved in Okazaki fragment maturation, replication fork processing, and end resection of DNA double‐strand breaks. Similar such helicase activity for resolving secondary structures and structure‐specific nuclease activity are needed during DNA replication to process the chromosome‐specific higher order repeat units present in the centromeres of human chromosomes. Here, we show that DNA2 binds preferentially to centromeric DNA. The nuclease and helicase activities of DNA2 are both essential for resolution of DNA structural obstacles to facilitate DNA replication fork movement. Loss of DNA2‐mediated clean‐up mechanisms impairs centromeric DNA replication and CENP‐A deposition, leading to activation of the ATR DNA damage checkpoints at centromeric DNA regions and late‐S/G2 cell cycle arrest. Cells that escape arrest show impaired metaphase plate formation and abnormal chromosomal segregation. Furthermore, the DNA2 inhibitor C5 mimics DNA2 knockout and synergistically kills cancer cells when combined with an ATR inhibitor. These findings provide mechanistic insights into how DNA2 supports replication of centromeric DNA and give further insights into new therapeutic strategies.
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Affiliation(s)
- Zhengke Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Bochao Liu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Weiwei Jin
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA.,Department of Gastroenterology & Pancreatic Surgery, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Mian Zhou
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Vincent Zewen Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA.,Department of Computer Science, Columbia University, New York, NY, USA
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott and White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Zhiyuan Shen
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
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89
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Wang YS, Chen J, Cui F, Wang H, Wang S, Hang W, Zeng Q, Quan CS, Zhai YX, Wang JW, Shen XF, Jian YP, Zhao RX, Werle KD, Cui R, Liang J, Li YL, Xu ZX. LKB1 is a DNA damage response protein that regulates cellular sensitivity to PARP inhibitors. Oncotarget 2018; 7:73389-73401. [PMID: 27705915 PMCID: PMC5341986 DOI: 10.18632/oncotarget.12334] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/17/2016] [Indexed: 12/30/2022] Open
Abstract
Liver kinase B1 (LKB1) functions as a tumor suppressor encoded by STK11, a gene that mutated in Peutz-Jeghers syndrome and in sporadic cancers. Previous studies showed that LKB1 participates in IR- and ROS-induced DNA damage response (DDR). However, the impact of LKB1 mutations on targeted cancer therapy remains unknown. Herein, we demonstrated that LKB1 formed DNA damage-induced nuclear foci and co-localized with ataxia telangiectasia mutated kinase (ATM), γ-H2AX, and breast cancer susceptibility 1 (BRCA1). ATM mediated LKB1 phosphorylation at Thr 363 following the exposure of cells to ionizing radiation (IR). LKB1 interacted with BRCA1, a downstream effector in DDR that is recruited to sites of DNA damage and functions directly in homologous recombination (HR) DNA repair. LKB1 deficient cells exhibited delayed DNA repair due to insufficient HR. Notably, LKB1 deficiency sensitized cells to poly (ADP-ribose) polymerase (PARP) inhibitors. Thus, we have demonstrated a novel function of LKB1 in DNA damage response. Cancer cells lacking LKB1 are more susceptible to DNA damage-based therapy and, in particular, to drugs that further impair DNA repair, such as PARP inhibitors.
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Affiliation(s)
- Yi-Shu Wang
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin 130021, China
| | - Jianfeng Chen
- Division of Hematology and Oncology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Fengmei Cui
- Division of Hematology and Oncology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Huibo Wang
- Division of Hematology and Oncology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shuai Wang
- Division of Hematology and Oncology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wei Hang
- Division of Hematology and Oncology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Qinghua Zeng
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin 130021, China.,Division of Hematology and Oncology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Cheng-Shi Quan
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin 130021, China
| | - Ying-Xian Zhai
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin 130021, China
| | - Jian-Wei Wang
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin 130021, China
| | - Xiang-Feng Shen
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin 130021, China
| | - Yong-Ping Jian
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin 130021, China
| | - Rui-Xun Zhao
- Division of Hematology and Oncology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kaitlin D Werle
- Division of Hematology and Oncology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rutao Cui
- Department of Pharmacology and Experimental Therapeutics, Boston University, School of Medicine, Boston, MA 02118, USA
| | - Jiyong Liang
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yu-Lin Li
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin 130021, China
| | - Zhi-Xiang Xu
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin 130021, China.,Division of Hematology and Oncology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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90
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The ATM and Rad3-Related (ATR) Protein Kinase Pathway Is Activated by Herpes Simplex Virus 1 and Required for Efficient Viral Replication. J Virol 2018; 92:JVI.01884-17. [PMID: 29263259 DOI: 10.1128/jvi.01884-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/13/2017] [Indexed: 12/16/2022] Open
Abstract
The ATM and Rad3-related (ATR) protein kinase and its downstream effector Chk1 are key sensors and organizers of the DNA damage response (DDR) to a variety of insults. Previous studies of herpes simplex virus 1 (HSV-1) showed no evidence for activation of the ATR pathway. Here we demonstrate that both Chk1 and ATR were phosphorylated by 3 h postinfection (h.p.i.). Activation of ATR and Chk1 was observed using 4 different HSV-1 strains in multiple cell types, while a specific ATR inhibitor blocked activation. Mechanistic studies point to early viral gene expression as a key trigger for ATR activation. Both pATR and pChk1 localized to the nucleus within viral replication centers, or associated with their periphery, by 3 h.p.i. Significant levels of pATR and pChk1 were also detected in the cytoplasm, where they colocalized with ICP4 and ICP0. Proximity ligation assays confirmed that pATR and pChk1 were closely and specifically associated with ICP4 and ICP0 in both the nucleus and cytoplasm by 3 h.p.i., but not with ICP8 or ICP27, presumably in a multiprotein complex. Chemically distinct ATR and Chk1 inhibitors blocked HSV-1 replication and infectious virion production, while inhibitors of ATM, Chk2, and DNA-dependent protein kinase (DNA-PK) did not. Together our data show that HSV-1 activates the ATR pathway at early stages of infection and that ATR and Chk1 kinase activities play important roles in HSV-1 replication fitness. These findings indicate that the ATR pathway may provide insight for therapeutic approaches.IMPORTANCE Viruses have evolved complex associations with cellular DNA damage response (DDR) pathways, which sense troublesome DNA structures formed during infection. The first evidence for activation of the ATR pathway by HSV-1 is presented. ATR is activated, and its downstream target Chk1 is robustly phosphorylated, during early stages of infection. Both activated proteins are found in the nucleus associated with viral replication compartments and in the cytoplasm associated with viral proteins. We also demonstrate that both ATR and Chk1 kinase activities are important for viral replication. The findings suggest that HSV-1 activates ATR and Chk1 during early stages of infection and utilizes the enzymes to promote its own replication. The observation may be exploitable for antiviral approaches.
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91
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Göder A, Emmerich C, Nikolova T, Kiweler N, Schreiber M, Kühl T, Imhof D, Christmann M, Heinzel T, Schneider G, Krämer OH. HDAC1 and HDAC2 integrate checkpoint kinase phosphorylation and cell fate through the phosphatase-2A subunit PR130. Nat Commun 2018; 9:764. [PMID: 29472538 PMCID: PMC5823910 DOI: 10.1038/s41467-018-03096-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 01/19/2018] [Indexed: 12/18/2022] Open
Abstract
Checkpoint kinases sense replicative stress to prevent DNA damage. Here we show that the histone deacetylases HDAC1/HDAC2 sustain the phosphorylation of the checkpoint kinases ATM, CHK1 and CHK2, activity of the cell cycle gatekeeper kinases WEE1 and CDK1, and induction of the tumour suppressor p53 in response to stalled DNA replication. Consequently, HDAC inhibition upon replicative stress promotes mitotic catastrophe. Mechanistically, HDAC1 and HDAC2 suppress the expression of PPP2R3A/PR130, a regulatory subunit of the trimeric serine/threonine phosphatase 2 (PP2A). Genetic elimination of PR130 reveals that PR130 promotes dephosphorylation of ATM by PP2A. Moreover, the ablation of PR130 slows G1/S phase transition and increases the levels of phosphorylated CHK1, replication protein A foci and DNA damage upon replicative stress. Accordingly, stressed PR130 null cells are very susceptible to HDAC inhibition, which abrogates the S phase checkpoint, induces apoptosis and reduces the homologous recombination protein RAD51. Thus, PR130 controls cell fate decisions upon replicative stress. Checkpoint kinases control cell cycle progression via the regulation of many key regulators. Here the authors demonstrate how HDAC1 and HDAC2 modulate checkpoint kinase signalling via the suppression of PR130, a regulatory subunit of the trimeric serine/threonine phosphatase 2.
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Affiliation(s)
- Anja Göder
- Institute of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, 55131, Mainz, Germany
| | - Claudia Emmerich
- University of Jena, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Hans-Knöll-Strasse 2, 07745, Jena, Germany
| | - Teodora Nikolova
- Institute of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, 55131, Mainz, Germany
| | - Nicole Kiweler
- Institute of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, 55131, Mainz, Germany
| | - Maria Schreiber
- University of Jena, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Hans-Knöll-Strasse 2, 07745, Jena, Germany
| | - Toni Kühl
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Markus Christmann
- Institute of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, 55131, Mainz, Germany
| | - Thorsten Heinzel
- University of Jena, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Hans-Knöll-Strasse 2, 07745, Jena, Germany
| | - Günter Schneider
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Ismaningerstrasse 22, 81675, Munich, Germany
| | - Oliver H Krämer
- Institute of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, 55131, Mainz, Germany.
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92
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Gupta D, Lin B, Cowan A, Heinen CD. ATR-Chk1 activation mitigates replication stress caused by mismatch repair-dependent processing of DNA damage. Proc Natl Acad Sci U S A 2018; 115:1523-1528. [PMID: 29378956 PMCID: PMC5816205 DOI: 10.1073/pnas.1720355115] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The mismatch repair pathway (MMR) is essential for removing DNA polymerase errors, thereby maintaining genomic stability. Loss of MMR function increases mutation frequency and is associated with tumorigenesis. However, how MMR is executed at active DNA replication forks is unclear. This has important implications for understanding how MMR repairs O6-methylguanine/thymidine (MeG/T) mismatches created upon exposure to DNA alkylating agents. If MeG/T lesion recognition by MMR initiates mismatch excision, the reinsertion of a mismatched thymidine during resynthesis could initiate futile repair cycles. One consequence of futile repair cycles might be a disruption of overall DNA replication in the affected cell. Herein, we show that in MMR-proficient HeLa cancer cells, treatment with a DNA alkylating agent slows S phase progression, yet cells still progress into the next cell cycle. In the first S phase following treatment, they activate ataxia telangiectasia and Rad3-related (ATR)-Checkpoint Kinase 1 (Chk1) signaling, which limits DNA damage, while inhibition of ATR kinase activity accelerates DNA damage accumulation and sensitivity to the DNA alkylating agent. We also observed that exposure of human embryonic stem cells to alkylation damage severely compromised DNA replication in a MMR-dependent manner. These cells fail to activate the ATR-Chk1 signaling axis, which may limit their ability to handle replication stress. Accordingly, they accumulate double-strand breaks and undergo immediate apoptosis. Our findings implicate the MMR-directed response to alkylation damage as a replication stress inducer, suggesting that repeated MMR processing of mismatches may occur that can disrupt S phase progression.
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Affiliation(s)
- Dipika Gupta
- Neag Comprehensive Cancer Center, UConn Health, Farmington, CT 06030-3101
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030-3101
| | - Bo Lin
- Neag Comprehensive Cancer Center, UConn Health, Farmington, CT 06030-3101
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030-3101
| | - Ann Cowan
- R. D. Berlin Center for Cell Analysis and Modeling, UConn Health, Farmington, CT 06030
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030
| | - Christopher D Heinen
- Neag Comprehensive Cancer Center, UConn Health, Farmington, CT 06030-3101;
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030-3101
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93
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Cupello S, Richardson C, Yan S. Cell-free Xenopus egg extracts for studying DNA damage response pathways. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2018; 60:229-236. [PMID: 27160070 DOI: 10.1387/ijdb.160113sy] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In response to a variety of DNA replication stress or DNA damaging agents, the DNA damage response (DDR) pathways are triggered for cells to coordinate DNA repair, cell cycle checkpoints, apoptosis, and senescence. Cell-free Xenopus egg extracts, derived from the eggs of African clawed frogs (Xenopus laevis), have been widely used for studies concerning DDR pathways. In this review, we focus on how different experimental systems have been established using Xenopus egg extracts to investigate the DDR pathways that are activated in response to DNA replication stress, double-strand breaks (DSBs), inter-strand crosslinks (ICLs), and oxidative stress. We summarize how molecular details of DDR pathways are dissected by the mechanistic studies with Xenopus egg extracts. We also provide an update on the regulation of translesion DNA synthesis (TLS) polymerases (Pol ĸ and REV1) in the DDR pathways. A better understanding of DDR pathways using Xenopus egg extracts has opened new avenues for future cancer therapeutics. Finally, we offer our perspectives of future directions for studies of DDR pathways with Xenopus egg extracts.
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Affiliation(s)
- Steven Cupello
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
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94
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Cryo-EM structure of human ATR-ATRIP complex. Cell Res 2017; 28:143-156. [PMID: 29271416 DOI: 10.1038/cr.2017.158] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/01/2017] [Accepted: 12/05/2017] [Indexed: 12/18/2022] Open
Abstract
ATR (ataxia telangiectasia-mutated and Rad3-related) protein kinase and ATRIP (ATR-interacting protein) form a complex and play a critical role in response to replication stress and DNA damage. Here, we determined the cryo-electron microscopy (EM) structure of the human ATR-ATRIP complex at 4.7 Å resolution and built an atomic model of the C-terminal catalytic core of ATR (residues 1 521-2 644) at 3.9 Å resolution. The complex adopts a hollow "heart" shape, consisting of two ATR monomers in distinct conformations. The EM map for ATRIP reveals 14 HEAT repeats in an extended "S" shape. The conformational flexibility of ATR allows ATRIP to properly lock the N-termini of the two ATR monomers to favor ATR-ATRIP complex formation and functional diversity. The isolated "head-head" and "tail-tail" each adopts a pseudo 2-fold symmetry. The catalytic pockets face outward and substrate access is not restricted by inhibitory elements. Our studies provide a structural basis for understanding the assembly of the ATR-ATRIP complex and a framework for characterizing ATR-mediated DNA repair pathways.
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95
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Wang X, Ran T, Zhang X, Xin J, Zhang Z, Wu T, Wang W, Cai G. 3.9 Å structure of the yeast Mec1-Ddc2 complex, a homolog of human ATR-ATRIP. Science 2017; 358:1206-1209. [DOI: 10.1126/science.aan8414] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
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96
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Gyori BM, Bachman JA, Subramanian K, Muhlich JL, Galescu L, Sorger PK. From word models to executable models of signaling networks using automated assembly. Mol Syst Biol 2017; 13:954. [PMID: 29175850 PMCID: PMC5731347 DOI: 10.15252/msb.20177651] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Word models (natural language descriptions of molecular mechanisms) are a common currency in spoken and written communication in biomedicine but are of limited use in predicting the behavior of complex biological networks. We present an approach to building computational models directly from natural language using automated assembly. Molecular mechanisms described in simple English are read by natural language processing algorithms, converted into an intermediate representation, and assembled into executable or network models. We have implemented this approach in the Integrated Network and Dynamical Reasoning Assembler (INDRA), which draws on existing natural language processing systems as well as pathway information in Pathway Commons and other online resources. We demonstrate the use of INDRA and natural language to model three biological processes of increasing scope: (i) p53 dynamics in response to DNA damage, (ii) adaptive drug resistance in BRAF‐V600E‐mutant melanomas, and (iii) the RAS signaling pathway. The use of natural language makes the task of developing a model more efficient and it increases model transparency, thereby promoting collaboration with the broader biology community.
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Affiliation(s)
- Benjamin M Gyori
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - John A Bachman
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kartik Subramanian
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jeremy L Muhlich
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lucian Galescu
- Institute for Human and Machine Cognition, Pensacola, FL, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
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97
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Sun L, Huang Y, Edwards RA, Yang S, Blackford AN, Niedzwiedz W, Glover JNM. Structural Insight into BLM Recognition by TopBP1. Structure 2017; 25:1582-1588.e3. [PMID: 28919440 PMCID: PMC6044410 DOI: 10.1016/j.str.2017.08.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/28/2017] [Accepted: 08/15/2017] [Indexed: 01/07/2023]
Abstract
Topoisomerase IIβ binding protein 1 (TopBP1) is a critical protein-protein interaction hub in DNA replication checkpoint control. It was proposed that TopBP1 BRCT5 interacts with Bloom syndrome helicase (BLM) to regulate genome stability through either phospho-Ser304 or phospho-Ser338 of BLM. Here we show that TopBP1 BRCT5 specifically interacts with the BLM region surrounding pSer304, not pSer338. Our crystal structure of TopBP1 BRCT4/5 bound to BLM reveals recognition of pSer304 by a conserved pSer-binding pocket, and interactions between an FVPP motif N-terminal to pSer304 and a hydrophobic groove on BRCT5. This interaction utilizes the same surface of BRCT5 that recognizes the DNA damage mediator, MDC1; however the binding orientations of MDC1 and BLM are reversed. While the MDC1 interactions are largely electrostatic, the interaction with BLM has higher affinity and relies on a mix of electrostatics and hydrophobicity. We suggest that similar evolutionarily conserved interactions may govern interactions between TopBP1 and 53BP1.
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Affiliation(s)
- Luxin Sun
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Yuhao Huang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ross A Edwards
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Sukmin Yang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Andrew N Blackford
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Wojciech Niedzwiedz
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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98
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Lin X, Wei F, Whyte P, Tang D. BMI1 reduces ATR activation and signalling caused by hydroxyurea. Oncotarget 2017; 8:89707-89721. [PMID: 29163782 PMCID: PMC5685703 DOI: 10.18632/oncotarget.21111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 09/03/2017] [Indexed: 01/31/2023] Open
Abstract
BMI1 facilitates DNA damage response (DDR) induced by double strand DNA breaks; however, it remains unknown whether BMI1 functions in single strand DNA (ssDNA) lesions-initiated DDR. We report here that BMI1 reduces hydroxyurea-elicited ATR activation, thereby reducing the S-phase checkpoints. Hydroxyurea induces ssDNA lesions, which activate ATR through binding TOPBP1 as evidenced by phosphorylation of ATR at threonine 1989 (ATRpT1989). ATR subsequently phosphorylates H2AX at serine 139 (γH2AX) and CHK1 at serine 345 (CHK1pS345), leading to phosphorylation of CDK1 at tyrosine 15 (CDK1pY15) and S-phase arrest. BMI1 overexpression reduced γH2AX, CHK1pS345, CDK1pY15, S-phase arrest, and ATR activation in HU-treated MCF7 and DU145 cells, whereas BMI1 knockdown enhanced these events. BMI1 contains a ring finger, helix-turn, proline/serine domain and two nuclear localization signals (NLS). Individual deletion of these domains did not abolish BMI1-derived reductions of CHK1pS345 in MCF7 cells following HU exposure, suggesting that these structural features are not essential for BMI1 to attenuate ATR-mediated CHK1pS345. BMI1 interacts with both TOPBP1 and ATR. Furthermore, all of our BMI1 mutants associate with endogenous TOPBP1. It has previously been established that association of TOPBP1 and ATR is required for ATR activation. Thus, our results suggest that BMI1 decreases ATR activation through a mechanism that involves binding to TOPBP1 and/or ATR.
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Affiliation(s)
- Xiaozeng Lin
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Ontario, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada
| | - Fengxiang Wei
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Ontario, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada.,The Genetics Laboratory, Longgang District Maternity and Child Healthcare Hospital, Longgang District, Shenzhen, Guangdong, P.R. China
| | - Peter Whyte
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Damu Tang
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Ontario, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada
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99
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Sirt7 promotes adipogenesis in the mouse by inhibiting autocatalytic activation of Sirt1. Proc Natl Acad Sci U S A 2017; 114:E8352-E8361. [PMID: 28923965 DOI: 10.1073/pnas.1706945114] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sirtuins (Sirt1-Sirt7) are NAD+-dependent protein deacetylases/ADP ribosyltransferases, which play decisive roles in chromatin silencing, cell cycle regulation, cellular differentiation, and metabolism. Different sirtuins control similar cellular processes, suggesting a coordinated mode of action but information about potential cross-regulatory interactions within the sirtuin family is still limited. Here, we demonstrate that Sirt1 requires autodeacetylation to efficiently deacetylate targets such as p53, H3K9, and H4K16. Sirt7 restricts Sirt1 activity by preventing Sirt1 autodeacetylation causing enhanced Sirt1 activity in Sirt7-/- mice. Increased Sirt1 activity in Sirt7-/- mice blocks PPARγ and adipocyte differentiation, thereby diminishing accumulation of white fat. Thus, reduction of Sirt1 activity restores adipogenesis in Sirt7-/- adipocytes in vitro and in vivo. We disclosed a principle controlling Sirt1 activity and uncovered an unexpected complexity in the crosstalk between two different sirtuins. We propose that antagonistic interactions between Sirt1 and Sirt7 are pivotal in controlling the signaling network required for maintenance of adipose tissue.
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100
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Groh IAM, Esselen M. Methyleugenol and selected oxidative metabolites affect DNA-Damage signalling pathways and induce apoptosis in human colon tumour HT29 cells. Food Chem Toxicol 2017; 108:267-275. [PMID: 28818686 DOI: 10.1016/j.fct.2017.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/01/2017] [Accepted: 08/11/2017] [Indexed: 12/13/2022]
Abstract
Previously the food carcinogen methyleugenol was found to be cytotoxic and genotoxic in multiple cell lines and in primary hepatocytes. In this study, the question addressed was whether methyleugenol and the selected oxidative metabolites, 1'-hydroxymethyleugenol, methyleugenol-2',3'-epoxide and 3'-oxomethylisoeugenol trigger a DNA damage response in the human colon carcinoma HT29 cell line. Most notably investigations by flow cytometry revealed that the metabolites induce an accumulation of HT29 cells in the G2 phase of the cell cycle. DNA damage response is characterised by a time-delayed phosphorylation of ATM (ataxia-telangiectasia, mutated)/ATR (ATM- and Rad3-related) kinases and checkpoint kinase 1 after 2 h of incubation, and the tumour suppressor protein p53 only after 24 h of incubation. The test compounds induced apoptotic cell death indicated by cleavage of caspase 3 and poly-(ADP-ribose)-polymerase after a prolonged incubation time up to 72 h. In addition, activation of ATM/ATR-signalling cascade might contribute to apoptosis induction to a certain extent. However, clarification of this relationship awaits experimental confirmation.
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Affiliation(s)
- Isabel Anna Maria Groh
- Institute of Food Chemistry and Toxicology, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Melanie Esselen
- Institute of Food Chemistry, Westfälische Wilhelms University of Münster, Münster, Germany.
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