1
|
Goff NJ, Mikhova M, Schmidt JC, Meek K. DNA-PK: A synopsis beyond synapsis. DNA Repair (Amst) 2024; 141:103716. [PMID: 38996771 DOI: 10.1016/j.dnarep.2024.103716] [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: 04/30/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024]
Abstract
Given its central role in life, DNA is remarkably easy to damage. Double strand breaks (DSBs) are the most toxic form of DNA damage, and DSBs pose the greatest danger to genomic integrity. In higher vertebrates, the non-homologous end joining pathway (NHEJ) is the predominate pathway that repairs DSBs. NHEJ has three steps: 1) DNA end recognition by the DNA dependent protein kinase [DNA-PK], 2) DNA end-processing by numerous NHEJ accessory factors, and 3) DNA end ligation by the DNA ligase IV complex (LX4). Although this would appear to be a relatively simple mechanism, it has become increasingly apparent that it is not. Recently, much insight has been derived regarding the mechanism of non-homologous end joining through a proliferation of cryo-EM studies, structure-function mutational experiments informed by these new structural data, and novel single-molecule imaging approaches. An emerging consensus in the field is that NHEJ progresses from initial DSB end recognition by DNA-PK to synapsis of the two DNA ends in a long-range synaptic complex where ends are held too far apart (115 Å) for ligation, and then progress to a short-range synaptic complex where ends are positioned close enough for ligation. What was surprising from these structural studies was the observation of two distinct types of DNA-PK dimers that represent NHEJ long-range complexes. In this review, we summarize current knowledge about the function of the distinct NHEJ synaptic complexes and align this new information with emerging cellular single-molecule microscopy studies as well as with previous studies of DNA-PK's function in repair.
Collapse
Affiliation(s)
- Noah J Goff
- College of Veterinary Medicine, Department of Microbiology Genetics & Immunology, Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
| | - Mariia Mikhova
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
| | - Jens C Schmidt
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA; Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI, USA
| | - Katheryn Meek
- College of Veterinary Medicine, Department of Microbiology Genetics & Immunology, Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
2
|
Qu H, Wang Y, Yan Q, Fan C, Zhang X, Wang D, Guo C, Chen P, Shi L, Liao Q, Zhou M, Wang F, Zeng Z, Xiang B, Xiong W. CircCDYL2 bolsters radiotherapy resistance in nasopharyngeal carcinoma by promoting RAD51 translation initiation for enhanced homologous recombination repair. J Exp Clin Cancer Res 2024; 43:122. [PMID: 38654320 PMCID: PMC11036759 DOI: 10.1186/s13046-024-03049-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Radiation therapy stands to be one of the primary approaches in the clinical treatment of malignant tumors. Nasopharyngeal Carcinoma, a malignancy predominantly treated with radiation therapy, provides an invaluable model for investigating the mechanisms underlying radiation therapy resistance in cancer. While some reports have suggested the involvement of circRNAs in modulating resistance to radiation therapy, the underpinning mechanisms remain unclear. METHODS RT-qPCR and in situ hybridization were used to detect the expression level of circCDYL2 in nasopharyngeal carcinoma tissue samples. The effect of circCDYL2 on radiotherapy resistance in nasopharyngeal carcinoma was demonstrated by in vitro and in vivo functional experiments. The HR-GFP reporter assay determined that circCDYL2 affected homologous recombination repair. RNA pull down, RIP, western blotting, IF, and polysome profiling assays were used to verify that circCDYL2 promoted the translation of RAD51 by binding to EIF3D protein. RESULTS We have identified circCDYL2 as highly expressed in nasopharyngeal carcinoma tissues, and it was closely associated with poor prognosis. In vitro and in vivo experiments demonstrate that circCDYL2 plays a pivotal role in promoting radiotherapy resistance in nasopharyngeal carcinoma. Our investigation unveils a specific mechanism by which circCDYL2, acting as a scaffold molecule, recruits eukaryotic translation initiation factor 3 subunit D protein (EIF3D) to the 5'-UTR of RAD51 mRNA, a crucial component of the DNA damage repair pathway to facilitate the initiation of RAD51 translation and enhance homologous recombination repair capability, and ultimately leads to radiotherapy resistance in nasopharyngeal carcinoma. CONCLUSIONS These findings establish a novel role of the circCDYL2/EIF3D/RAD51 axis in nasopharyngeal carcinoma radiotherapy resistance. Our work not only sheds light on the underlying molecular mechanism but also highlights the potential of circCDYL2 as a therapeutic sensitization target and a promising prognostic molecular marker for nasopharyngeal carcinoma.
Collapse
Affiliation(s)
- Hongke Qu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Yumin Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
| | - Qijia Yan
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
| | - Chunmei Fan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Xiangyan Zhang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Dan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Pan Chen
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Lei Shi
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China.
| |
Collapse
|
3
|
Locke AJ, Abou Farraj R, Tran C, Zeinali E, Mashayekhi F, Ali JYH, Glover JNM, Ismail IH. The role of RNF138 in DNA end resection is regulated by ubiquitylation and CDK phosphorylation. J Biol Chem 2024; 300:105709. [PMID: 38309501 PMCID: PMC10910129 DOI: 10.1016/j.jbc.2024.105709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 01/02/2024] [Accepted: 01/18/2024] [Indexed: 02/05/2024] Open
Abstract
Double-strand breaks (DSBs) are DNA lesions that pose a significant threat to genomic stability. The repair of DSBs by the homologous recombination (HR) pathway is preceded by DNA end resection, the 5' to 3' nucleolytic degradation of DNA away from the DSB. We and others previously identified a role for RNF138, a really interesting new gene finger E3 ubiquitin ligase, in stimulating DNA end resection and HR. Yet, little is known about how RNF138's function is regulated in the context of DSB repair. Here, we show that RNF138 is phosphorylated at residue T27 by cyclin-dependent kinase (CDK) activity during the S and G2 phases of the cell cycle. We also observe that RNF138 is ubiquitylated constitutively, with ubiquitylation occurring in part on residue K158 and rising during the S/G2 phases. Interestingly, RNF138 ubiquitylation decreases upon genotoxic stress. By mutating RNF138 at residues T27, K158, and the previously identified S124 ataxia telangiectasia mutated phosphorylation site (Han et al., 2016, ref. 22), we find that post-translational modifications at all three positions mediate DSB repair. Cells expressing the T27A, K158R, and S124A variants of RNF138 are impaired in DNA end resection, HR activity, and are more sensitive to ionizing radiation compared to those expressing wildtype RNF138. Our findings shed more light on how RNF138 activity is controlled by the cell during HR.
Collapse
Affiliation(s)
- Andrew J Locke
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Rabih Abou Farraj
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Caroline Tran
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Elham Zeinali
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Fatemeh Mashayekhi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Jana Yasser Hafez Ali
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - J N Mark Glover
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Ismail Hassan Ismail
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada; Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt.
| |
Collapse
|
4
|
Koike M, Yamashita H, Yutoku Y, Koike A. Molecular cloning, subcellular localization, and rapid recruitment to DNA damage sites of chicken Ku70. Sci Rep 2024; 14:1188. [PMID: 38216643 PMCID: PMC10786929 DOI: 10.1038/s41598-024-51501-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/05/2024] [Indexed: 01/14/2024] Open
Abstract
Ku70 is a multifunctional protein with pivotal roles in DNA repair via non-homologous end-joining, V(D)J recombination, telomere maintenance, and neuronal apoptosis control. Nonetheless, its regulatory mechanisms remain elusive. Chicken Ku70 (GdKu70) cDNA has been previously cloned, and DT40 cells expressing it have significantly contributed to critical biological discoveries. GdKu70 features an additional 18 amino acids at its N-terminus compared to mammalian Ku70, the biological significance of which remains uncertain. Here, we show that the 5' flanking sequence of GdKu70 cDNA is not nearly encoded in the chicken genome. Notably, these 18 amino acids result from fusion events involving the NFE2L1 gene on chromosome 27 and the Ku70 gene on chromosome 1. Through experiments using newly cloned chicken Ku70 cDNA and specific antibodies, we demonstrated that Ku70 localizes within the cell nucleus as a heterodimer with Ku80 and promptly accumulates at DNA damage sites following injury. This suggests that the functions and spatiotemporal regulatory mechanisms of Ku70 in chickens closely resemble those in mammals. The insights and resources acquired will contribute to elucidate the various mechanisms by which Ku functions. Meanwhile, caution is advised when interpreting the previous numerous key studies that relied on GdKu70 cDNA and its expressing cells.
Collapse
Affiliation(s)
- Manabu Koike
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan.
- Life Science Course, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, 338-8570, Japan.
| | - Hideji Yamashita
- Department of Food and Life Sciences, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto, 862-8652, Japan
| | - Yasutomo Yutoku
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Aki Koike
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
| |
Collapse
|
5
|
Bossaert M, Moreno A, Peixoto A, Pillaire MJ, Chanut P, Frit P, Calsou P, Loparo JJ, Britton S. Identification of the main barriers to Ku accumulation in chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574002. [PMID: 38260538 PMCID: PMC10802386 DOI: 10.1101/2024.01.03.574002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Repair of DNA double strand breaks by the non-homologous end-joining pathway is initiated by the binding of Ku to DNA ends. Given its high affinity for ends, multiple Ku proteins load onto linear DNAs in vitro. However, in cells, Ku loading is limited to ~1-2 molecules per DNA end. The mechanisms enforcing this limit are currently unknown. Here we show that the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs), but not its protein kinase activity, is required to prevent excessive Ku entry into chromatin. Ku accumulation is further restricted by two mechanisms: a neddylation/FBXL12-dependent process which actively removes loaded Ku molecules throughout the cell cycle and a CtIP/ATM-dependent mechanism which operates in S-phase. Finally, we demonstrate that the misregulation of Ku loading leads to impaired transcription in the vicinity of DNA ends. Together our data shed light on the multiple layers of coordinated mechanisms operating to prevent Ku from invading chromatin and interfering with other DNA transactions.
Collapse
Affiliation(s)
- Madeleine Bossaert
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe labélisée la Ligue contre le Cancer 2018
| | - Andrew Moreno
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Antonio Peixoto
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe labélisée la Ligue contre le Cancer 2018
| | - Marie-Jeanne Pillaire
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe labélisée la Ligue contre le Cancer 2018
| | - Pauline Chanut
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe labélisée la Ligue contre le Cancer 2018
| | - Philippe Frit
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe labélisée la Ligue contre le Cancer 2018
| | - Patrick Calsou
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe labélisée la Ligue contre le Cancer 2018
| | - Joseph John Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Sébastien Britton
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe labélisée la Ligue contre le Cancer 2018
| |
Collapse
|
6
|
Tang GLQ, Lai JXH, Pervaiz S. Ubiquitin-proteasome pathway-mediated regulation of the Bcl-2 family: effects and therapeutic approaches. Haematologica 2024; 109:33-43. [PMID: 37584295 PMCID: PMC10772529 DOI: 10.3324/haematol.2023.283730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/10/2023] [Indexed: 08/17/2023] Open
Abstract
Proteasomal degradation of proteins represents an important regulatory mechanism in maintaining healthy homeostasis in cells. Deregulation of the ubiquitin-proteasome system is associated with various diseases as it controls protein abundance and turnover in cells. Furthermore, proteasomal regulation of protein turnover rate can determine a cell's response to external stimuli. The Bcl-2 family of proteins is an important group of proteins involved in mediating cell survival or cell death in response to external stimuli. Aberrant overexpression of anti-apoptotic proteins or deletion of pro-apoptotic proteins can lead to the development of cancer. Unsurprisingly, proteasomal degradation of Bcl-2 proteins also serves as an important factor regulating the level of Bcl-2 proteins and thereby affecting the functional outcome of cell death. This review aims to highlight the regulation of the Bcl-2 family of proteins with particular emphasis on proteasomal-mediated degradation pathways and the current literature on the therapeutic approaches targeting the proteasome system.
Collapse
Affiliation(s)
- Galvin Le Qian Tang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore
| | - Jolin Xiao Hui Lai
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore
| | - Shazib Pervaiz
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Integrative Science and Engineering Programme (ISEP), NUS Graduate School (NUSGS), National University of Singapore, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Medicine Healthy Longevity Program, National University of Singapore, Singapore; National University Cancer Institute, National University Health System.
| |
Collapse
|
7
|
Warmenhoven JW, Henthorn NT, McNamara AL, Ingram SP, Merchant MJ, Kirkby KJ, Schuemann J, Paganetti H, Prise KM, McMahon SJ. Effects of Differing Underlying Assumptions in In Silico Models on Predictions of DNA Damage and Repair. Radiat Res 2023; 200:509-522. [PMID: 38014593 DOI: 10.1667/rade-21-00147.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/05/2023] [Indexed: 11/29/2023]
Abstract
The induction and repair of DNA double-strand breaks (DSBs) are critical factors in the treatment of cancer by radiotherapy. To investigate the relationship between incident radiation and cell death through DSB induction many in silico models have been developed. These models produce and use custom formats of data, specific to the investigative aims of the researchers, and often focus on particular pairings of damage and repair models. In this work we use a standard format for reporting DNA damage to evaluate combinations of different, independently developed, models. We demonstrate the capacity of such inter-comparison to determine the sensitivity of models to both known and implicit assumptions. Specifically, we report on the impact of differences in assumptions regarding patterns of DNA damage induction on predicted initial DSB yield, and the subsequent effects this has on derived DNA repair models. The observed differences highlight the importance of considering initial DNA damage on the scale of nanometres rather than micrometres. We show that the differences in DNA damage models result in subsequent repair models assuming significantly different rates of random DSB end diffusion to compensate. This in turn leads to disagreement on the mechanisms responsible for different biological endpoints, particularly when different damage and repair models are combined, demonstrating the importance of inter-model comparisons to explore underlying model assumptions.
Collapse
Affiliation(s)
- John W Warmenhoven
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Nicholas T Henthorn
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Aimee L McNamara
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Samuel P Ingram
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Michael J Merchant
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Karen J Kirkby
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Jan Schuemann
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Harald Paganetti
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Kevin M Prise
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| |
Collapse
|
8
|
Kefala Stavridi A, Gontier A, Morin V, Frit P, Ropars V, Barboule N, Racca C, Jonchhe S, Morten M, Andreani J, Rak A, Legrand P, Bourand-Plantefol A, Hardwick S, Chirgadze D, Davey P, De Oliveira TM, Rothenberg E, Britton S, Calsou P, Blundell T, Varela P, Chaplin A, Charbonnier JB. Structural and functional basis of inositol hexaphosphate stimulation of NHEJ through stabilization of Ku-XLF interaction. Nucleic Acids Res 2023; 51:11732-11747. [PMID: 37870477 PMCID: PMC10682503 DOI: 10.1093/nar/gkad863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
The classical Non-Homologous End Joining (c-NHEJ) pathway is the predominant process in mammals for repairing endogenous, accidental or programmed DNA Double-Strand Breaks. c-NHEJ is regulated by several accessory factors, post-translational modifications, endogenous chemical agents and metabolites. The metabolite inositol-hexaphosphate (IP6) stimulates c-NHEJ by interacting with the Ku70-Ku80 heterodimer (Ku). We report cryo-EM structures of apo- and DNA-bound Ku in complex with IP6, at 3.5 Å and 2.74 Å resolutions respectively, and an X-ray crystallography structure of a Ku in complex with DNA and IP6 at 3.7 Å. The Ku-IP6 interaction is mediated predominantly via salt bridges at the interface of the Ku70 and Ku80 subunits. This interaction is distant from the DNA, DNA-PKcs, APLF and PAXX binding sites and in close proximity to XLF binding site. Biophysical experiments show that IP6 binding increases the thermal stability of Ku by 2°C in a DNA-dependent manner, stabilizes Ku on DNA and enhances XLF affinity for Ku. In cells, selected mutagenesis of the IP6 binding pocket reduces both Ku accrual at damaged sites and XLF enrolment in the NHEJ complex, which translate into a lower end-joining efficiency. Thus, this study defines the molecular bases of the IP6 metabolite stimulatory effect on the c-NHEJ repair activity.
Collapse
Affiliation(s)
- Antonia Kefala Stavridi
- Heartand Lung Research Institute, University of Cambridge, Biomedical Campus, Papworth Road, Trumpington, Cambridge CB2 0BB, UK
| | - Amandine Gontier
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Univ.Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Vincent Morin
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Univ.Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Philippe Frit
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Univ.Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Nadia Barboule
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Carine Racca
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Sagun Jonchhe
- NYU Langone Medical Center, 450 East 29th Street, NY, NY, USA York University, USA
| | - Michael J Morten
- NYU Langone Medical Center, 450 East 29th Street, NY, NY, USA York University, USA
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Univ.Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Alexey Rak
- Structure-Design-Informatics, Sanofi R&D, Vitry sur Seine, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette, France
| | - Alexa Bourand-Plantefol
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Univ.Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Steven W Hardwick
- Cryo-EM Facility, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Dimitri Y Chirgadze
- Cryo-EM Facility, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Paul Davey
- Oncology, R&D, AstraZeneca, Cambridge, UK
| | | | - Eli Rothenberg
- NYU Langone Medical Center, 450 East 29th Street, NY, NY, USA York University, USA
| | - Sebastien Britton
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Patrick Calsou
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Tom L Blundell
- Heartand Lung Research Institute, University of Cambridge, Biomedical Campus, Papworth Road, Trumpington, Cambridge CB2 0BB, UK
| | - Paloma F Varela
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Univ.Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Amanda K Chaplin
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Univ.Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| |
Collapse
|
9
|
Park SH, Kim N, Kang N, Ryu E, Lee EA, Ra JS, Gartner A, Kang S, Myung K, Lee KY. Short-range end resection requires ATAD5-mediated PCNA unloading for faithful homologous recombination. Nucleic Acids Res 2023; 51:10519-10535. [PMID: 37739427 PMCID: PMC10602867 DOI: 10.1093/nar/gkad776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
Homologous recombination (HR) requires bidirectional end resection initiated by a nick formed close to a DNA double-strand break (DSB), dysregulation favoring error-prone DNA end-joining pathways. Here we investigate the role of the ATAD5, a PCNA unloading protein, in short-range end resection, long-range resection not being affected by ATAD5 deficiency. Rapid PCNA loading onto DNA at DSB sites depends on the RFC PCNA loader complex and MRE11-RAD50-NBS1 nuclease complexes bound to CtIP. Based on our cytological analyses and on an in vitro system for short-range end resection, we propose that PCNA unloading by ATAD5 is required for the completion of short-range resection. Hampering PCNA unloading also leads to failure to remove the KU70/80 complex from the termini of DSBs hindering DNA repair synthesis and the completion of HR. In line with this model, ATAD5-depleted cells are defective for HR, show increased sensitivity to camptothecin, a drug forming protein-DNA adducts, and an augmented dependency on end-joining pathways. Our study highlights the importance of PCNA regulation at DSB for proper end resection and HR.
Collapse
Affiliation(s)
- Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Namwoo Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Nalae Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Eun A Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Anton Gartner
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Kyoo-young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon 24252, Korea
| |
Collapse
|
10
|
Loparo JJ. Holding it together: DNA end synapsis during non-homologous end joining. DNA Repair (Amst) 2023; 130:103553. [PMID: 37572577 PMCID: PMC10530278 DOI: 10.1016/j.dnarep.2023.103553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/04/2023] [Accepted: 08/06/2023] [Indexed: 08/14/2023]
Abstract
DNA double strand breaks (DSBs) are common lesions whose misrepair are drivers of oncogenic transformations. The non-homologous end joining (NHEJ) pathway repairs the majority of these breaks in vertebrates by directly ligating DNA ends back together. Upon formation of a DSB, a multiprotein complex is assembled on DNA ends which tethers them together within a synaptic complex. Synapsis is a critical step of the NHEJ pathway as loss of synapsis can result in mispairing of DNA ends and chromosome translocations. As DNA ends are commonly incompatible for ligation, the NHEJ machinery must also process ends to enable rejoining. This review describes how recent progress in single-molecule approaches and cryo-EM have advanced our molecular understanding of DNA end synapsis during NHEJ and how synapsis is coordinated with end processing to determine the fidelity of repair.
Collapse
Affiliation(s)
- Joseph J Loparo
- Dept. of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
11
|
Deshpande RA, Marin-Gonzalez A, Barnes HK, Woolley PR, Ha T, Paull TT. Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice. Nat Commun 2023; 14:5759. [PMID: 37717054 PMCID: PMC10505227 DOI: 10.1038/s41467-023-41544-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
The Mre11-Rad50-Nbs1 (MRN) complex recognizes and processes DNA double-strand breaks for homologous recombination by performing short-range removal of 5' strands. Endonucleolytic processing by MRN requires a stably bound protein at the break site-a role we postulate is played by DNA-dependent protein kinase (DNA-PK) in mammals. Here we interrogate sites of MRN-dependent processing by identifying sites of CtIP association and by sequencing DNA-PK-bound DNA fragments that are products of MRN cleavage. These intermediates are generated most efficiently when DNA-PK is catalytically blocked, yielding products within 200 bp of the break site, whereas DNA-PK products in the absence of kinase inhibition show greater dispersal. Use of light-activated Cas9 to induce breaks facilitates temporal resolution of DNA-PK and Mre11 binding, showing that both complexes bind to DNA ends before release of DNA-PK-bound products. These results support a sequential model of double-strand break repair involving collaborative interactions between homologous and non-homologous repair complexes.
Collapse
Affiliation(s)
| | - Alberto Marin-Gonzalez
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Hannah K Barnes
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Phillip R Woolley
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Tanya T Paull
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
12
|
Li Z, Wang Y. Short Double-Stranded DNA (≤40-bp) Affects Repair Pathway Choice. Int J Mol Sci 2023; 24:11836. [PMID: 37511594 PMCID: PMC10380458 DOI: 10.3390/ijms241411836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
To repair ionizing radiation (IR)-induced double strand breaks (DSBs), mammalian cells primarily use canonical non-homologous end-joining (cNHEJ), the homologous recombination (HR) pathway, and the alternative non-homologous end-joining (aEJ) as a backup. These pathways function either compensatively or competitively. High linear energy transfer (LET) compared to low-LET IR kills more cells at the same doses by inhibiting only cNHEJ, but not HR or aEJ. The mechanism remains unclear. The activation of each repair pathway requires the binding of different proteins to DNA fragments of varying lengths. We previously observed an increased generation of small DNA fragments (≤40 bp) in cells following high-LET IR compared to low-LET IR, suggesting that short DNA fragments were one of the major factors interfering with cNHEJ. To provide direct evidence, here we compare the efficiencies of cNHEJ, HR, or aEJ in repairing DSBs containing 30- or 60-bp fragments in vitro and in cells. We show that only cNHEJ but not HR or a-EJ was inefficient for repairing DSBs with 30-bp fragments compared to 60-bp ones, which strongly supports our hypothesis. These results not only enhance our understanding of the DSB repair pathway choice but also hold potential benefits for protection against high-LET IR-induced damage or improving high-LET radiotherapy.
Collapse
Affiliation(s)
- Zhentian Li
- Department of Radiation Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ya Wang
- Department of Radiation Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
13
|
Chae K, Overcash JM, Dawson C, Valentin C, Tsujimoto H, Myles KM, Adelman ZN. CRISPR-based gene editing of non-homologous end joining factors biases DNA repair pathway choice toward single-strand annealing in Aedes aegypti. CURRENT RESEARCH IN BIOTECHNOLOGY 2023; 5:100133. [PMID: 37475832 PMCID: PMC10357993 DOI: 10.1016/j.crbiot.2023.100133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Abstract
To maintain genome stability, eukaryotic cells orchestrate DNA repair pathways to process DNA double-strand breaks (DSBs) that result from diverse developmental or environmental stimuli. Bias in the selection of DSB repair pathways, either non-homologous end joining (NHEJ) or homology-directed repair (HDR), is also critical for efficient gene editing and for homing-based gene drive approaches developed for the control of disease-transmitting vector mosquitoes. However, little is understood about DNA repair homeostasis in the mosquito genome. Here, we utilized CRISPR/Cas9 to generate indel mutant strains for core NHEJ factors ku80, DNA ligase IV (lig4), and DNA-PKcs in the mosquito Aedes aegypti and evaluated the corresponding effects on DNA repair. In a plasmid-based assay, disruption of ku80 or lig4, but not DNA-PKcs, reduced both NHEJ and SSA. However, a transgenic reporter strain-based test revealed that those mutations significantly biased DNA repair events toward SSA. Interestingly, ku80 mutation also significantly increased the end joining rate by a yet-characterized mechanism in males. Our study provides evidence that the core NHEJ factors have an antagonistic effect on SSA-based DSB repair of the Ae. aegypti genome. Down-modulating the NHEJ pathway can enhance the efficiency of nuclease-based genetic control approaches, as most of those operate by homology-based repair processes along with extensive DNA end resection that is antagonized by NHEJ.
Collapse
Affiliation(s)
- Keun Chae
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Justin M. Overcash
- U.S. Department of Agriculture-Animal and Plant Health Inspection Service (USDA-APHIS), Biotechnology Regulatory Services, Riverdale, MD 20737, United States
| | - Chanell Dawson
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Collin Valentin
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Hitoshi Tsujimoto
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Kevin M. Myles
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Zach N. Adelman
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| |
Collapse
|
14
|
Kloeber JA, Lou Z. Critical DNA damaging pathways in tumorigenesis. Semin Cancer Biol 2022; 85:164-184. [PMID: 33905873 PMCID: PMC8542061 DOI: 10.1016/j.semcancer.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/22/2022]
Abstract
The acquisition of DNA damage is an early driving event in tumorigenesis. Premalignant lesions show activated DNA damage responses and inactivation of DNA damage checkpoints promotes malignant transformation. However, DNA damage is also a targetable vulnerability in cancer cells. This requires a detailed understanding of the cellular and molecular mechanisms governing DNA integrity. Here, we review current work on DNA damage in tumorigenesis. We discuss DNA double strand break repair, how repair pathways contribute to tumorigenesis, and how double strand breaks are linked to the tumor microenvironment. Next, we discuss the role of oncogenes in promoting DNA damage through replication stress. Finally, we discuss our current understanding on DNA damage in micronuclei and discuss therapies targeting these DNA damage pathways.
Collapse
Affiliation(s)
- Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
| |
Collapse
|
15
|
Abstract
In mammalian cells, DNA double-strand breaks (DSBs) are mainly repaired by nonhomologous end joining (NHEJ) pathway. Ku (a heterodimer formed by Ku70 and Ku80 proteins) and DNA ligase IV are the core NHEJ factors. Ku could also be involved in other cellular processes, including telomere length regulation, DNA replication, transcription, and translation control. Leishmania, an early branching eukaryote and the causative agent of leishmaniasis, has no functional NHEJ pathway due to its lack of DNA ligase IV and other NHEJ factors but retains Ku70 and Ku80 proteins. In this study, we generated Leishmania donovani Ku70 disruption mutants and Ku70 and Ku80 double gene (Ku70/80) disruption mutants. We found that Leishmania Ku is still involved in DSB repair, possibly through its binding to DNA ends to block and slowdown 5′ end resections and Ku-Ku or other protein interactions. Depending on location of a DSB between the direct repeat genomic sequences, Leishmania Ku could have an inhibiting effect, no effect or a promoting effect on the DSB repair mediated by single strand annealing (SSA), the most frequently used DSB repair pathway in Leishmania. Ku70/80 proteins are also required for the healthy proliferation of Leishmania cells. Interestingly, unlike in Trypanosoma brucei and L. mexicana, Ku70/80 proteins are dispensable for maintaining the normal lengths of telomeres in L. donovani. We also show it is possible to reconstitute the two components (Ku and Ligase D) NHEJ pathway derived from Mycobacterium marinum in Leishmania. This improved DSB repair fidelity and efficiency in Leishmania and sets up an example that the bacterial NHEJ pathway can be successfully reconstructed in an NHEJ-deficient eukaryotic parasite. IMPORTANCE Nonhomologous end joining (NHEJ) is the most efficient double-stranded DNA break (DSB) repair pathway in mammalian cells. In contrast, the protozoan parasite Leishmania has no functional NHEJ pathway but retains the core NHEJ factors of Ku70 and Ku80 proteins. In this study, we found that Leishmania Ku heterodimers are still participating in DSB repair possibly through blocking 5′ end resections and Ku-Ku protein interactions. Depending on the DSB location, Ku could have an inhibiting or promoting effect on DSB repair mediated by the single-strand annealing repair pathway. Ku is also required for the normal growth of the parasite but surprisingly dispensable for maintaining the telomere lengths. Further, we show it is possible to introduce Mycobacterium marinum NHEJ pathway into Leishmania. Understanding DSB repair mechanisms of Leishmania may improve the CRISPR gene targeting specificity and efficiency and help identify new drug targets for this important human parasite.
Collapse
|
16
|
Lu H, Guan J, Wang SY, Li GM, Bohr VA, Davis AJ. DNA-PKcs-dependent phosphorylation of RECQL4 promotes NHEJ by stabilizing the NHEJ machinery at DNA double-strand breaks. Nucleic Acids Res 2022; 50:5635-5651. [PMID: 35580045 PMCID: PMC9178012 DOI: 10.1093/nar/gkac375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/25/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
Non-homologous end joining (NHEJ) is the major pathway that mediates the repair of DNA double-strand breaks (DSBs) generated by ionizing radiation (IR). Previously, the DNA helicase RECQL4 was implicated in promoting NHEJ, but its role in the pathway remains unresolved. In this study, we report that RECQL4 stabilizes the NHEJ machinery at DSBs to promote repair. Specifically, we find that RECQL4 interacts with the NHEJ core factor DNA-PKcs and the interaction is increased following IR. RECQL4 promotes DNA end bridging mediated by DNA-PKcs and Ku70/80 in vitro and the accumulation/retention of NHEJ factors at DSBs in vivo. Moreover, interaction between DNA-PKcs and the other core NHEJ proteins following IR treatment is attenuated in the absence of RECQL4. These data indicate that RECQL4 promotes the stabilization of the NHEJ factors at DSBs to support formation of the NHEJ long-range synaptic complex. In addition, we observed that the kinase activity of DNA-PKcs is required for accumulation of RECQL4 to DSBs and that DNA-PKcs phosphorylates RECQL4 at six serine/threonine residues. Blocking phosphorylation at these sites reduced the recruitment of RECQL4 to DSBs, attenuated the interaction between RECQL4 and NHEJ factors, destabilized interactions between the NHEJ machinery, and resulted in decreased NHEJ. Collectively, these data illustrate reciprocal regulation between RECQL4 and DNA-PKcs in NHEJ.
Collapse
Affiliation(s)
- Huiming Lu
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Junhong Guan
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shih-Ya Wang
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Guo-Min Li
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vilhelm A Bohr
- DNA Repair Section, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Anthony J Davis
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
17
|
Wang Y, Liu B, Lu H, Liu J, Romanienko PJ, Montelione GT, Shen Z. SETD4-mediated KU70 methylation suppresses apoptosis. Cell Rep 2022; 39:110794. [PMID: 35545041 PMCID: PMC9201767 DOI: 10.1016/j.celrep.2022.110794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/28/2021] [Accepted: 04/15/2022] [Indexed: 12/12/2022] Open
Abstract
The mammalian KU70 is a pleiotropic protein functioning in DNA repair and cytoplasmic suppression of apoptosis. We report a regulatory mechanism by which KU70’s cytoplasmic function is enabled due to a methylation at K570 of KU70 by SET-domain-containing protein 4 (SETD4). While SETD4 silencing reduces the level of methylated KU70, over-expression of SETD4 enhances methylation of KU70. Mutations of Y272 and Y284 of SETD4 abrogate methylation of KU70. Although SETD4 is predominantly a nuclear protein, the methylated KU70 is enriched in the cytoplasm. SETD4 knockdown enhances staurosporine (STS)-induced apoptosis and cell killing. Over-expression of the wild-type (WT) SETD4, but not the SETD4-Y272/Y284F mutant, suppresses STS-induced apoptosis. The KU70-K570R (mouse Ku70-K568R) mutation dampens the anti-apoptosis activity of KU70. Our study identifies KU70 as a non-histone substrate of SETD4, discovers a post-translational modification of KU70, and uncovers a role for SETD4 and KU70-K570 methylation in the suppression of apoptosis. Wang et al. identify the methylation of mammalian KU70 by SETD4. This post-translational modification is critical for KU70 localization to the cytoplasm and subsequent suppression of apoptosis.
Collapse
Affiliation(s)
- Yuan Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Bochao Liu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Huimei Lu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Jingmei Liu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Peter J Romanienko
- Genome Editing Shared Resource, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180, USA
| | - Zhiyuan Shen
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA.
| |
Collapse
|
18
|
Gong L, Zhang Y, Zhao J, Zhang Y, Tu K, Jiao L, Xu Q, Zhang M, Han S. All-In-One Biomimetic Nanoplatform Based on Hollow Polydopamine Nanoparticles for Synergistically Enhanced Radiotherapy of Colon Cancer. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107656. [PMID: 35150039 DOI: 10.1002/smll.202107656] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Even though radiotherapy is the most important therapeutic strategy for colon cancer treatment, there is an enormous demand to improve radiosensitivity in solid tumor destruction. For this purpose, a biomimetic nanoplatform based on hollow polydopamine nanoparticles (HP) with homologous targeting and pH-responsive drug release properties is designed. In this work, HP is constructed by using a chelation competition-induced polymerization strategy and then modified with the cancer cell membrane. Hollow polydopamine integrated with Pt nanoparticles (Pt@HP) has a catalase-like activity, which can be used to trigger endogenous H2 O2 into O2 , relieving hypoxia of the tumor microenvironment (TME). With mesoporous shells and large cavities, Pt@HP shows efficient apoptin100-109 (AP) and verteporfin (VP) loading to form AVPt@HP@M. Under X-ray irradiation, AVPt@HP@M exerts a radiosensitization effect via multiple strategies, including relieving hypoxia (Pt NPs), enhancing tumor apoptosis (AP), and X-ray-induced photodynamic therapy (X-PDT) (VP). Further metabonomics analysis shows that the specific mechanism of the AVPt@HP@M is through influencing purine metabolism. Without appreciable systemic toxicity, this nanoplatform highlights a new strategy for effective radiosensitization and provides a reference for treating malignant tumors.
Collapse
Affiliation(s)
- Liuyun Gong
- Department of Radiotherapy, the First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Yujie Zhang
- School of Basic Medical Sciences, Xi'an Key Laboratory of Immune Related Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, 710061, China
| | - Jing Zhao
- Department of Radiotherapy, the First Affiliated Hospital, Soochow University, Suzhou, Jiangsu, 215000, China
| | - Yilei Zhang
- School of Basic Medical Sciences, Xi'an Key Laboratory of Immune Related Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, 710061, China
| | - Kangsheng Tu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Lianying Jiao
- School of Basic Medical Sciences, Xi'an Key Laboratory of Immune Related Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, 710061, China
| | - Qiuran Xu
- Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou, Zhejiang, 310009, China
| | - Mingzhen Zhang
- School of Basic Medical Sciences, Xi'an Key Laboratory of Immune Related Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, 710061, China
| | - Suxia Han
- Department of Radiotherapy, the First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| |
Collapse
|
19
|
Kciuk M, Gielecińska A, Mujwar S, Mojzych M, Kontek R. Cyclin-dependent kinases in DNA damage response. Biochim Biophys Acta Rev Cancer 2022; 1877:188716. [DOI: 10.1016/j.bbcan.2022.188716] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 02/06/2023]
|
20
|
Finelli R, Moreira BP, Alves MG, Agarwal A. Unraveling the Molecular Impact of Sperm DNA Damage on Human Reproduction. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1358:77-113. [DOI: 10.1007/978-3-030-89340-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
21
|
Penninckx S, Pariset E, Cekanaviciute E, Costes SV. Quantification of radiation-induced DNA double strand break repair foci to evaluate and predict biological responses to ionizing radiation. NAR Cancer 2021; 3:zcab046. [PMID: 35692378 PMCID: PMC8693576 DOI: 10.1093/narcan/zcab046] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/08/2021] [Accepted: 12/17/2021] [Indexed: 08/08/2023] Open
Abstract
Radiation-induced foci (RIF) are nuclear puncta visualized by immunostaining of proteins that regulate DNA double-strand break (DSB) repair after exposure to ionizing radiation. RIF are a standard metric for measuring DSB formation and repair in clinical, environmental and space radiobiology. The time course and dose dependence of their formation has great potential to predict in vivo responses to ionizing radiation, predisposition to cancer and probability of adverse reactions to radiotherapy. However, increasing complexity of experimentally and therapeutically setups (charged particle, FLASH …) is associated with several confounding factors that must be taken into account when interpreting RIF values. In this review, we discuss the spatiotemporal characteristics of RIF development after irradiation, addressing the common confounding factors, including cell proliferation and foci merging. We also describe the relevant endpoints and mathematical models that enable accurate biological interpretation of RIF formation and resolution. Finally, we discuss the use of RIF as a biomarker for quantification and prediction of in vivo radiation responses, including important caveats relating to the choice of the biological endpoint and the detection method. This review intends to help scientific community design radiobiology experiments using RIF as a key metric and to provide suggestions for their biological interpretation.
Collapse
Affiliation(s)
- Sébastien Penninckx
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Medical Physics Department, Jules Bordet Institute, Université Libre de Bruxelles, 1 Rue Héger-Bordet, 1000 Brussels, Belgium
| | - Eloise Pariset
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Universities Space Research Association, 615 National Avenue, Mountain View, CA 94043, USA
| | - Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sylvain V Costes
- To whom correspondence should be addressed. Tel: +1 650 604 5343;
| |
Collapse
|
22
|
Schellenbauer A, Guilly MN, Grall R, Le Bars R, Paget V, Kortulewski T, Sutcu H, Mathé C, Hullo M, Biard D, Leteurtre F, Barroca V, Corre Y, Irbah L, Rass E, Theze B, Bertrand P, Demmers JAA, Guirouilh-Barbat J, Lopez BS, Chevillard S, Delic J. Phospho-Ku70 induced by DNA damage interacts with RNA Pol II and promotes the formation of phospho-53BP1 foci to ensure optimal cNHEJ. Nucleic Acids Res 2021; 49:11728-11745. [PMID: 34718776 PMCID: PMC8599715 DOI: 10.1093/nar/gkab980] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/15/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022] Open
Abstract
Canonical non-homologous end-joining (cNHEJ) is the prominent mammalian DNA double-strand breaks (DSBs) repair pathway operative throughout the cell cycle. Phosphorylation of Ku70 at ser27-ser33 (pKu70) is induced by DNA DSBs and has been shown to regulate cNHEJ activity, but the underlying mechanism remained unknown. Here, we established that following DNA damage induction, Ku70 moves from nucleoli to the sites of damage, and once linked to DNA, it is phosphorylated. Notably, the novel emanating functions of pKu70 are evidenced through the recruitment of RNA Pol II and concomitant formation of phospho-53BP1 foci. Phosphorylation is also a prerequisite for the dynamic release of Ku70 from the repair complex through neddylation-dependent ubiquitylation. Although the non-phosphorylable ala-Ku70 form does not compromise the formation of the NHEJ core complex per se, cells expressing this form displayed constitutive and stress-inducible chromosomal instability. Consistently, upon targeted induction of DSBs by the I-SceI meganuclease into an intrachromosomal reporter substrate, cells expressing pKu70, rather than ala-Ku70, are protected against the joining of distal DNA ends. Collectively, our results underpin the essential role of pKu70 in the orchestration of DNA repair execution in living cells and substantiated the way it paves the maintenance of genome stability.
Collapse
Affiliation(s)
- Amelie Schellenbauer
- Laboratoire de Cancérologie Expérimentale, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, 18, Av. du Panorama, 92265 Fontenay aux Roses, *Université Paris Descartes, 75006 Paris, France
| | - Marie-Noelle Guilly
- Laboratoire de Cancérologie Expérimentale, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, 18, Av. du Panorama, 92265 Fontenay aux Roses, *Université Paris Descartes, 75006 Paris, France
| | - Romain Grall
- Laboratoire de Cancérologie Expérimentale, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, 18, Av. du Panorama, 92265 Fontenay aux Roses, *Université Paris Descartes, 75006 Paris, France
| | - Romain Le Bars
- Light Microscopy Facility, Imagerie-Gif, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Vincent Paget
- IRS[N]/PSE-SANTE/SERAMED/LRMed, 31, Av. De la Division Leclerc, 92260 Fontenay aux Roses, France
| | - Thierry Kortulewski
- Laboratoire de Radiopathologie, UMR Stabilité Génétique Cellules Souches et Radiations, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, UMRE008-U1274, 18 Av. du Panorama, 92265 Fontenay aux Roses, France
| | - Haser Sutcu
- IRS[N]/PSE-SANTE/SERAMED/LRAcc, 31, Av. De la Division Leclerc, 92260 Fontenay aux Roses, France
| | - Cécile Mathé
- Laboratoire de Cancérologie Expérimentale, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, 18, Av. du Panorama, 92265 Fontenay aux Roses, *Université Paris Descartes, 75006 Paris, France
| | - Marie Hullo
- Laboratoire de Cancérologie Expérimentale, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, 18, Av. du Panorama, 92265 Fontenay aux Roses, *Université Paris Descartes, 75006 Paris, France
| | - Denis Biard
- Service d'étude des prions et maladies atypiques (SEPIA), DRF, Institut de Biologie François Jacob (IBFJ), IRCM, 18, Av. du Panorama, 92265 Fontenay aux Roses, France
| | - François Leteurtre
- Laboratoire de Cancérologie Expérimentale, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, 18, Av. du Panorama, 92265 Fontenay aux Roses, *Université Paris Descartes, 75006 Paris, France
| | - Vilma Barroca
- Laboratoire Réparation et Transcription dans les cellules Souches, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, UMRE008-U1274, 18, Av. du Panorama, 92265 Fontenay aux Roses, France
| | - Youenn Corre
- Laboratoire de Cancérologie Expérimentale, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, 18, Av. du Panorama, 92265 Fontenay aux Roses, *Université Paris Descartes, 75006 Paris, France
| | - Lamya Irbah
- Plateforme de Microscopie, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, UMRE008-U12745, 18, Av. du Panorama, 92265 Fontenay aux Roses, France
| | - Emilie Rass
- Laboratoire de Réparation et Vieillissement; Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, UMRE008-U1274, 18, Av. du Panorama, 92265 Fontenay aux Roses, France
| | - Benoit Theze
- Laboratoire de Réparation et Vieillissement; Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, UMRE008-U1274, 18, Av. du Panorama, 92265 Fontenay aux Roses, France
| | - Pascale Bertrand
- Laboratoire de Réparation et Vieillissement; Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, UMRE008-U1274, 18, Av. du Panorama, 92265 Fontenay aux Roses, France
| | - Jeroen A A Demmers
- Proteomics Center, Room Ee-679A | Faculty Building, Erasmus University Medical Center Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Josée Guirouilh-Barbat
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, 24 rue du Faubourg St Jacques, 75014 Paris, France
| | - Bernard S Lopez
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, 24 rue du Faubourg St Jacques, 75014 Paris, France
| | - Sylvie Chevillard
- Laboratoire de Cancérologie Expérimentale, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris-Saclay, DRF, Institut de Biologie François Jacob (IBFJ), IRCM, 18, Av. du Panorama, 92265 Fontenay aux Roses, *Université Paris Descartes, 75006 Paris, France
| | - Jozo Delic
- To whom correspondence should be addressed. Tel: +33 1 4654 7552;
| |
Collapse
|
23
|
Singh JK, Smith R, Rother MB, de Groot AJL, Wiegant WW, Vreeken K, D’Augustin O, Kim RQ, Qian H, Krawczyk PM, González-Prieto R, Vertegaal ACO, Lamers M, Huet S, van Attikum H. Zinc finger protein ZNF384 is an adaptor of Ku to DNA during classical non-homologous end-joining. Nat Commun 2021; 12:6560. [PMID: 34772923 PMCID: PMC8589989 DOI: 10.1038/s41467-021-26691-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/19/2021] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are among the most deleterious types of DNA damage as they can lead to mutations and chromosomal rearrangements, which underlie cancer development. Classical non-homologous end-joining (cNHEJ) is the dominant pathway for DSB repair in human cells, involving the DNA-binding proteins XRCC6 (Ku70) and XRCC5 (Ku80). Other DNA-binding proteins such as Zinc Finger (ZnF) domain-containing proteins have also been implicated in DNA repair, but their role in cNHEJ remained elusive. Here we show that ZNF384, a member of the C2H2 family of ZnF proteins, binds DNA ends in vitro and is recruited to DSBs in vivo. ZNF384 recruitment requires the poly(ADP-ribosyl) polymerase 1 (PARP1)-dependent expansion of damaged chromatin, followed by binding of its C2H2 motifs to the exposed DNA. Moreover, ZNF384 interacts with Ku70/Ku80 via its N-terminus, thereby promoting Ku70/Ku80 assembly and the accrual of downstream cNHEJ factors, including APLF and XRCC4/LIG4, for efficient repair at DSBs. Altogether, our data suggest that ZNF384 acts as a 'Ku-adaptor' that binds damaged DNA and Ku70/Ku80 to facilitate the build-up of a cNHEJ repairosome, highlighting a role for ZNF384 in DSB repair and genome maintenance.
Collapse
Affiliation(s)
- Jenny Kaur Singh
- grid.10419.3d0000000089452978Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rebecca Smith
- grid.410368.80000 0001 2191 9284Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, BIOSIT–UMS3480, F-35000 Rennes, France
| | - Magdalena B. Rother
- grid.10419.3d0000000089452978Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anton J. L. de Groot
- grid.10419.3d0000000089452978Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Wouter W. Wiegant
- grid.10419.3d0000000089452978Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kees Vreeken
- grid.10419.3d0000000089452978Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ostiane D’Augustin
- grid.410368.80000 0001 2191 9284Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, BIOSIT–UMS3480, F-35000 Rennes, France ,grid.457349.80000 0004 0623 0579Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, F-92265 Fontenay-aux-Roses, France
| | - Robbert Q. Kim
- grid.10419.3d0000000089452978Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Haibin Qian
- grid.16872.3a0000 0004 0435 165XDepartment of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Przemek M. Krawczyk
- grid.16872.3a0000 0004 0435 165XDepartment of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Román González-Prieto
- grid.16872.3a0000 0004 0435 165XDepartment of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Alfred C. O. Vertegaal
- grid.16872.3a0000 0004 0435 165XDepartment of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Meindert Lamers
- grid.16872.3a0000 0004 0435 165XDepartment of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Sébastien Huet
- grid.410368.80000 0001 2191 9284Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, BIOSIT–UMS3480, F-35000 Rennes, France ,grid.440891.00000 0001 1931 4817Institut Universitaire de France, F-75000 Paris, France
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| |
Collapse
|
24
|
Frock RL, Sadeghi C, Meng J, Wang JL. DNA End Joining: G0-ing to the Core. Biomolecules 2021; 11:biom11101487. [PMID: 34680120 PMCID: PMC8533500 DOI: 10.3390/biom11101487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/28/2022] Open
Abstract
Humans have evolved a series of DNA double-strand break (DSB) repair pathways to efficiently and accurately rejoin nascently formed pairs of double-stranded DNA ends (DSEs). In G0/G1-phase cells, non-homologous end joining (NHEJ) and alternative end joining (A-EJ) operate to support covalent rejoining of DSEs. While NHEJ is predominantly utilized and collaborates extensively with the DNA damage response (DDR) to support pairing of DSEs, much less is known about A-EJ collaboration with DDR factors when NHEJ is absent. Non-cycling lymphocyte progenitor cells use NHEJ to complete V(D)J recombination of antigen receptor genes, initiated by the RAG1/2 endonuclease which holds its pair of targeted DSBs in a synapse until each specified pair of DSEs is handed off to the NHEJ DSB sensor complex, Ku. Similar to designer endonuclease DSBs, the absence of Ku allows for A-EJ to access RAG1/2 DSEs but with random pairing to complete their repair. Here, we describe recent insights into the major phases of DSB end joining, with an emphasis on synapsis and tethering mechanisms, and bring together new and old concepts of NHEJ vs. A-EJ and on RAG2-mediated repair pathway choice.
Collapse
|
25
|
Saha J, Bae J, Wang SY, Lu H, Chappell LJ, Gopal P, Davis AJ. Ablating putative Ku70 phosphorylation sites results in defective DNA damage repair and spontaneous induction of hepatocellular carcinoma. Nucleic Acids Res 2021; 49:9836-9850. [PMID: 34428289 PMCID: PMC8464062 DOI: 10.1093/nar/gkab743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/31/2022] Open
Abstract
Multiple pathways mediate the repair of DNA double-strand breaks (DSBs), with numerous mechanisms responsible for driving choice between the pathways. Previously, we reported that mutating five putative phosphorylation sites on the non-homologous end joining (NHEJ) factor, Ku70, results in sustained retention of human Ku70/80 at DSB ends and attenuation of DSB repair via homologous recombination (HR). In this study, we generated a knock-in mouse, in which the three conserved putative phosphorylation sites of Ku70 were mutated to alanine to ablate potential phosphorylation (Ku703A/3A), in order to examine if disrupting DSB repair pathway choice by modulating Ku70/80 dynamics at DSB ends results in enhanced genomic instability and tumorigenesis. The Ku703A/3A mice developed spontaneous and have accelerated chemical-induced hepatocellular carcinoma (HCC) compared to wild-type (Ku70+/+) littermates. The HCC tumors from the Ku703A/3A mice have increased γH2AX and 8-oxo-G staining, suggesting decreased DNA repair. Spontaneous transformed cell lines from Ku703A/3A mice are more radiosensitive, have a significant decrease in DNA end resection, and are more sensitive to the DNA cross-linking agent mitomycin C compared to cells from Ku70+/+ littermates. Collectively, these findings demonstrate that mutating the putative Ku70 phosphorylation sites results in defective DNA damage repair and disruption of this process drives genomic instability and accelerated development of HCC.
Collapse
Affiliation(s)
- Janapriya Saha
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jinsung Bae
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Shih-Ya Wang
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Huiming Lu
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | | | - Purva Gopal
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Anthony J Davis
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
26
|
Paull TT. Reconsidering pathway choice: a sequential model of mammalian DNA double-strand break pathway decisions. Curr Opin Genet Dev 2021; 71:55-62. [PMID: 34293662 DOI: 10.1016/j.gde.2021.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/14/2021] [Accepted: 06/29/2021] [Indexed: 12/27/2022]
Abstract
DNA double-strand breaks can be repaired through ligation-based pathways (non-homologous end-joining) or replication-based pathways (homologous recombination) in eukaryotic cells. The decisions that govern these outcomes are widely viewed as a competition between factors that recognize DNA ends and physically promote association of factors specific to each pathway, commonly known as 'pathway choice'. Here I review recent results in the literature and propose that this decision is better described as a sequential set of binding and end processing events, with non-homologous end joining as the first decision point. Physical association and co-localization of end resection factors with non-homologous end-joining factors suggests that ends are transferred between these complexes, thus the ultimate outcome is not the result of a competition but is more akin to a relay race that is determined by the efficiency of the initial end-joining event and the availability of activated DNA end-processing enzymes.
Collapse
Affiliation(s)
- Tanya T Paull
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712, United States.
| |
Collapse
|
27
|
Ackerson SM, Romney C, Schuck PL, Stewart JA. To Join or Not to Join: Decision Points Along the Pathway to Double-Strand Break Repair vs. Chromosome End Protection. Front Cell Dev Biol 2021; 9:708763. [PMID: 34322492 PMCID: PMC8311741 DOI: 10.3389/fcell.2021.708763] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/17/2021] [Indexed: 01/01/2023] Open
Abstract
The regulation of DNA double-strand breaks (DSBs) and telomeres are diametrically opposed in the cell. DSBs are considered one of the most deleterious forms of DNA damage and must be quickly recognized and repaired. Telomeres, on the other hand, are specialized, stable DNA ends that must be protected from recognition as DSBs to inhibit unwanted chromosome fusions. Decisions to join DNA ends, or not, are therefore critical to genome stability. Yet, the processing of telomeres and DSBs share many commonalities. Accordingly, key decision points are used to shift DNA ends toward DSB repair vs. end protection. Additionally, DSBs can be repaired by two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ). The choice of which repair pathway is employed is also dictated by a series of decision points that shift the break toward HR or NHEJ. In this review, we will focus on these decision points and the mechanisms that dictate end protection vs. DSB repair and DSB repair choice.
Collapse
Affiliation(s)
- Stephanie M Ackerson
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Carlan Romney
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - P Logan Schuck
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Jason A Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| |
Collapse
|
28
|
Xue C, Greene EC. DNA Repair Pathway Choices in CRISPR-Cas9-Mediated Genome Editing. Trends Genet 2021; 37:639-656. [PMID: 33896583 PMCID: PMC8187289 DOI: 10.1016/j.tig.2021.02.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
Many clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-based genome editing technologies take advantage of Cas nucleases to induce DNA double-strand breaks (DSBs) at desired locations within a genome. Further processing of the DSBs by the cellular DSB repair machinery is then necessary to introduce desired mutations, sequence insertions, or gene deletions. Thus, the accuracy and efficiency of genome editing are influenced by the cellular DSB repair pathways. DSBs are themselves highly genotoxic lesions and as such cells have evolved multiple mechanisms for their repair. These repair pathways include homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single-strand annealing (SSA). In this review, we briefly highlight CRISPR-Cas9 and then describe the mechanisms of DSB repair. Finally, we summarize recent findings of factors that can influence the choice of DNA repair pathway in response to Cas9-induced DSBs.
Collapse
Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
29
|
Hammel M, Tainer JA. X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology. Protein Sci 2021; 30:1735-1756. [PMID: 34056803 PMCID: PMC8376411 DOI: 10.1002/pro.4133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022]
Abstract
Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIVBRCT–Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.
Collapse
Affiliation(s)
- Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
30
|
Qi Y, Warmenhoven JW, Henthorn NT, Ingram SP, Xu XG, Kirkby KJ, Merchant MJ. Mechanistic Modelling of Slow and Fast NHEJ DNA Repair Pathways Following Radiation for G0/G1 Normal Tissue Cells. Cancers (Basel) 2021; 13:2202. [PMID: 34063683 PMCID: PMC8124137 DOI: 10.3390/cancers13092202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/23/2021] [Accepted: 04/29/2021] [Indexed: 01/12/2023] Open
Abstract
Mechanistic in silico models can provide insight into biological mechanisms and highlight uncertainties for experimental investigation. Radiation-induced double-strand breaks (DSBs) are known to be toxic lesions if not repaired correctly. Non-homologous end joining (NHEJ) is the major DSB-repair pathway available throughout the cell cycle and, recently, has been hypothesised to consist of a fast and slow component in G0/G1. The slow component has been shown to be resection-dependent, requiring the nuclease Artemis to function. However, the pathway is not yet fully understood. This study compares two hypothesised models, simulating the action of individual repair proteins on DSB ends in a step-by-step manner, enabling the modelling of both wild-type and protein-deficient cell systems. Performance is benchmarked against experimental data from 21 cell lines and 18 radiation qualities. A model where resection-dependent and independent pathways are entirely separated can only reproduce experimental repair kinetics with additional restraints on end motion and protein recruitment. However, a model where the pathways are entwined was found to effectively fit without needing additional mechanisms. It has been shown that DaMaRiS is a useful tool when analysing the connections between resection-dependent and independent NHEJ repair pathways and robustly matches with experimental results from several sources.
Collapse
Affiliation(s)
- Yaping Qi
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026, China;
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
| | - John William Warmenhoven
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Nicholas Thomas Henthorn
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Samuel Peter Ingram
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester M13 9PL, UK
| | - Xie George Xu
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026, China;
| | - Karen Joy Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Michael John Merchant
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| |
Collapse
|
31
|
Abbasi S, Parmar G, Kelly RD, Balasuriya N, Schild-Poulter C. The Ku complex: recent advances and emerging roles outside of non-homologous end-joining. Cell Mol Life Sci 2021; 78:4589-4613. [PMID: 33855626 PMCID: PMC11071882 DOI: 10.1007/s00018-021-03801-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/29/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022]
Abstract
Since its discovery in 1981, the Ku complex has been extensively studied under multiple cellular contexts, with most work focusing on Ku in terms of its essential role in non-homologous end-joining (NHEJ). In this process, Ku is well-known as the DNA-binding subunit for DNA-PK, which is central to the NHEJ repair process. However, in addition to the extensive study of Ku's role in DNA repair, Ku has also been implicated in various other cellular processes including transcription, the DNA damage response, DNA replication, telomere maintenance, and has since been studied in multiple contexts, growing into a multidisciplinary point of research across various fields. Some advances have been driven by clarification of Ku's structure, including the original Ku crystal structure and the more recent Ku-DNA-PKcs crystallography, cryogenic electron microscopy (cryoEM) studies, and the identification of various post-translational modifications. Here, we focus on the advances made in understanding the Ku heterodimer outside of non-homologous end-joining, and across a variety of model organisms. We explore unique structural and functional aspects, detail Ku expression, conservation, and essentiality in different species, discuss the evidence for its involvement in a diverse range of cellular functions, highlight Ku protein interactions and recent work concerning Ku-binding motifs, and finally, we summarize the clinical Ku-related research to date.
Collapse
Affiliation(s)
- Sanna Abbasi
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Gursimran Parmar
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Rachel D Kelly
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Nileeka Balasuriya
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada.
| |
Collapse
|
32
|
Zahid S, Seif El Dahan M, Iehl F, Fernandez-Varela P, Le Du MH, Ropars V, Charbonnier JB. The Multifaceted Roles of Ku70/80. Int J Mol Sci 2021; 22:ijms22084134. [PMID: 33923616 PMCID: PMC8073936 DOI: 10.3390/ijms22084134] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/11/2022] Open
Abstract
DNA double-strand breaks (DSBs) are accidental lesions generated by various endogenous or exogenous stresses. DSBs are also genetically programmed events during the V(D)J recombination process, meiosis, or other genome rearrangements, and they are intentionally generated to kill cancer during chemo- and radiotherapy. Most DSBs are processed in mammalian cells by the classical nonhomologous end-joining (c-NHEJ) pathway. Understanding the molecular basis of c-NHEJ has major outcomes in several fields, including radiobiology, cancer therapy, immune disease, and genome editing. The heterodimer Ku70/80 (Ku) is a central actor of the c-NHEJ as it rapidly recognizes broken DNA ends in the cell and protects them from nuclease activity. It subsequently recruits many c-NHEJ effectors, including nucleases, polymerases, and the DNA ligase 4 complex. Beyond its DNA repair function, Ku is also involved in several other DNA metabolism processes. Here, we review the structural and functional data on the DNA and RNA recognition properties of Ku implicated in DNA repair and in telomeres maintenance.
Collapse
|
33
|
Tsuyama T, Fujita K, Sasaki R, Hamanaka S, Sotoyama Y, Ogawa A, Kusuzaki K, Azuma Y, Tada S. N-terminal region of RecQ4 inhibits non-homologous end joining and chromatin association of the Ku heterodimer in Xenopus egg extracts. Gene 2021; 787:145647. [PMID: 33845136 DOI: 10.1016/j.gene.2021.145647] [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: 11/13/2020] [Revised: 03/30/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
RecQ4, a member of the RecQ helicase family, is required for the maintenance of genome integrity. RecQ4 has been shown to promote the following two DNA double-strand break (DSB) repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). However, its molecular function has not been fully elucidated. In the present study, we aimed to investigate the role of RecQ4 in NHEJ using Xenopus egg extracts. The N-terminal 598 amino acid region of Xenopus RecQ4 (N598), which lacks a central helicase domain and a downstream C-terminal region, was added to the extracts and its effect on the joining of DNA ends was analyzed. We found that N598 inhibited the joining of linearized DNA ends in the extracts. In addition, N598 inhibited DSB-induced chromatin binding of Ku70, which is essential for NHEJ, while the DSB-induced chromatin binding of the HR-associated proteins, replication protein A (RPA) and Rad51, increased upon the addition of N598. These results suggest that RecQ4 possibly influences the choice of the DSB repair pathway by influencing the association of the Ku heterodimer with the DNA ends.
Collapse
Affiliation(s)
- Takashi Tsuyama
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Toho University, Funabashi-shi, Chiba 274-8510, Japan
| | - Kumiko Fujita
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Toho University, Funabashi-shi, Chiba 274-8510, Japan
| | - Ryosuke Sasaki
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Toho University, Funabashi-shi, Chiba 274-8510, Japan
| | - Shiori Hamanaka
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Toho University, Funabashi-shi, Chiba 274-8510, Japan
| | - Yuki Sotoyama
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Toho University, Funabashi-shi, Chiba 274-8510, Japan
| | - Akira Ogawa
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Toho University, Funabashi-shi, Chiba 274-8510, Japan
| | - Kana Kusuzaki
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Toho University, Funabashi-shi, Chiba 274-8510, Japan
| | - Yutaro Azuma
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Toho University, Funabashi-shi, Chiba 274-8510, Japan
| | - Shusuke Tada
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Toho University, Funabashi-shi, Chiba 274-8510, Japan.
| |
Collapse
|
34
|
Ghosh D, Raghavan SC. Nonhomologous end joining: new accessory factors fine tune the machinery. Trends Genet 2021; 37:582-599. [PMID: 33785198 DOI: 10.1016/j.tig.2021.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 01/08/2023]
Abstract
Nonhomologous DNA end joining (NHEJ) is one of the major DNA double-strand break (DSB) repair pathways in eukaryotes. The well-known critical proteins involved in NHEJ include Ku70/80, DNA-PKcs, Artemis, DNA pol λ/μ, DNA ligase IV-XRCC4, and XLF. Recent studies have added a number of new proteins to the NHEJ repertoire namely paralog of XRCC4 and XLF (PAXX), modulator of retroviral infection (MRI)/ cell cycle regulator of NHEJ (CYREN), transactivation response DNA-binding protein (TARDBP) of 43 kDa (TDP-43), intermediate filament family orphan (IFFO1), ERCC excision repair 6 like 2 (ERCC6L2), and RNase H2. PAXX acts as a stabilizing factor for the main NHEJ components. MRI/CYREN seems to play a dual role stimulating NHEJ in the G1 phase of the cell cycle, while inhibiting the pathway in the S and G2 phases. TDP-43 can recruit the ligase IV-XRCC4 complex to the DSB sites and stimulate ligation in neuronal cells. RNase H2 excises out the ribonucleotides inserted during repair by DNA polymerase μ/TdT. This review provides a brief glimpse into how these new partners were discovered and their contribution to the mechanism and regulation of NHEJ.
Collapse
Affiliation(s)
- Dipayan Ghosh
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
35
|
Stinson BM, Loparo JJ. Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway. Annu Rev Biochem 2021; 90:137-164. [PMID: 33556282 DOI: 10.1146/annurev-biochem-080320-110356] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA double-strand breaks pose a serious threat to genome stability. In vertebrates, these breaks are predominantly repaired by nonhomologous end joining (NHEJ), which pairs DNA ends in a multiprotein synaptic complex to promote their direct ligation. NHEJ is a highly versatile pathway that uses an array of processing enzymes to modify damaged DNA ends and enable their ligation. The mechanisms of end synapsis and end processing have important implications for genome stability. Rapid and stable synapsis is necessary to limit chromosome translocations that result from the mispairing of DNA ends. Furthermore, end processing must be tightly regulated to minimize mutations at the break site. Here, we review our current mechanistic understanding of vertebrate NHEJ, with a particular focus on end synapsis and processing.
Collapse
Affiliation(s)
- Benjamin M Stinson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| |
Collapse
|
36
|
Nie S, Wang A, Yuan Y. Comparison of clinicopathological parameters, prognosis, micro-ecological environment and metabolic function of Gastric Cancer with or without Fusobacterium sp. Infection. J Cancer 2021; 12:1023-1032. [PMID: 33442401 PMCID: PMC7797643 DOI: 10.7150/jca.50918] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Fusobacterium sp. plays a crucial role in the tumorigenesis and development of gastrointestinal tumors. Our research group previously disclosed that Fusobacterium sp. was more abundant in gastric cancer (GC) tissues than adjacent non-cancerous (NC) tissues. However, Fusobacterium sp. did not exist in all GC tissues and the differentiated features of GC with or without Fusobacterium sp. infection is not clear. Methods: The expression data of 61 GC tissues came from 16S rRNA gene sequencing. Comparison groups were defined based on sOTU at the genus level of Fusobacterium sp., which was performed by the Qiime2 microbiome bioinformatics platform. We used Chi-square and Fisher's exact test to compare clinicopathological parameters, and used Kaplan-Meier analysis, Cox univariate and multivariate analysis to compare prognosis. Micro-ecological environment comparison was characterized by 16S rRNA gene sequencing, and the metabolic function prediction was applied by PICRUSt2. Results of microbial diversity, differential enrichment genus and metabolic function in GC with or without Fusobacterium sp. infection was validated with 229 GC tissues downloaded from an independent cohort in ENA database (PRJNA428883). Results: The infection rate of Fusobacterium sp. in 61 GC tissues was 52.46% and elderly GC patients were more prone to Fusobacterium sp. infection. GC patients infected with Fusobacterium sp. were more likely to have tumor-infiltrating lymphocytes and p53 expression. The microbial diversity and microbial structure showed significant differences between two GC tissue groups with 42 differential enrichment genera. The metabolic function of Fusobacterium sp.-positive GC tissues was related to the biosynthesis of lysine, peptidoglycan, and tRNA. The differences in microbial structure, the existence of some differential enrichment genera and the metabolic function of Fusobacterium sp.-positive GC tissues, were then validated by 229 GC tissues of an independent cohort. Conclusions: Fusobacterium sp. infection can affect the phenotypic characteristics, micro-ecological environment, and metabolic functions of GC, which may provide a basis for further exploring the relationship between Fusobacterium sp. infection and carcinogenesis of GC.
Collapse
Affiliation(s)
- Siru Nie
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Ang Wang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| |
Collapse
|
37
|
Finelli R, Darbandi S, Pushparaj PN, Henkel R, Ko E, Agarwal A. In Silico Sperm Proteome Analysis to Investigate DNA Repair Mechanisms in Varicocele Patients. Front Endocrinol (Lausanne) 2021; 12:757592. [PMID: 34975746 PMCID: PMC8719329 DOI: 10.3389/fendo.2021.757592] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/30/2021] [Indexed: 01/19/2023] Open
Abstract
Varicocele, a condition associated with increased oxidative stress, negatively affects sperm DNA integrity and reduces pregnancy rates. However, the molecular mechanisms related to DNA integrity, damage, and repair in varicocele patients remain unclear. This study aimed to determine the role of DNA repair molecular mechanisms in varicocele-related infertility by combining an in silico proteomics approach with wet-laboratory techniques. Proteomics results previously generated from varicocele patients (n=50) and fertile controls (n=10) attending our Andrology Center were reanalyzed using bioinformatics tools, including the WEB-based Gene SeT AnaLysis Toolkit, Open Target Platform, and Ingenuity Pathway Analysis (IPA), to identify differentially expressed proteins (DEPs) involved in DNA repair. Subsequently, selected DEPs in spermatozoa were validated using western blotting in varicocele (n = 13) and fertile control (n = 5) samples. We identified 99 DEPs mainly involved in male reproductive system disease (n=66) and male infertility (n=47). IPA analysis identified five proteins [fatty acid synthase (FASN), myeloperoxidase (MPO), mitochondrial aconitate hydratase (ACO2), nucleoporin 93 (NUP93), and 26S proteasome non-ATPase regulatory subunit 14 (PSMD14)] associated with DNA repair deficiency, which showed altered expression in varicocele (P <0.03). We validated ACO2 downregulation (fold change=0.37, change%=-62.7%, P=0.0001) and FASN overexpression (fold change = 4.04, change %= 303.7%, P = 0.014) in men with varicocele compared to controls. This study combined a unique in silico approach with an in vitro validation of the molecular mechanisms that may be responsible for varicocele-associated infertility. We identified ACO2 and FASN as possible proteins involved in DNA repair, whose altered expression may contribute to DNA damage in varicocele pathophysiology.
Collapse
Affiliation(s)
- Renata Finelli
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, United States
| | - Sara Darbandi
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
- Gene Therapy and Regenerative Medicine Research Center, Hope Generation Foundation, Tehran, Iran
| | - Peter Natesan Pushparaj
- Center of Excellence in Genomic Medicine Research and Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ralf Henkel
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, United States
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Department of Medical Bioscience, University of the Western Cape, Bellville, South Africa
- LogixX Pharma, Reading, United Kingdom
| | - Edmund Ko
- Department of Urology, Loma Linda University Health, Loma Linda, CA, United States
| | - Ashok Agarwal
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, United States
- *Correspondence: Ashok Agarwal,
| |
Collapse
|
38
|
Whelan DR, Lee WTC, Marks F, Kong YT, Yin Y, Rothenberg E. Super-resolution visualization of distinct stalled and broken replication fork structures. PLoS Genet 2020; 16:e1009256. [PMID: 33370257 PMCID: PMC7793303 DOI: 10.1371/journal.pgen.1009256] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 01/08/2021] [Accepted: 11/03/2020] [Indexed: 12/25/2022] Open
Abstract
Endogenous genotoxic stress occurs in healthy cells due to competition between DNA replication machinery, and transcription and topographic relaxation processes. This causes replication fork stalling and regression, which can further collapse to form single-ended double strand breaks (seDSBs). Super-resolution microscopy has made it possible to directly observe replication stress and DNA damage inside cells, however new approaches to sample preparation and analysis are required. Here we develop and apply multicolor single molecule microscopy to visualize individual replication forks under mild stress from the trapping of Topoisomerase I cleavage complexes, a damage induction which closely mimics endogenous replicative stress. We observe RAD51 and RAD52, alongside RECQ1, as the first responder proteins to stalled but unbroken forks, whereas Ku and MRE11 are initially recruited to seDSBs. By implementing novel super-resolution imaging assays, we are thus able to discern closely related replication fork stress motifs and their repair pathways.
Collapse
Affiliation(s)
- Donna R. Whelan
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, Victoria, Australia
- * E-mail: (DRW); (ER)
| | - Wei Ting C. Lee
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, New York, United States of America
| | - Frances Marks
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, New York, United States of America
| | - Yu Tina Kong
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, New York, United States of America
| | - Yandong Yin
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, New York, United States of America
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, New York, United States of America
- * E-mail: (DRW); (ER)
| |
Collapse
|
39
|
Thapar R, Wang JL, Hammel M, Ye R, Liang K, Sun C, Hnizda A, Liang S, Maw SS, Lee L, Villarreal H, Forrester I, Fang S, Tsai MS, Blundell TL, Davis AJ, Lin C, Lees-Miller SP, Strick TR, Tainer J. Mechanism of efficient double-strand break repair by a long non-coding RNA. Nucleic Acids Res 2020; 48:10953-10972. [PMID: 33045735 PMCID: PMC7641761 DOI: 10.1093/nar/gkaa784] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/26/2020] [Accepted: 09/09/2020] [Indexed: 12/28/2022] Open
Abstract
Mechanistic studies in DNA repair have focused on roles of multi-protein DNA complexes, so how long non-coding RNAs (lncRNAs) regulate DNA repair is less well understood. Yet, lncRNA LINP1 is over-expressed in multiple cancers and confers resistance to ionizing radiation and chemotherapeutic drugs. Here, we unveil structural and mechanistic insights into LINP1's ability to facilitate non-homologous end joining (NHEJ). We characterized LINP1 structure and flexibility and analyzed interactions with the NHEJ factor Ku70/Ku80 (Ku) and Ku complexes that direct NHEJ. LINP1 self-assembles into phase-separated condensates via RNA-RNA interactions that reorganize to form filamentous Ku-containing aggregates. Structured motifs in LINP1 bind Ku, promoting Ku multimerization and stabilization of the initial synaptic event for NHEJ. Significantly, LINP1 acts as an effective proxy for PAXX. Collective results reveal how lncRNA effectively replaces a DNA repair protein for efficient NHEJ with implications for development of resistance to cancer therapy.
Collapse
Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing L Wang
- Ecole Normale Supérieure, IBENS, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Ruiqiong Ye
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Alberta, T2N 4N1, Canada
| | - Ke Liang
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Chengcao Sun
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Ales Hnizda
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Shikang Liang
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Su S Maw
- Biological Systems and Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Linda Lee
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Alberta, T2N 4N1, Canada
| | | | - Isaac Forrester
- CryoEM Core at Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shujuan Fang
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Alberta, T2N 4N1, Canada
| | - Miaw-Sheue Tsai
- Biological Systems and Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Anthony J Davis
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Alberta, T2N 4N1, Canada
| | - Terence R Strick
- Ecole Normale Supérieure, IBENS, CNRS, INSERM, PSL Research University, Paris 75005, France
- Programme “Equipe Labellisée’’, Ligue Nationale Contre le Cancer, Paris 75005, France
| | - John A Tainer
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
- Department of Cancer Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
40
|
The molecular basis and disease relevance of non-homologous DNA end joining. Nat Rev Mol Cell Biol 2020; 21:765-781. [PMID: 33077885 DOI: 10.1038/s41580-020-00297-8] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 12/26/2022]
Abstract
Non-homologous DNA end joining (NHEJ) is the predominant repair mechanism of any type of DNA double-strand break (DSB) during most of the cell cycle and is essential for the development of antigen receptors. Defects in NHEJ result in sensitivity to ionizing radiation and loss of lymphocytes. The most critical step of NHEJ is synapsis, or the juxtaposition of the two DNA ends of a DSB, because all subsequent steps rely on it. Recent findings show that, like the end processing step, synapsis can be achieved through several mechanisms. In this Review, we first discuss repair pathway choice between NHEJ and other DSB repair pathways. We then integrate recent insights into the mechanisms of NHEJ synapsis with updates on other steps of NHEJ, such as DNA end processing and ligation. Finally, we discuss NHEJ-related human diseases, including inherited disorders and neoplasia, which arise from rare failures at different NHEJ steps.
Collapse
|
41
|
DNA double-strand break end resection: a critical relay point for determining the pathway of repair and signaling. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s42764-020-00017-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
AbstractA DNA double-strand break (DSB) is considered the most critical DNA lesion because it causes cell death and severe mutations if it is not repaired or repaired incorrectly. Accumulating evidence has shown that the majority of DSBs are repaired by DNA non-homologous end joining (NHEJ), the first utilized repair pathway in human cells. In contrast, the repair pathway is sometimes diverted into using homologous recombination (HR), which has increased precision under specific circumstances: e.g., when DSBs are generated at transcriptionally active loci or are not readily repaired due to the complexity of damage at the DSB ends or due to highly compacted chromatin. DSB end resection (resection) is considered the most critical turning point for directing repair towards HR. After resection, the HR process is finalized by RAD51 loading and recombination. Thus, understanding the process of resection is critically important to understand the regulation of the choice of DSB repair pathway. In addition, resection is also an important factor influencing DNA damage signaling because unresected ends preferentially activate ATM, whereas longer resected ends activate ATR. Thus, DSB end resection is a key relay point that determines the repair pathway and the signal balance. In this review, we summarize the mechanism underlying DSB end resection and further discuss how it is involved in cancer therapy.
Collapse
|
42
|
DNA-PK in human malignant disorders: Mechanisms and implications for pharmacological interventions. Pharmacol Ther 2020; 215:107617. [PMID: 32610116 DOI: 10.1016/j.pharmthera.2020.107617] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022]
Abstract
The DNA-PK holoenzyme is a fundamental element of the DNA damage response machinery (DDR), which is responsible for cellular genomic stability. Consequently, and predictably, over the last decades since its identification and characterization, numerous pre-clinical and clinical studies reported observations correlating aberrant DNA-PK status and activity with cancer onset, progression and responses to therapeutic modalities. Notably, various studies have established in recent years the role of DNA-PK outside the DDR network, corroborating its role as a pleiotropic complex involved in transcriptional programs that operate biologic processes as epithelial to mesenchymal transition (EMT), hypoxia, metabolism, nuclear receptors signaling and inflammatory responses. In particular tumor entities as prostate cancer, immense research efforts assisted mapping and describing the overall signaling networks regulated by DNA-PK that control metastasis and tumor progression. Correspondingly, DNA-PK emerges as an obvious therapeutic target in cancer and data pertaining to various pharmacological approaches have been published, largely in context of combination with DNA-damaging agents (DDAs) that act by inflicting DNA double strand breaks (DSBs). Currently, new generation inhibitors are tested in clinical trials. Several excellent reviews have been published in recent years covering the biology of DNA-PK and its role in cancer. In the current article we are aiming to systematically describe the main findings on DNA-PK signaling in major cancer types, focusing on both preclinical and clinical reports and present a detailed current status of the DNA-PK inhibitors repertoire.
Collapse
|
43
|
Improving Precise CRISPR Genome Editing by Small Molecules: Is there a Magic Potion? Cells 2020; 9:cells9051318. [PMID: 32466303 PMCID: PMC7291049 DOI: 10.3390/cells9051318] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/01/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) genome editing has become a standard method in molecular biology, for the establishment of genetically modified cellular and animal models, for the identification and validation of drug targets in animals, and is heavily tested for use in gene therapy of humans. While the efficiency of CRISPR mediated gene targeting is much higher than of classical targeted mutagenesis, the efficiency of CRISPR genome editing to introduce defined changes into the genome is still low. Overcoming this problem will have a great impact on the use of CRISPR genome editing in academic and industrial research and the clinic. This review will present efforts to achieve this goal by small molecules, which modify the DNA repair mechanisms to facilitate the precise alteration of the genome.
Collapse
|
44
|
Gonzalez V, Spampinato CP. The mismatch repair protein MSH6 regulates somatic recombination in Arabidopsis thaliana. DNA Repair (Amst) 2020; 87:102789. [PMID: 31945543 DOI: 10.1016/j.dnarep.2020.102789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/29/2019] [Accepted: 01/08/2020] [Indexed: 11/28/2022]
Abstract
The mismatch repair (MMR) pathway promotes genome stability by controlling the fidelity of replication and recombination. The first step of the pathway involves recognition of the mismatch by heterodimers composed of MutS homologs (MSH). Although MSH6 has been well characterized in yeasts and humans, the role of the plant protein has not been extensively studied. We first analyzed gene expression in Arabidopsis thaliana. The use of transgenic plants expressing the β-glucuronidase (GUS) reporter gene under the control of approximately 1-kb region upstream of the start codon of the AtMSH6 gene demonstrated that MSH6 is preferentially expressed in undifferentiated cells with an intense cell division rate. We then examined protein function in meiotic and somatic recombination. Suppression of AtMSH6 did not affect the rate of meiotic recombination, but increased the frequency of recombination between two homeologous repeats of a marker gene by 3-fold relative to wild-type plants. Expression of the AtMSH6 gene under the control of its own promoter in msh6 homozygous mutant plants rescued the altered somatic recombination phenotype. We conclude that MSH6 shows a functional conservation across different biological kingdoms and a functional specificity in plants.
Collapse
Affiliation(s)
- Valentina Gonzalez
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Claudia P Spampinato
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
| |
Collapse
|
45
|
Warmenhoven JW, Henthorn NT, Ingram SP, Chadwick AL, Sotiropoulos M, Korabel N, Fedotov S, Mackay RI, Kirkby KJ, Merchant MJ. Insights into the non-homologous end joining pathway and double strand break end mobility provided by mechanistic in silico modelling. DNA Repair (Amst) 2020; 85:102743. [DOI: 10.1016/j.dnarep.2019.102743] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 12/26/2022]
|
46
|
Deshpande RA, Myler LR, Soniat MM, Makharashvili N, Lee L, Lees-Miller SP, Finkelstein IJ, Paull TT. DNA-dependent protein kinase promotes DNA end processing by MRN and CtIP. SCIENCE ADVANCES 2020; 6:eaay0922. [PMID: 31934630 PMCID: PMC6949041 DOI: 10.1126/sciadv.aay0922] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
The repair of DNA double-strand breaks occurs through nonhomologous end joining or homologous recombination in vertebrate cells-a choice that is thought to be decided by a competition between DNA-dependent protein kinase (DNA-PK) and the Mre11/Rad50/Nbs1 (MRN) complex but is not well understood. Using ensemble biochemistry and single-molecule approaches, here, we show that the MRN complex is dependent on DNA-PK and phosphorylated CtIP to perform efficient processing and resection of DNA ends in physiological conditions, thus eliminating the competition model. Endonucleolytic removal of DNA-PK-bound DNA ends is also observed at double-strand break sites in human cells. The involvement of DNA-PK in MRN-mediated end processing promotes an efficient and sequential transition from nonhomologous end joining to homologous recombination by facilitating DNA-PK removal.
Collapse
Affiliation(s)
- Rajashree A. Deshpande
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan R. Myler
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY 10065, USA
| | - Michael M. Soniat
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Nodar Makharashvili
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Linda Lee
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Susan P. Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T. Paull
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
47
|
Harpprecht L, Baldi S, Schauer T, Schmidt A, Bange T, Robles MS, Kremmer E, Imhof A, Becker PB. A Drosophila cell-free system that senses DNA breaks and triggers phosphorylation signalling. Nucleic Acids Res 2019; 47:7444-7459. [PMID: 31147711 PMCID: PMC6698661 DOI: 10.1093/nar/gkz473] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 11/23/2022] Open
Abstract
Preblastoderm Drosophila embryo development is characterized by fast cycles of nuclear divisions. Extracts from these embryos can be used to reconstitute complex chromatin with high efficiency. We now discovered that this chromatin assembly system contains activities that recognize unprotected DNA ends and signal DNA damage through phosphorylation. DNA ends are initially bound by Ku and MRN complexes. Within minutes, the phosphorylation of H2A.V (homologous to γH2A.X) initiates from DNA breaks and spreads over tens of thousands DNA base pairs. The γH2A.V phosphorylation remains tightly associated with the damaged DNA and does not spread to undamaged DNA in the same reaction. This first observation of long-range γH2A.X spreading along damaged chromatin in an in vitro system provides a unique opportunity for mechanistic dissection. Upon further incubation, DNA ends are rendered single-stranded and bound by the RPA complex. Phosphoproteome analyses reveal damage-dependent phosphorylation of numerous DNA-end-associated proteins including Ku70, RPA2, CHRAC16, the exonuclease Rrp1 and the telomer capping complex. Phosphorylation of spindle assembly checkpoint components and of microtubule-associated proteins required for centrosome integrity suggests this cell-free system recapitulates processes involved in the regulated elimination of fatally damaged syncytial nuclei.
Collapse
Affiliation(s)
- Lisa Harpprecht
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Sandro Baldi
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich, LMU Munich, 81377 Munich, Germany
| | - Tamas Schauer
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
- Bioinformatics Unit, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Andreas Schmidt
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
- Protein Analysis Unit, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Tanja Bange
- Institute of Medical Psychology, LMU Munich, 80336 Munich, Germany
| | - Maria S Robles
- Institute of Medical Psychology, LMU Munich, 80336 Munich, Germany
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, German Research Center for Environmental Health, 81377 Munich, Germany
| | - Axel Imhof
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich, LMU Munich, 81377 Munich, Germany
- Protein Analysis Unit, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich, LMU Munich, 81377 Munich, Germany
- To whom correspondence should be addressed. Tel: +49 89 2180 75427; Fax: +49 89 2180 75425;
| |
Collapse
|
48
|
Lu H, Saha J, Beckmann PJ, Hendrickson EA, Davis AJ. DNA-PKcs promotes chromatin decondensation to facilitate initiation of the DNA damage response. Nucleic Acids Res 2019; 47:9467-9479. [PMID: 31396623 PMCID: PMC6765147 DOI: 10.1093/nar/gkz694] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 11/14/2022] Open
Abstract
The DNA damage response (DDR) encompasses the cellular response to DNA double-stranded breaks (DSBs), and includes recognition of the DSB, recruitment of numerous factors to the DNA damage site, initiation of signaling cascades, chromatin remodeling, cell-cycle checkpoint activation, and repair of the DSB. Key drivers of the DDR are multiple members of the phosphatidylinositol 3-kinase-related kinase family, including ataxia telangiectasia mutated (ATM), ataxia telangiectasia and Rad3-related (ATR), and the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). ATM and ATR modulate multiple portions of the DDR, but DNA-PKcs is believed to primarily function in the DSB repair pathway, non-homologous end joining. Utilizing a human cell line in which the kinase domain of DNA-PKcs is inactivated, we show here that DNA-PKcs kinase activity is required for the cellular response to DSBs immediately after their induction. Specifically, DNA-PKcs kinase activity initiates phosphorylation of the chromatin factors H2AX and KAP1 following ionizing radiation exposure and drives local chromatin decondensation near the DSB site. Furthermore, loss of DNA-PKcs kinase activity results in a marked decrease in the recruitment of numerous members of the DDR machinery to DSBs. Collectively, these results provide clear evidence that DNA-PKcs activity is pivotal for the initiation of the DDR.
Collapse
Affiliation(s)
- Huiming Lu
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Janapriya Saha
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pauline J Beckmann
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Anthony J Davis
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
49
|
Xie Y, Liu YK, Guo ZP, Guan H, Liu XD, Xie DF, Jiang YG, Ma T, Zhou PK. RBX1 prompts degradation of EXO1 to limit the homologous recombination pathway of DNA double-strand break repair in G1 phase. Cell Death Differ 2019; 27:1383-1397. [PMID: 31562368 PMCID: PMC7205894 DOI: 10.1038/s41418-019-0424-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 09/06/2019] [Accepted: 09/12/2019] [Indexed: 01/12/2023] Open
Abstract
End resection of DNA double-strand breaks (DSBs) to form 3′ single-strand DNA (ssDNA) is critical to initiate the homologous recombination (HR) pathway of DSB repair. HR pathway is strictly limited in the G1-phase cells because of lack of homologous DNA as the templates. Exonuclease 1 (EXO1) is the key molecule responsible for 3′ ssDNA formation of DSB end resection. We revealed that EXO1 is inactivated in G1-phase cells via ubiquitination-mediated degradation, resulting from an elevated expression level of RING-box protein 1 (RBX1) in G1 phase. The increased RBX1 significantly prompted the neddylation of Cullin1 and contributed to the G1 phase-specific degradation of EXO1. Knockdown of RBX1 remarkedly attenuated the degradation of EXO1 and increased the end resection and HR activity in γ-irradiated G1-phase cells, as demonstrated by the increased formation of RPA32, BrdU, and RAD51 foci. And EXO1 depletion mitigated DNA repair defects due to RBX1 reduction. Moreover, increased autophosphorylation of DNA-PKcs at S2056 was found to be responsible for the higher expression level of the RBX1 in the G1 phase. Inactivation of DNA-PKcs decreased RBX1 expression, and simultaneously increased EXO1 expression and DSB end resection in G1-phase cells. This study demonstrates a new mechanism for restraining the HR pathway of DNA DSB repair in G1 phase via RBX1-prompted inactivation of EXO1.
Collapse
Affiliation(s)
- Ying Xie
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 100850, Beijing, China.,Key Laboratory of Molecular Epidemiology of Hunan Province, School of Medicine, Hunan Normal University, 410013, Changsha, China
| | - Yi-Ke Liu
- Institute for Chemical Carcinogenesis, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, 511436, Guangzhou, China
| | - Zong-Pei Guo
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 100850, Beijing, China
| | - Hua Guan
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 100850, Beijing, China
| | - Xiao-Dan Liu
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 100850, Beijing, China
| | - Da-Fei Xie
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 100850, Beijing, China
| | - Yi-Guo Jiang
- Institute for Chemical Carcinogenesis, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, 511436, Guangzhou, China
| | - Teng Ma
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 100850, Beijing, China. .,Department of Cellular and Molecular Biology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, 101149, Beijing, China.
| | - Ping-Kun Zhou
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 100850, Beijing, China. .,Institute for Chemical Carcinogenesis, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, 511436, Guangzhou, China.
| |
Collapse
|
50
|
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: 3.2] [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.
Collapse
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
| |
Collapse
|