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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.
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2
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Li G, Yang X, Wang L, Pan Y, Chen S, Shang L, Zhang Y, Wu Y, Zhou Z, Chen Q, Zhang X, Zhang L, Wang Y, Li J, Jin L, Wu Y, Zhang X, Zhang F. Haploinsufficiency in non-homologous end joining factor 1 induces ovarian dysfunction in humans and mice. J Med Genet 2021; 59:579-588. [PMID: 33888552 DOI: 10.1136/jmedgenet-2020-107398] [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: 08/12/2020] [Revised: 02/16/2021] [Accepted: 03/18/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND Premature ovarian insufficiency (POI) is a common disease in women that leads to a reduced reproductive lifespan. The aetiology of POI is genetically heterogeneous, with certain double-strand break (DSB) repair genes being implicated in POI. Although non-homologous end joining (NHEJ) is an efficient DSB repair pathway, the functional relationship between this pathway and POI remains unknown. METHODS AND RESULTS We conducted whole-exome sequencing in a Chinese family and identified a rare heterozygous loss-of-function variant in non-homologous end joining factor 1 (NHEJ1): c.532C>T (p.R178*), which co-segregated with POI and irregular menstruation. The amount of NHEJ1 protein in the proband was half of the normal level, indicating a link between NHEJ1 haploinsufficiency and POI. Furthermore, another rare heterozygous NHEJ1 variant c.500A>G (p.Y167C) was identified in one of 100 sporadic POI cases. Both variants were predicted to be deleterious by multiple in silico tools. In vitro assays showed that knock-down of NHEJ1 in human KGN ovarian cells impaired DNA repair capacity. We also generated a knock-in mouse model with a heterozygous Nhej1 variant equivalent to NHEJ1 p.R178* in familial patients. Compared with wild-type mice, heterozygous Nhej1-mutated female mice required a longer time to first birth, and displayed reduced numbers of primordial and growing follicles. Moreover, these mice exhibited higher sensitivity to DSB-inducing drugs. All these phenotypes are analogous to the progressive loss of ovarian function observed in POI. CONCLUSIONS Our observations in both humans and mice suggest that NHEJ1 haploinsufficiency is associated with non-syndromic POI, providing novel insights into genetic counselling and clinical prevention of POI.
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Affiliation(s)
- Guoqing Li
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Xi Yang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Lingbo Wang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Yuncheng Pan
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Siyuan Chen
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Lingyue Shang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Yicheng Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Yucheng Wu
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Zixue Zhou
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Qing Chen
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Xue Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Ling Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Yingchen Wang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Li Jin
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Yanhua Wu
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China .,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China.,National Demonstration Center for Experimental Biology Education, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaojin Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China .,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China .,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
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3
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Macedo-Silva C, Miranda-Gonçalves V, Lameirinhas A, Lencart J, Pereira A, Lobo J, Guimarães R, Martins AT, Henrique R, Bravo I, Jerónimo C. JmjC-KDMs KDM3A and KDM6B modulate radioresistance under hypoxic conditions in esophageal squamous cell carcinoma. Cell Death Dis 2020; 11:1068. [PMID: 33318475 PMCID: PMC7736883 DOI: 10.1038/s41419-020-03279-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC), the most frequent esophageal cancer (EC) subtype, entails dismal prognosis. Hypoxia, a common feature of advanced ESCC, is involved in resistance to radiotherapy (RT). RT response in hypoxia might be modulated through epigenetic mechanisms, constituting novel targets to improve patient outcome. Post-translational methylation in histone can be partially modulated by histone lysine demethylases (KDMs), which specifically removes methyl groups in certain lysine residues. KDMs deregulation was associated with tumor aggressiveness and therapy failure. Thus, we sought to unveil the role of Jumonji C domain histone lysine demethylases (JmjC-KDMs) in ESCC radioresistance acquisition. The effectiveness of RT upon ESCC cells under hypoxic conditions was assessed by colony formation assay. KDM3A/KDM6B expression, and respective H3K9me2 and H3K27me3 target marks, were evaluated by RT-qPCR, Western blot, and immunofluorescence. Effect of JmjC-KDM inhibitor IOX1, as well as KDM3A knockdown, in in vitro functional cell behavior and RT response was assessed in ESCC under hypoxic conditions. In vivo effect of combined IOX1 and ionizing radiation treatment was evaluated in ESCC cells using CAM assay. KDM3A, KDM6B, HIF-1α, and CAIX immunoexpression was assessed in primary ESCC and normal esophagus. Herein, we found that hypoxia promoted ESCC radioresistance through increased KDM3A/KDM6B expression, enhancing cell survival and migration and decreasing DNA damage and apoptosis, in vitro. Exposure to IOX1 reverted these features, increasing ESCC radiosensitivity and decreasing ESCC microtumors size, in vivo. KDM3A was upregulated in ESCC tissues compared to the normal esophagus, associating and colocalizing with hypoxic markers (HIF-1α and CAIX). Therefore, KDM3A upregulation in ESCC cell lines and primary tumors associated with hypoxia, playing a critical role in EC aggressiveness and radioresistance. KDM3A targeting, concomitant with conventional RT, constitutes a promising strategy to improve ESCC patients' survival.
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Affiliation(s)
- Catarina Macedo-Silva
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal
| | - Vera Miranda-Gonçalves
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal
| | - Ana Lameirinhas
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal
| | - Joana Lencart
- Medical Physics, Radiobiology and Radiation Protection Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal
- Departments of Medical Physics, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Alexandre Pereira
- Medical Physics, Radiobiology and Radiation Protection Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal
- Departments of Medical Physics, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - João Lobo
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal
- Departments of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar - University of Porto (ICBAS-UP), Porto, Portugal
| | - Rita Guimarães
- Departments of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Ana Teresa Martins
- Departments of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal
- Departments of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar - University of Porto (ICBAS-UP), Porto, Portugal
| | - Isabel Bravo
- Medical Physics, Radiobiology and Radiation Protection Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar - University of Porto (ICBAS-UP), Porto, Portugal.
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4
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Ruis B, Molan A, Takasugi T, Hendrickson EA. Absence of XRCC4 and its paralogs in human cells reveal differences in outcomes for DNA repair and V(D)J recombination. DNA Repair (Amst) 2019; 85:102738. [PMID: 31731258 DOI: 10.1016/j.dnarep.2019.102738] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023]
Abstract
The repair of DNA double-stranded breaks (DSBs) is an essential function performed by the Classical Non-Homologous End-Joining (C-NHEJ) pathway in higher eukaryotes. C-NHEJ, in fact, does double duty as it is also required for the repair of the intermediates formed during lymphoid B- and T-cell recombination. Consequently, the failure to properly repair DSBs leads to both genomic instability and immunodeficiency. A critical DSB protein required for C-NHEJ is the DNA Ligase IV (LIGIV) accessory factor, X-Ray Cross Complementing 4 (XRCC4). XRCC4 is believed to stabilize LIGIV, participate in LIGIV activation, and to help tether the broken DSB ends together. XRCC4's role in these processes has been muddied by the identification of two additional XRCC4 paralogs, XRCC4-Like Factor (XLF), and Paralog of XRCC4 and XLF (PAXX). The roles that these paralogs play in C-NHEJ is partially understood, but, in turn, has itself been obscured by species-specific differences observed in the absence of one or the other paralogs. In order to investigate the role(s) that XRCC4 may play, with or without XLF and/or PAXX, in lymphoid variable(diversity)joining [V(D)J] recombination as well as in DNA DSB repair in human somatic cells, we utilized gene targeting to inactivate the XRCC4 gene in both parental and XLF- HCT116 cells and then inactivated PAXX in those same cell lines. The loss of XRCC4 expression by itself led, as anticipated, to increased sensitivity to DNA damaging agents as well as an increased dependence on microhomology-mediated DNA repair whether in the context of DSB repair or during V(D)J recombination. The additional loss of XLF in these cell lines sensitized the cells even more whereas the presence or absence of PAXX was scarcely negligible. These studies demonstrate that, of the three LIG4 accessory factor paralogs, the absence of XRCC4 influences DNA repair and recombination the most in human cells.
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Affiliation(s)
- Brian Ruis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Amy Molan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Taylor Takasugi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States.
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5
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Chen BR, Quinet A, Byrum AK, Jackson J, Berti M, Thangavel S, Bredemeyer AL, Hindi I, Mosammaparast N, Tyler JK, Vindigni A, Sleckman BP. XLF and H2AX function in series to promote replication fork stability. J Cell Biol 2019; 218:2113-2123. [PMID: 31123184 PMCID: PMC6605786 DOI: 10.1083/jcb.201808134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/03/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022] Open
Abstract
Chen et al. show that XLF functions to limit fork reversal during DNA replication. H2AX prevents MRE11-dependent replication stress in XLF-deficient cells, suggesting that H2AX prevents the resection of regressed arms at reversed forks. XRCC4-like factor (XLF) is a non-homologous end joining (NHEJ) DNA double strand break repair protein. However, XLF deficiency leads to phenotypes in mice and humans that are not necessarily consistent with an isolated defect in NHEJ. Here we show that XLF functions during DNA replication. XLF undergoes cell division cycle 7–dependent phosphorylation; associates with the replication factor C complex, a critical component of the replisome; and is found at replication forks. XLF deficiency leads to defects in replication fork progression and an increase in fork reversal. The additional loss of H2AX, which protects DNA ends from resection, leads to a requirement for ATR to prevent an MRE11-dependent loss of newly synthesized DNA and activation of DNA damage response. Moreover, H2ax−/−:Xlf−/− cells exhibit a marked dependence on the ATR kinase for survival. We propose that XLF and H2AX function in series to prevent replication stress induced by the MRE11-dependent resection of regressed arms at reversed replication forks.
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Affiliation(s)
- Bo-Ruei Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Annabel Quinet
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Andrea K Byrum
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jessica Jackson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Matteo Berti
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Saravanabhavan Thangavel
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Andrea L Bredemeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Issa Hindi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Alessandro Vindigni
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Barry P Sleckman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
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6
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A single XLF dimer bridges DNA ends during nonhomologous end joining. Nat Struct Mol Biol 2018; 25:877-884. [PMID: 30177755 PMCID: PMC6128732 DOI: 10.1038/s41594-018-0120-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/05/2018] [Indexed: 01/09/2023]
Abstract
Non-homologous end joining (NHEJ) is the primary pathway of DNA double-strand break repair in vertebrate cells, yet it remains unclear how NHEJ factors assemble a synaptic complex that bridges DNA ends. To address the role of XRCC4-like factor (XLF) in synaptic complex assembly, we employed single-molecule fluorescence imaging in Xenopus laevis egg extract, a system that efficiently joins DNA ends. We find that a single XLF dimer binds to DNA substrates just prior to formation of a ligation-competent synaptic complex between DNA ends. The interaction of both globular head domains of the XLF dimer with XRCC4 is required for efficient formation of this synaptic complex. In contrast to a model in which filaments of XLF and XRCC4 bridge DNA ends, our results indicate that binding of a single XLF dimer facilitates the assembly of a stoichiometrically well-defined synaptic complex.
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Sulkowski PL, Scanlon SE, Oeck S, Glazer PM. PTEN Regulates Nonhomologous End Joining By Epigenetic Induction of NHEJ1/XLF. Mol Cancer Res 2018; 16:1241-1254. [PMID: 29739874 DOI: 10.1158/1541-7786.mcr-17-0581] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/23/2018] [Accepted: 04/23/2018] [Indexed: 11/16/2022]
Abstract
DNA double-strand breaks (DSB) are the most cytotoxic DNA lesions, and up to 90% of DSBs require repair by nonhomologous end joining (NHEJ). Functional and genomic analyses of patient-derived melanomas revealed that PTEN loss is associated with NHEJ deficiency. In PTEN-null melanomas, PTEN complementation rescued the NHEJ defect; conversely, suppression of PTEN compromised NHEJ. Mechanistic studies revealed that PTEN promotes NHEJ through direct induction of expression of XRCC4-like factor (NHEJ1/XLF), which functions in DNA end bridging and ligation. PTEN was found to occupy the NHEJ1 gene promoter and to recruit the histone acetyltransferases, PCAF and CBP, inducing XLF expression. This recruitment activity was found to be independent of its phosphatase activity, but dependent on K128, a site of regulatory acetylation on PTEN. These findings define a novel function for PTEN in regulating NHEJ DSB repair, and therefore may assist in the design of individualized strategies for cancer therapy.Implications: PTEN is the second most frequently lost tumor suppressor gene. Here it is demonstrated that PTEN has a direct and novel regulatory role in NHEJ, a key DNA repair pathway in response to radiation and chemotherapy. Mol Cancer Res; 16(8); 1241-54. ©2018 AACR.
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Affiliation(s)
| | - Susan E Scanlon
- Department of Experimental Pathology, Yale University, New Haven, Connecticut
| | - Sebastian Oeck
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut.,Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Peter M Glazer
- Department of Genetics, Yale University, New Haven, Connecticut. .,Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
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Thompson EL, Yeo JE, Lee EA, Kan Y, Raghunandan M, Wiek C, Hanenberg H, Schärer OD, Hendrickson EA, Sobeck A. FANCI and FANCD2 have common as well as independent functions during the cellular replication stress response. Nucleic Acids Res 2017; 45:11837-11857. [PMID: 29059323 PMCID: PMC5714191 DOI: 10.1093/nar/gkx847] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 09/16/2017] [Indexed: 11/18/2022] Open
Abstract
Fanconi anemia (FA) is an inherited cancer predisposition syndrome characterized by cellular hypersensitivity to DNA interstrand crosslinks (ICLs). To repair these lesions, the FA proteins act in a linear hierarchy: following ICL detection on chromatin, the FA core complex monoubiquitinates and recruits the central FANCI and FANCD2 proteins that subsequently coordinate ICL removal and repair of the ensuing DNA double-stranded break by homology-dependent repair (HDR). FANCD2 also functions during the replication stress response by mediating the restart of temporarily stalled replication forks thereby suppressing the firing of new replication origins. To address if FANCI is also involved in these FANCD2-dependent mechanisms, we generated isogenic FANCI-, FANCD2- and FANCI:FANCD2 double-null cells. We show that FANCI and FANCD2 are partially independent regarding their protein stability, nuclear localization and chromatin recruitment and contribute independently to cellular proliferation. Simultaneously, FANCD2—but not FANCI—plays a major role in HDR-mediated replication restart and in suppressing new origin firing. Consistent with this observation, deficiencies in HDR-mediated DNA DSB repair can be overcome by stabilizing RAD51 filament formation in cells lacking functional FANCD2. We propose that FANCI and FANCD2 have partially non-overlapping and possibly even opposing roles during the replication stress response.
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Affiliation(s)
- Elizabeth L Thompson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jung E Yeo
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Eun-A Lee
- Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Yinan Kan
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Maya Raghunandan
- Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Constanze Wiek
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, 40225 Düsseldorf, Germany.,Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Orlando D Schärer
- Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alexandra Sobeck
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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9
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Tadi SK, Tellier-Lebègue C, Nemoz C, Drevet P, Audebert S, Roy S, Meek K, Charbonnier JB, Modesti M. PAXX Is an Accessory c-NHEJ Factor that Associates with Ku70 and Has Overlapping Functions with XLF. Cell Rep 2017; 17:541-555. [PMID: 27705800 DOI: 10.1016/j.celrep.2016.09.026] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 08/31/2016] [Accepted: 09/09/2016] [Indexed: 01/19/2023] Open
Abstract
In mammalian cells, classical non-homologous end joining (c-NHEJ) is critical for DNA double-strand break repair induced by ionizing radiation and during V(D)J recombination in developing B and T lymphocytes. Recently, PAXX was identified as a c-NHEJ core component. We report here that PAXX-deficient cells exhibit a cellular phenotype uncharacteristic of a deficiency in c-NHEJ core components. PAXX-deficient cells display normal sensitivity to radiomimetic drugs, are proficient in transient V(D)J recombination assays, and do not shift toward higher micro-homology usage in plasmid repair assays. Although PAXX-deficient cells lack c-NHEJ phenotypes, PAXX forms a stable ternary complex with Ku bound to DNA. Formation of this complex involves an interaction with Ku70 and requires a bare DNA extension for stability. Moreover, the relatively weak Ku-dependent stimulation of LIG4/XRCC4 activity by PAXX is unmasked by XLF ablation. Thus, PAXX plays an accessory role during c-NHEJ that is largely overlapped by XLF's function.
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Affiliation(s)
- Satish K Tadi
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, 13273 Marseille, France
| | - Carine Tellier-Lebègue
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, University Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Clément Nemoz
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, University Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Pascal Drevet
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, University Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Stéphane Audebert
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, 13273 Marseille, France
| | - Sunetra Roy
- Department of Microbiology & Molecular Genetics, and Department of Pathobiology & Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Katheryn Meek
- Department of Microbiology & Molecular Genetics, and Department of Pathobiology & Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, University Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, 13273 Marseille, France.
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10
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Jaafar L, Li Z, Li S, Dynan WS. SFPQ•NONO and XLF function separately and together to promote DNA double-strand break repair via canonical nonhomologous end joining. Nucleic Acids Res 2017; 45:1848-1859. [PMID: 27924002 PMCID: PMC5605232 DOI: 10.1093/nar/gkw1209] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/28/2016] [Indexed: 01/10/2023] Open
Abstract
A complex of two related mammalian proteins, SFPQ and NONO, promotes DNA double-strand break repair via the canonical nonhomologous end joining (c-NHEJ) pathway. However, its mechanism of action is not fully understood. Here we describe an improved SFPQ•NONO-dependent in vitro end joining assay. We use this system to demonstrate that the SFPQ•NONO complex substitutes in vitro for the core c-NHEJ factor, XLF. Results are consistent with a model where SFPQ•NONO promotes sequence-independent pairing of DNA substrates, albeit in a way that differs in detail from XLF. Although SFPQ•NONO and XLF function redundantly in vitro, shRNA-mediated knockdown experiments indicate that NONO and XLF are both required for efficient end joining and radioresistance in cell-based assays. In addition, knockdown of NONO sensitizes cells to the interstrand crosslinking agent, cisplatin, whereas knockdown of XLF does not, and indeed suppresses the effect of NONO deficiency. These findings suggest that each protein has one or more unique activities, in addition to the DNA pairing revealed in vitro, that contribute to DNA repair in the more complex cellular milieu. The SFPQ•NONO complex contains an RNA binding domain, and prior work has demonstrated diverse roles in RNA metabolism. It is thus plausible that the additional repair function of NONO, revealed in cell-based assays, could involve RNA interaction.
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Affiliation(s)
- Lahcen Jaafar
- Departments of Radiation Oncology and Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Zhentian Li
- Departments of Radiation Oncology and Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Shuyi Li
- Departments of Radiation Oncology and Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - William S Dynan
- Departments of Radiation Oncology and Biochemistry, Emory University, Atlanta, GA 30322, USA
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11
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Menon V, Povirk LF. XLF/Cernunnos: An important but puzzling participant in the nonhomologous end joining DNA repair pathway. DNA Repair (Amst) 2017; 58:29-37. [PMID: 28846869 DOI: 10.1016/j.dnarep.2017.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/24/2017] [Accepted: 08/07/2017] [Indexed: 01/15/2023]
Abstract
DNA double strand breaks (DSBs) are one of the most deleterious DNA lesions that promote cell death, genomic instability and carcinogenesis. The two major cellular mechanisms that repair DSBs are Nonhomologous End-Joining (NHEJ) and Homologous Recombination Repair (HRR). NHEJ is the predominant pathway, in which XLF (also called Cernunnos) is a key player. Patients with XLF mutation exhibit microcephaly, lymphopenia, and growth retardation, and are immunodeficient and radiosensitive. During NHEJ, XLF interacts with XRCC4-Ligase IV, stimulates its ligase activity, and forms DNA-binding filaments of alternating XLF and XRCC4 dimers that may serve to align broken DNA and promote ligation of noncomplementary ends. Despite its central role in NHEJ, the effects of XLF deficiency are surprisingly variable in different biological contexts, and different individual cell lines. This review summarizes the role of XLF in NHEJ, and the unexpected complexity of its interplay with other repair factors in supporting radiosurvival and V(D)J recombination.
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Affiliation(s)
- Vijay Menon
- Goodwin Research Laboratory, Massey Cancer Center, Virginia Commonwealth University, VA, USA
| | - Lawrence F Povirk
- Goodwin Research Laboratory, Massey Cancer Center, Virginia Commonwealth University, VA, USA; Department of Pharmacology and Toxicology, Virginia Commonwealth University, VA, USA.
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12
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Yang S, Wang XQ. XLF-mediated NHEJ activity in hepatocellular carcinoma therapy resistance. BMC Cancer 2017; 17:344. [PMID: 28526069 PMCID: PMC5437682 DOI: 10.1186/s12885-017-3345-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 05/11/2017] [Indexed: 11/16/2022] Open
Abstract
Background DNA repair pathways are used by cancer cells to overcome many standard anticancer treatments, causing therapy resistance. Here, we investigated the role of XRCC4-like factor (XLF), a core member of the non-homologous end joining (NHEJ) repair pathway, in chemoresistance in hepatocellular carcinoma (HCC). Methods qRT-PCR analysis and western blotting were performed to detect expression levels of genes and proteins related to NHEJ. NHEJ repair capacity was assessed in vitro (cell-free) and in vivo by monitoring the activity of the NHEJ pathway. Cell viability and IC50 assays were used to measure sensitivity to drug therapy. A xenograft HCC model was used to develop methods of targeting XLF-induced chemosensitization. Clinicopathological analysis was conducted on patients with HCC treated with transarterial chemoembolization (TACE). Results Many conventional cancer chemotherapeutics induce DNA double-strand breaks (DSBs). HCC cells respond to these breaks by increasing their NHEJ activity, resulting in resistance. XLF-knockdown cells show an inhibition of NHEJ activity in both cell-free and live-cell assays as well as a high level of unrepaired cellular DSBs. These results indicate that XLF facilitates DNA end-joining and therefore promotes NHEJ activity in cancer cells. Consequently, knockdown of XLF significantly chemosensitized resistant cells both in vitro and in xenograft tumors. A low rate of XLF genomic alteration was found in patients with primary HCC, but XLF expression was induced after drug treatment. Clinically, a high level of XLF expression is significantly associated with advanced HCC and shorter overall survival. Conclusion Chemotherapy-induced overexpression of XLF and XLF-mediated enhancements in NHEJ activity contribute to chemoresistance in HCC cells and patients with HCC. Targeting XLF to modulate DSB repair could enhance drug sensitivity and may be a therapeutically useful addition to conventional therapy. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3345-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sitian Yang
- Department of Surgery, The University of Hong Kong, 21 Sassoon Road, Hong Kong, China
| | - Xiao Qi Wang
- Department of Surgery, The University of Hong Kong, 21 Sassoon Road, Hong Kong, China. .,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China.
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13
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Normanno D, Négrel A, de Melo AJ, Betzi S, Meek K, Modesti M. Mutational phospho-mimicry reveals a regulatory role for the XRCC4 and XLF C-terminal tails in modulating DNA bridging during classical non-homologous end joining. eLife 2017; 6. [PMID: 28500754 PMCID: PMC5468090 DOI: 10.7554/elife.22900] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/12/2017] [Indexed: 12/23/2022] Open
Abstract
XRCC4 and DNA Ligase 4 (LIG4) form a tight complex that provides DNA ligase activity for classical non-homologous end joining (the predominant DNA double-strand break repair pathway in higher eukaryotes) and is stimulated by XLF. Independently of LIG4, XLF also associates with XRCC4 to form filaments that bridge DNA. These XRCC4/XLF complexes rapidly load and connect broken DNA, thereby stimulating intermolecular ligation. XRCC4 and XLF both include disordered C-terminal tails that are functionally dispensable in isolation but are phosphorylated in response to DNA damage by DNA-PK and/or ATM. Here we concomitantly modify the tails of XRCC4 and XLF by substituting fourteen previously identified phosphorylation sites with either alanine or aspartate residues. These phospho-blocking and -mimicking mutations impact both the stability and DNA bridging capacity of XRCC4/XLF complexes, but without affecting their ability to stimulate LIG4 activity. Implicit in this finding is that phosphorylation may regulate DNA bridging by XRCC4/XLF filaments.
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Affiliation(s)
- Davide Normanno
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Aurélie Négrel
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Abinadabe J de Melo
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Stéphane Betzi
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Katheryn Meek
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States.,Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, United States
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
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14
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Ma J, Setton J, Morris L, Carrillo Albornoz PB, Barker C, Lok BH, Sherman E, Katabi N, Beal K, Ganly I, Powell SN, Lee N, Chan TA, Riaz N. Genomic analysis of exceptional responders to radiotherapy reveals somatic mutations in ATM. Oncotarget 2017; 8:10312-10323. [PMID: 28055970 PMCID: PMC5354661 DOI: 10.18632/oncotarget.14400] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/30/2016] [Indexed: 12/04/2022] Open
Abstract
Radiation therapy is a mainstay of cancer treatment, yet the molecular determinants of clinical response are poorly understood. We identified exceptional responders to radiotherapy based on clinical response, and investigated the associated tumor sequencing data in order to identify additional patients with similar mutations. Among head and neck squamous cell cancer patients receiving palliative radiotherapy at our institution, we identified one patient with documented complete metabolic response. Targeted sequencing analysis of the tumor identified a somatic frame-shift mutation in ATM, a gene known to be associated with radio-sensitivity in the germline. To validate the association of somatic ATM mutation with radiotherapy response, we identified eight patients with ATM truncating mutations who received radiotherapy, all of whom demonstrated excellent responses with a median local control period of 4.62 years. Analysis of 22 DNA repair genes in The Cancer Genome Atlas (TCGA) data revealed mutations in 15.9% of 9064 tumors across 24 cancer types, with ATM mutations being the most prevalent. This is the first study to suggest that exceptional responses to radiotherapy may be determined by mutations in DNA repair genes. Sequencing of DNA repair genes merits attention in larger cohorts and may have significant implications for the personalization of radiotherapy.
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MESH Headings
- Aged
- Aged, 80 and over
- Ataxia Telangiectasia Mutated Proteins/genetics
- Biomarkers, Tumor/genetics
- Carcinoma, Non-Small-Cell Lung/diagnostic imaging
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/radiotherapy
- Carcinoma, Squamous Cell/diagnostic imaging
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/radiotherapy
- Computational Biology
- DNA Mutational Analysis
- Databases, Genetic
- Endometrial Neoplasms/diagnostic imaging
- Endometrial Neoplasms/genetics
- Endometrial Neoplasms/pathology
- Endometrial Neoplasms/radiotherapy
- Female
- Head and Neck Neoplasms/diagnostic imaging
- Head and Neck Neoplasms/genetics
- Head and Neck Neoplasms/pathology
- Head and Neck Neoplasms/radiotherapy
- Humans
- Lung Neoplasms/diagnostic imaging
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/radiotherapy
- Middle Aged
- Mutation
- Palliative Care
- Patient Selection
- Precision Medicine
- Radiation Tolerance/genetics
- Radiotherapy Dosage
- Retrospective Studies
- Squamous Cell Carcinoma of Head and Neck
- Treatment Outcome
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Affiliation(s)
- Jennifer Ma
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeremy Setton
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luc Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Christopher Barker
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin H. Lok
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Sherman
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nora Katabi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn Beal
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ian Ganly
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon N. Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Lee
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A. Chan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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15
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Hung PJ, Chen BR, George R, Liberman C, Morales AJ, Colon-Ortiz P, Tyler JK, Sleckman BP, Bredemeyer AL. Deficiency of XLF and PAXX prevents DNA double-strand break repair by non-homologous end joining in lymphocytes. Cell Cycle 2016; 16:286-295. [PMID: 27830975 DOI: 10.1080/15384101.2016.1253640] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Non-homologous end joining (NHEJ) is a major DNA double-strand break (DSB) repair pathway that functions in all phases of the cell cycle. NHEJ repairs genotoxic and physiological DSBs, such as those generated by ionizing radiation and during V(D)J recombination at antigen receptor loci, respectively. DNA end joining by NHEJ relies on the core factors Ku70, Ku80, XRCC4, and DNA Ligase IV. Additional proteins also play important roles in NHEJ. The XRCC4-like factor (XLF) participates in NHEJ through its interaction with XRCC4, and XLF deficiency in humans leads to immunodeficiency and increased sensitivity to ionizing radiation. However, XLF is dispensable for NHEJ-mediated DSB repair during V(D)J recombination in murine lymphocytes, where it may have redundant functions with other DSB repair factors. Paralog of XRCC4 and XLF (PAXX) is a recently identified NHEJ factor that has structural similarity to XRCC4 and XLF. Here we show that PAXX is also dispensable for NHEJ during V(D)J recombination and during the repair of genotoxic DSBs in lymphocytes. However, a combined deficiency of PAXX and XLF blocks NHEJ with a severity comparable to that observed in DNA Ligase IV-deficient cells. Similar to XLF, PAXX interacts with Ku through its C-terminal region, and mutations that disrupt Ku binding prevent PAXX from promoting NHEJ in XLF-deficient lymphocytes. Our findings suggest that the PAXX and XLF proteins may have redundant functions during NHEJ.
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Affiliation(s)
- Putzer J Hung
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA.,b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Bo-Ruei Chen
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA.,b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Rosmy George
- b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Caleb Liberman
- b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Abigail J Morales
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA.,b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Pedro Colon-Ortiz
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA
| | - Jessica K Tyler
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA
| | - Barry P Sleckman
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA.,b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Andrea L Bredemeyer
- b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
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16
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Czochor JR, Sulkowski P, Glazer PM. miR-155 Overexpression Promotes Genomic Instability by Reducing High-fidelity Polymerase Delta Expression and Activating Error-Prone DSB Repair. Mol Cancer Res 2016; 14:363-73. [PMID: 26850462 PMCID: PMC5021065 DOI: 10.1158/1541-7786.mcr-15-0399] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/28/2016] [Indexed: 12/21/2022]
Abstract
UNLABELLED miR-155 is an oncogenic miRNA that is often overexpressed in cancer and is associated with poor prognosis. miR-155 can target several DNA repair factors, including RAD51, MLH1, and MSH6, and its overexpression results in an increased mutation frequency in vitro, although the mechanism has yet to be fully understood. Here, we demonstrate that overexpression of miR-155 drives an increased mutation frequency both in vitro and in vivo, promoting genomic instability by affecting multiple DNA repair pathways. miR-155 overexpression causes a decrease in homologous recombination, but yields a concurrent increase in the error-prone nonhomologous end-joining pathway. Despite repressing established targets MLH1 and MSH6, the identified mutation pattern upon miR-155 overexpression does not resemble that of a mismatch repair-deficient background. Further investigation revealed that all four subunits of polymerase delta, a high-fidelity DNA replication, and repair polymerase are downregulated at the mRNA level in the context of miR-155 overexpression. FOXO3a, a transcription factor and known target of miR-155, has one or more putative binding site(s) in the promoter of all four polymerase delta subunits. Finally, suppression of FOXO3a by miR-155 or by siRNA knockdown is sufficient to repress the expression of the catalytic subunit of polymerase delta, POLD1, at the protein level, indicating that FOXO3a contributes to the regulation of polymerase delta levels. IMPLICATIONS Taken together, miR-155 overexpression drives an increase in mutation frequency via multifaceted impact on DNA damage response and DNA repair pathways.
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Affiliation(s)
| | | | - Peter M. Glazer
- Department of Genetics, Yale University, New Haven, CT
- Department of Therapeutic Radiology, Yale University, New Haven, CT
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17
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Borrego-Soto G, Ortiz-López R, Rojas-Martínez A. Ionizing radiation-induced DNA injury and damage detection in patients with breast cancer. Genet Mol Biol 2015; 38:420-32. [PMID: 26692152 PMCID: PMC4763322 DOI: 10.1590/s1415-475738420150019] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 07/15/2015] [Indexed: 12/26/2022] Open
Abstract
Breast cancer is the most common malignancy in women. Radiotherapy is frequently used in patients with breast cancer, but some patients may be more susceptible to ionizing radiation, and increased exposure to radiation sources may be associated to radiation adverse events. This susceptibility may be related to deficiencies in DNA repair mechanisms that are activated after cell-radiation, which causes DNA damage, particularly DNA double strand breaks. Some of these genetic susceptibilities in DNA-repair mechanisms are implicated in the etiology of hereditary breast/ovarian cancer (pathologic mutations in the BRCA 1 and 2 genes), but other less penetrant variants in genes involved in sporadic breast cancer have been described. These same genetic susceptibilities may be involved in negative radiotherapeutic outcomes. For these reasons, it is necessary to implement methods for detecting patients who are susceptible to radiotherapy-related adverse events. This review discusses mechanisms of DNA damage and repair, genes related to these functions, and the diagnosis methods designed and under research for detection of breast cancer patients with increased radiosensitivity.
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Affiliation(s)
- Gissela Borrego-Soto
- Departamento de Bioquímica y Medicina Molecular, Facultad de
Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
- Centro de Investigación y Desarrollo en Ciencias de la Salud,
Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Rocío Ortiz-López
- Departamento de Bioquímica y Medicina Molecular, Facultad de
Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
- Centro de Investigación y Desarrollo en Ciencias de la Salud,
Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Augusto Rojas-Martínez
- Departamento de Bioquímica y Medicina Molecular, Facultad de
Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
- Centro de Investigación y Desarrollo en Ciencias de la Salud,
Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
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18
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XRCC4/XLF Interaction Is Variably Required for DNA Repair and Is Not Required for Ligase IV Stimulation. Mol Cell Biol 2015; 35:3017-28. [PMID: 26100018 DOI: 10.1128/mcb.01503-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 06/15/2015] [Indexed: 01/21/2023] Open
Abstract
The classic nonhomologous end-joining (c-NHEJ) pathway is largely responsible for repairing double-strand breaks (DSBs) in mammalian cells. XLF stimulates the XRCC4/DNA ligase IV complex by an unknown mechanism. XLF interacts with XRCC4 to form filaments of alternating XRCC4 and XLF dimers that bridge DNA ends in vitro, providing a mechanism by which XLF might stimulate ligation. Here, we characterize two XLF mutants that do not interact with XRCC4 and cannot form filaments or bridge DNA in vitro. One mutant is fully sufficient in stimulating ligation by XRCC4/Lig4 in vitro; the other is not. This separation-of-function mutant (which must function as an XLF homodimer) fully complements the c-NHEJ deficits of some XLF-deficient cell strains but not others, suggesting a variable requirement for XRCC4/XLF interaction in living cells. To determine whether the lack of XRCC4/XLF interaction (and potential bridging) can be compensated for by other factors, candidate repair factors were disrupted in XLF- or XRCC4-deficient cells. The loss of either ATM or the newly described XRCC4/XLF-like factor, PAXX, accentuates the requirement for XLF. However, in the case of ATM/XLF loss (but not PAXX/XLF loss), this reflects a greater requirement for XRCC4/XLF interaction.
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19
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Craxton A, Somers J, Munnur D, Jukes-Jones R, Cain K, Malewicz M. XLS (c9orf142) is a new component of mammalian DNA double-stranded break repair. Cell Death Differ 2015; 22:890-7. [PMID: 25941166 PMCID: PMC4423191 DOI: 10.1038/cdd.2015.22] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 02/09/2015] [Indexed: 12/18/2022] Open
Abstract
Repair of double-stranded DNA breaks (DSBs) in mammalian cells primarily occurs by the non-homologous end-joining (NHEJ) pathway, which requires seven core proteins (Ku70/Ku86, DNA-PKcs (DNA-dependent protein kinase catalytic subunit), Artemis, XRCC4-like factor (XLF), XRCC4 and DNA ligase IV). Here we show using combined affinity purification and mass spectrometry that DNA-PKcs co-purifies with all known core NHEJ factors. Furthermore, we have identified a novel evolutionary conserved protein associated with DNA-PKcs—c9orf142. Computer-based modelling of c9orf142 predicted a structure very similar to XRCC4, hence we have named c9orf142—XLS (XRCC4-like small protein). Depletion of c9orf142/XLS in cells impaired DSB repair consistent with a defect in NHEJ. Furthermore, c9orf142/XLS interacted with other core NHEJ factors. These results demonstrate the existence of a new component of the NHEJ DNA repair pathway in mammalian cells.
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Affiliation(s)
- A Craxton
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - J Somers
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - D Munnur
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - R Jukes-Jones
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - K Cain
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - M Malewicz
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
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