1
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Lavi ES, Lin ZP, Ratner ES. Gene expression of non-homologous end-joining pathways in the prognosis of ovarian cancer. iScience 2023; 26:107934. [PMID: 37810216 PMCID: PMC10558711 DOI: 10.1016/j.isci.2023.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/04/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Ovarian cancer is the deadliest gynecologic malignancy in women, with a 46% five-year overall survival rate. The objective of the study was to investigate the effects of non-homologous end-joining (NHEJ) genes on clinical outcomes of ovarian cancer patients. To determine if these genes act as prognostic biomarkers of mortality and disease progression, the expression profiles of 48 NHEJ-associated genes were analyzed using an array of statistical and machine learning techniques: logistic regression models, decision trees, naive-Bayes, two sample t-tests, support vector machines, hierarchical clustering, principal component analysis, and neural networks. In this process, the correlation of genes with patient survival and disease progression and recurrence was noted. Also, multiple features from the gene set were found to have significant predictive capabilities. APTX, BRCA1, PAXX, LIG1, and TP53 were identified as most important out of all the candidate genes for predicting clinical outcomes of ovarian cancer patients.
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Affiliation(s)
- Ethan S. Lavi
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Z. Ping Lin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Elena S. Ratner
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
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2
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Richardson RR, Steyert M, Khim SN, Crutcher GW, Brandenburg C, Robertson CD, Romanowski AJ, Inen J, Altas B, Poulopoulos A. Enhancing Precision and Efficiency of Cas9-Mediated Knockin Through Combinatorial Fusions of DNA Repair Proteins. CRISPR J 2023; 6:447-461. [PMID: 37713292 PMCID: PMC10611978 DOI: 10.1089/crispr.2023.0036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/14/2023] [Indexed: 09/17/2023] Open
Abstract
Cas9 targets genomic loci with high specificity. For knockin with double-strand break repair, however, Cas9 often leads to unintended on-target knockout rather than intended edits. This imprecision is a barrier for direct in vivo editing where clonal selection is not feasible. In this study, we demonstrate a high-throughput workflow to comparatively assess on-target efficiency and precision of editing outcomes. Using this workflow, we screened combinations of donor DNA and Cas9 variants, as well as fusions to DNA repair proteins. This yielded novel high-performance double-strand break repair editing agents and combinatorial optimizations, yielding increases in knockin efficiency and precision. Cas9-RC, a novel fusion Cas9 flanked by eRad18 and CtIP[HE], increased knockin performance in vitro and in vivo in the developing mouse brain. Continued comparative assessment of editing efficiency and precision with this framework will further the development of high-performance editing agents for in vivo knockin and future genome therapeutics.
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Affiliation(s)
- Ryan R. Richardson
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marilyn Steyert
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Saovleak N. Khim
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Garrett W. Crutcher
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cheryl Brandenburg
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Colin D. Robertson
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrea J. Romanowski
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jeffrey Inen
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Bekir Altas
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Alexandros Poulopoulos
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
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3
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Shi M, Hou J, Liang W, Li Q, Shao S, Ci S, Shu C, Zhao X, Zhao S, Huang M, Wu C, Hu Z, He L, Guo Z, Pan F. GAPDH facilitates homologous recombination repair by stabilizing RAD51 in an HDAC1-dependent manner. EMBO Rep 2023; 24:e56437. [PMID: 37306047 PMCID: PMC10398663 DOI: 10.15252/embr.202256437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/13/2023] Open
Abstract
Homologous recombination (HR), a form of error-free DNA double-strand break (DSB) repair, is important for the maintenance of genomic integrity. Here, we identify a moonlighting protein, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), as a regulator of HR repair, which is mediated through HDAC1-dependent regulation of RAD51 stability. Mechanistically, in response to DSBs, Src signaling is activated and mediates GAPDH nuclear translocation. Then, GAPDH directly binds with HDAC1, releasing it from its suppressor. Subsequently, activated HDAC1 deacetylates RAD51 and prevents it from undergoing proteasomal degradation. GAPDH knockdown decreases RAD51 protein levels and inhibits HR, which is re-established by overexpression of HDAC1 but not SIRT1. Notably, K40 is an important acetylation site of RAD51, which facilitates stability maintenance. Collectively, our findings provide new insights into the importance of GAPDH in HR repair, in addition to its glycolytic activity, and they show that GAPDH stabilizes RAD51 by interacting with HDAC1 and promoting HDAC1 deacetylation of RAD51.
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Affiliation(s)
- Munan Shi
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Jiajia Hou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Weichu Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Qianwen Li
- Department of Radiotherapy, Taikang Xianlin Drum Tower HospitalNanjing UniversityNanjingChina
| | - Shan Shao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Shusheng Ci
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
- School of Basic Medical SciencesNanjing Medical UniversityNanjingChina
| | - Chuanjun Shu
- Department of Bioinformatics, School of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjingChina
| | - Xingqi Zhao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Shanmeizi Zhao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Miaoling Huang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Congye Wu
- Department of Oncology, Nanjing First HospitalNanjing Medical UniversityNanjingChina
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
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4
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Jiang Y. Contribution of Microhomology to Genome Instability: Connection between DNA Repair and Replication Stress. Int J Mol Sci 2022; 23:12937. [PMID: 36361724 PMCID: PMC9657218 DOI: 10.3390/ijms232112937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/23/2022] [Accepted: 10/23/2022] [Indexed: 11/23/2023] Open
Abstract
Microhomology-mediated end joining (MMEJ) is a highly mutagenic pathway to repair double-strand breaks (DSBs). MMEJ was thought to be a backup pathway of homologous recombination (HR) and canonical nonhomologous end joining (C-NHEJ). However, it attracts more attention in cancer research due to its special function of microhomology in many different aspects of cancer. In particular, it is initiated with DNA end resection and upregulated in homologous recombination-deficient cancers. In this review, I summarize the following: (1) the recent findings and contributions of MMEJ to genome instability, including phenotypes relevant to MMEJ; (2) the interaction between MMEJ and other DNA repair pathways; (3) the proposed mechanistic model of MMEJ in DNA DSB repair and a new connection with microhomology-mediated break-induced replication (MMBIR); and (4) the potential clinical application by targeting MMEJ based on synthetic lethality for cancer therapy.
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Affiliation(s)
- Yuning Jiang
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22903, USA
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5
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Potential Molecular Mechanisms behind the Ultra-High Dose Rate "FLASH" Effect. Int J Mol Sci 2022; 23:ijms232012109. [PMID: 36292961 PMCID: PMC9602825 DOI: 10.3390/ijms232012109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/26/2022] [Accepted: 10/08/2022] [Indexed: 11/17/2022] Open
Abstract
FLASH radiotherapy, or the delivery of a dose at an ultra-high dose rate (>40 Gy/s), has recently emerged as a promising tool to enhance the therapeutic index in cancer treatment. The remarkable sparing of normal tissues and equivalent tumor control by FLASH irradiation compared to conventional dose rate irradiation—the FLASH effect—has already been demonstrated in several preclinical models and even in a first patient with T-cell cutaneous lymphoma. However, the biological mechanisms responsible for the differential effect produced by FLASH irradiation in normal and cancer cells remain to be elucidated. This is of great importance because a good understanding of the underlying radiobiological mechanisms and characterization of the specific beam parameters is required for a successful clinical translation of FLASH radiotherapy. In this review, we summarize the FLASH investigations performed so far and critically evaluate the current hypotheses explaining the FLASH effect, including oxygen depletion, the production of reactive oxygen species, and an altered immune response. We also propose a new theory that assumes an important role of mitochondria in mediating the normal tissue and tumor response to FLASH dose rates.
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6
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Huang J, Cook DE. The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens. FEMS Microbiol Rev 2022; 46:6638986. [PMID: 35810003 PMCID: PMC9779921 DOI: 10.1093/femsre/fuac035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks require repair or risk corrupting the language of life. To ensure genome integrity and viability, multiple DNA double-strand break repair pathways function in eukaryotes. Two such repair pathways, canonical non-homologous end joining and homologous recombination, have been extensively studied, while other pathways such as microhomology-mediated end joint and single-strand annealing, once thought to serve as back-ups, now appear to play a fundamental role in DNA repair. Here, we review the molecular details and hierarchy of these four DNA repair pathways, and where possible, a comparison for what is known between animal and fungal models. We address the factors contributing to break repair pathway choice, and aim to explore our understanding and knowledge gaps regarding mechanisms and regulation in filamentous pathogens. We additionally discuss how DNA double-strand break repair pathways influence genome engineering results, including unexpected mutation outcomes. Finally, we review the concept of biased genome evolution in filamentous pathogens, and provide a model, termed Biased Variation, that links DNA double-strand break repair pathways with properties of genome evolution. Despite our extensive knowledge for this universal process, there remain many unanswered questions, for which the answers may improve genome engineering and our understanding of genome evolution.
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Affiliation(s)
- Jun Huang
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS 66506, United States
| | - David E Cook
- Corresponding author: 1712 Claflin Road, 4004 Throckmorton Hall, Manhattan, KS 66502, United States. E-mail:
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7
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Friedl AA, Prise KM, Butterworth KT, Montay-Gruel P, Favaudon V. Radiobiology of the FLASH effect. Med Phys 2022; 49:1993-2013. [PMID: 34426981 DOI: 10.1002/mp.15184] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Radiation exposures at ultrahigh dose rates (UHDRs) at several orders of magnitude greater than in current clinical radiotherapy (RT) have been shown to manifest differential radiobiological responses compared to conventional (CONV) dose rates. This has led to studies investigating the application of UHDR for therapeutic advantage (FLASH-RT) that have gained significant interest since the initial discovery in 2014 that demonstrated reduced lung toxicity with equivalent levels of tumor control compared with conventional dose-rate RT. Many subsequent studies have demonstrated the potential protective role of FLASH-RT in normal tissues, yet the underlying molecular and cellular mechanisms of the FLASH effect remain to be fully elucidated. Here, we summarize the current evidence of the FLASH effect and review FLASH-RT studies performed in preclinical models of normal tissue response. To critically examine the underlying biological mechanisms of responses to UHDR radiation exposures, we evaluate in vitro studies performed with normal and tumor cells. Differential responses to UHDR versus CONV irradiation recurrently involve reduced inflammatory processes and differential expression of pro- and anti-inflammatory genes. In addition, frequently reduced levels of DNA damage or misrepair products are seen after UHDR irradiation. So far, it is not clear what signal elicits these differential responses, but there are indications for involvement of reactive species. Different susceptibility to FLASH effects observed between normal and tumor cells may result from altered metabolic and detoxification pathways and/or repair pathways used by tumor cells. We summarize the current theories that may explain the FLASH effect and highlight important research questions that are key to a better mechanistic understanding and, thus, the future implementation of FLASH-RT in the clinic.
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Affiliation(s)
- Anna A Friedl
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Kevin M Prise
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Karl T Butterworth
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Pierre Montay-Gruel
- Department of Radiation Oncology, University of California at Irvine, Irvine, California, USA
| | - Vincent Favaudon
- Institut Curie, Inserm U 1021-CNRS UMR 3347, Université Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France
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8
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Targeting PARP proteins in acute leukemia: DNA damage response inhibition and therapeutic strategies. J Hematol Oncol 2022; 15:10. [PMID: 35065680 PMCID: PMC8783444 DOI: 10.1186/s13045-022-01228-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
The members of the Poly(ADP‐ribose) polymerase (PARP) superfamily are involved in several biological processes and, in particular, in the DNA damage response (DDR). The most studied members, PARP1, PARP2 and PARP3, act as sensors of DNA damages, in order to activate different intracellular repair pathways, including single-strand repair, homologous recombination, conventional and alternative non-homologous end joining. This review recapitulates the functional role of PARPs in the DDR pathways, also in relationship with the cell cycle phases, which drives our knowledge of the mechanisms of action of PARP inhibitors (PARPi), encompassing inhibition of single-strand breaks and base excision repair, PARP trapping and sensitization to antileukemia immune responses. Several studies have demonstrated a preclinical activity of the current available PARPi, olaparib, rucaparib, niraparib, veliparib and talazoparib, as single agent and/or in combination with cytotoxic, hypomethylating or targeted drugs in acute leukemia, thus encouraging the development of clinical trials. We here summarize the most recent preclinical and clinical findings and discuss the synthetic lethal interactions of PARPi in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). Despite the low frequency of genomic alterations of PARP and other DDR-related genes in acute leukemia, selective vulnerabilities have been reported in several disease subgroups, along with a “BRCAness phenotype.” AML carrying the RUNX1-RUNX1T1 or PML-RARA fusion genes or mutations in signaling genes (FLT3-ITD in combination with TET2 or TET2 and DNMT3A deficiency), cohesin complex members (STAG2), TP53 and BCOR as co-occurring lesions, IDH1/2 and ALL cases expressing the TCF3-HLF chimera or TET1 was highly sensitive to PARPi in preclinical studies. These data, along with the warning coming from the observation of cases of therapy-related myeloid malignancies among patients receiving PARPi for solid tumors treatment, indicate that PARPi represents a promising strategy in a personalized medicine setting. The characterization of the clonal and subclonal genetic background and of the DDR functionality is crucial to select acute leukemia patients that will likely benefit of PARPi-based therapeutic regimens.
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9
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Trichodysplasia spinulosa polyomavirus small T antigen synergistically modulates S6 protein translation and DNA damage response pathways to shape host cell environment. Virus Genes 2022; 58:35-41. [PMID: 35000075 DOI: 10.1007/s11262-021-01880-7] [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: 02/02/2021] [Accepted: 11/24/2021] [Indexed: 11/27/2022]
Abstract
TSPyV is a viral agent linked to Trichodysplasia spinulosa, a disfiguring human skin disease which presents with hyperkeratotic spicule eruption in immunocompromised hosts. This proliferative disease state requires extensive modulation of the host cell environment. While the small T (sT) antigen of TSPyV has been postulated to cause widespread cellular perturbation, its specific substrates and their mechanistic connection are unclear. To identify the cellular substrates and pathways perturbed by TSPyV sT and propose a nuanced model that reconciles the multiple arms of TSPyV pathogenesis, changes in expression of several proteins and phospho-proteins in TSPyV sT expressing and TSPyV sT deletion mutant-expressing cell lysates were interrogated using Western blot assays. TSPyV sT expression exploits the DNA damage response pathway, by inducing hyperphosphorylation of ATM and 53BP1 and upregulation of BMI-1. Concurrently, sT dysregulates the S6 protein translation pathway via hyperphosphorylation of CDC2, p70 S6 kinase, S6, and PP1α. The S6S244/247 and p-PP1αT320 phospho-forms are points of overlap between the DDR and S6 networks. We propose a mechanistic rationale for previous reports positioning sT antigen as the key driver of TSPyV pathogenesis. We illuminate novel targets in the S6 and DDR pathways and recognize a potential synergy between these pathways. TSPyV may sensitize the cell to both unrestricted translation and genomic instability. This multi-pronged infection model may inform future therapeutic modalities against TSPyV and possibly other viruses with overlapping host substrates.
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10
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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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11
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Curik N, Polivkova V, Burda P, Koblihova J, Laznicka A, Kalina T, Kanderova V, Brezinova J, Ransdorfova S, Karasova D, Rejlova K, Bakardjieva M, Kuzilkova D, Kundrat D, Linhartova J, Klamova H, Salek C, Klener P, Hrusak O, Machova Polakova K. Somatic Mutations in Oncogenes Are in Chronic Myeloid Leukemia Acquired De Novo via Deregulated Base-Excision Repair and Alternative Non-Homologous End Joining. Front Oncol 2021; 11:744373. [PMID: 34616685 PMCID: PMC8488388 DOI: 10.3389/fonc.2021.744373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/02/2021] [Indexed: 12/16/2022] Open
Abstract
Somatic mutations are a common molecular mechanism through which chronic myeloid leukemia (CML) cells acquire resistance to tyrosine kinase inhibitors (TKIs) therapy. While most of the mutations in the kinase domain of BCR-ABL1 can be successfully managed, the recurrent somatic mutations in other genes may be therapeutically challenging. Despite the major clinical relevance of mutation-associated resistance in CML, the mechanisms underlying mutation acquisition in TKI-treated leukemic cells are not well understood. This work demonstrated de novo acquisition of mutations on isolated single-cell sorted CML clones growing in the presence of imatinib. The acquisition of mutations was associated with the significantly increased expression of the LIG1 and PARP1 genes involved in the error-prone alternative nonhomologous end-joining pathway, leading to genomic instability, and increased expression of the UNG, FEN and POLD3 genes involved in the base-excision repair (long patch) pathway, allowing point mutagenesis. This work showed in vitro and in vivo that de novo acquisition of resistance-associated mutations in oncogenes is the prevalent method of somatic mutation development in CML under TKIs treatment.
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Affiliation(s)
- Nikola Curik
- Institute of Hematology and Blood Transfusion, Prague, Czechia.,Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czechia
| | | | - Pavel Burda
- Institute of Hematology and Blood Transfusion, Prague, Czechia.,Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Jitka Koblihova
- Institute of Hematology and Blood Transfusion, Prague, Czechia
| | - Adam Laznicka
- Institute of Hematology and Blood Transfusion, Prague, Czechia.,Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Tomas Kalina
- CLIP-Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Veronika Kanderova
- CLIP-Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Jana Brezinova
- Institute of Hematology and Blood Transfusion, Prague, Czechia
| | | | | | - Katerina Rejlova
- CLIP-Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Marina Bakardjieva
- CLIP-Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Daniela Kuzilkova
- CLIP-Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - David Kundrat
- Institute of Hematology and Blood Transfusion, Prague, Czechia
| | - Jana Linhartova
- Institute of Hematology and Blood Transfusion, Prague, Czechia
| | - Hana Klamova
- Institute of Hematology and Blood Transfusion, Prague, Czechia
| | - Cyril Salek
- Institute of Hematology and Blood Transfusion, Prague, Czechia
| | - Pavel Klener
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czechia.,First Department of Internal Medicine-Department of Hematology, Charles University General Hospital in Prague, Prague, Czechia
| | - Ondrej Hrusak
- CLIP-Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Katerina Machova Polakova
- Institute of Hematology and Blood Transfusion, Prague, Czechia.,Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czechia
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12
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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.
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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
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13
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Tatin X, Muggiolu G, Sauvaigo S, Breton J. Evaluation of DNA double-strand break repair capacity in human cells: Critical overview of current functional methods. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108388. [PMID: 34893153 DOI: 10.1016/j.mrrev.2021.108388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 02/05/2023]
Abstract
DNA double-strand breaks (DSBs) are highly deleterious lesions, responsible for mutagenesis, chromosomal translocation or cell death. DSB repair (DSBR) is therefore a critical part of the DNA damage response (DDR) to restore molecular and genomic integrity. In humans, this process is achieved through different pathways with various outcomes. The balance between DSB repair activities varies depending on cell types, tissues or individuals. Over the years, several methods have been developed to study variations in DSBR capacity. Here, we mainly focus on functional techniques, which provide dynamic information regarding global DSB repair proficiency or the activity of specific pathways. These methods rely on two kinds of approaches. Indirect techniques, such as pulse field gel electrophoresis (PFGE), the comet assay and immunofluorescence (IF), measure DSB repair capacity by quantifying the time-dependent decrease in DSB levels after exposure to a DNA-damaging agent. On the other hand, cell-free assays and reporter-based methods directly track the repair of an artificial DNA substrate. Each approach has intrinsic advantages and limitations and despite considerable efforts, there is currently no ideal method to quantify DSBR capacity. All techniques provide different information and can be regarded as complementary, but some studies report conflicting results. Parameters such as the type of biological material, the required equipment or the cost of analysis may also limit available options. Improving currently available methods measuring DSBR capacity would be a major step forward and we present direct applications in mechanistic studies, drug development, human biomonitoring and personalized medicine, where DSBR analysis may improve the identification of patients eligible for chemo- and radiotherapy.
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Affiliation(s)
- Xavier Tatin
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France; LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | | | - Sylvie Sauvaigo
- LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | - Jean Breton
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France.
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14
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Tomasini PP, Guecheva TN, Leguisamo NM, Péricart S, Brunac AC, Hoffmann JS, Saffi J. Analyzing the Opportunities to Target DNA Double-Strand Breaks Repair and Replicative Stress Responses to Improve Therapeutic Index of Colorectal Cancer. Cancers (Basel) 2021; 13:3130. [PMID: 34201502 PMCID: PMC8268241 DOI: 10.3390/cancers13133130] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/15/2021] [Accepted: 06/18/2021] [Indexed: 12/22/2022] Open
Abstract
Despite the ample improvements of CRC molecular landscape, the therapeutic options still rely on conventional chemotherapy-based regimens for early disease, and few targeted agents are recommended for clinical use in the metastatic setting. Moreover, the impact of cytotoxic, targeted agents, and immunotherapy combinations in the metastatic scenario is not fully satisfactory, especially the outcomes for patients who develop resistance to these treatments need to be improved. Here, we examine the opportunity to consider therapeutic agents targeting DNA repair and DNA replication stress response as strategies to exploit genetic or functional defects in the DNA damage response (DDR) pathways through synthetic lethal mechanisms, still not explored in CRC. These include the multiple actors involved in the repair of DNA double-strand breaks (DSBs) through homologous recombination (HR), classical non-homologous end joining (NHEJ), and microhomology-mediated end-joining (MMEJ), inhibitors of the base excision repair (BER) protein poly (ADP-ribose) polymerase (PARP), as well as inhibitors of the DNA damage kinases ataxia-telangiectasia and Rad3 related (ATR), CHK1, WEE1, and ataxia-telangiectasia mutated (ATM). We also review the biomarkers that guide the use of these agents, and current clinical trials with targeted DDR therapies.
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Affiliation(s)
- Paula Pellenz Tomasini
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Avenida Sarmento Leite, 245, Porto Alegre 90050-170, Brazil; (P.P.T.); (N.M.L.)
- Post-Graduation Program in Cell and Molecular Biology, Federal University of Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre 91501-970, Brazil
| | - Temenouga Nikolova Guecheva
- Cardiology Institute of Rio Grande do Sul, University Foundation of Cardiology (IC-FUC), Porto Alegre 90620-000, Brazil;
| | - Natalia Motta Leguisamo
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Avenida Sarmento Leite, 245, Porto Alegre 90050-170, Brazil; (P.P.T.); (N.M.L.)
| | - Sarah Péricart
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France; (S.P.); (A.-C.B.); (J.S.H.)
| | - Anne-Cécile Brunac
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France; (S.P.); (A.-C.B.); (J.S.H.)
| | - Jean Sébastien Hoffmann
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France; (S.P.); (A.-C.B.); (J.S.H.)
| | - Jenifer Saffi
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Avenida Sarmento Leite, 245, Porto Alegre 90050-170, Brazil; (P.P.T.); (N.M.L.)
- Post-Graduation Program in Cell and Molecular Biology, Federal University of Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre 91501-970, Brazil
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15
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Michelena J, Pellegrino S, Spegg V, Altmeyer M. Replicated chromatin curtails 53BP1 recruitment in BRCA1-proficient and BRCA1-deficient cells. Life Sci Alliance 2021; 4:4/6/e202101023. [PMID: 33811064 PMCID: PMC8046418 DOI: 10.26508/lsa.202101023] [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: 01/18/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
This study demonstrates how single cell normalization to genome size provides insight into genome function, here in the context of DNA double-strand break repair by 53BP1 versus BRCA1–BARD1. DNA double-strand breaks can be repaired by non-homologous end-joining or homologous recombination. Which pathway is used depends on the balance between the tumor suppressors 53BP1 and BRCA1 and on the availability of an undamaged template DNA for homology-directed repair. How cells switch from a 53BP1-dominated to a BRCA1-governed homologous recombination response as they progress through the cell cycle is incompletely understood. Here we reveal, using high-throughput microscopy and applying single cell normalization to control for increased genome size as cells replicate their DNA, that 53BP1 recruitment to damaged replicated chromatin is inefficient in both BRCA1-proficient and BRCA1-deficient cells. Our results substantiate a dual switch model from a 53BP1-dominated response in unreplicated chromatin to a BRCA1–BARD1–dominated response in replicated chromatin, in which replication-coupled dilution of 53BP1’s binding mark H4K20me2 functionally cooperates with BRCA1–BARD1–mediated suppression of 53BP1 binding. More generally, we suggest that appropriate normalization of single cell data, for example, to DNA content, provides additional layers of information, which can be critical for quantifying and interpreting cellular phenotypes.
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Affiliation(s)
- Jone Michelena
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Stefania Pellegrino
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School (LSZGS), Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School (LSZGS), Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
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16
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Nelson CB, Alturki TM, Luxton JJ, Taylor LE, Maranon DG, Muraki K, Murnane JP, Bailey SM. Telomeric Double Strand Breaks in G1 Human Cells Facilitate Formation of 5' C-Rich Overhangs and Recruitment of TERRA. Front Genet 2021; 12:644803. [PMID: 33841503 PMCID: PMC8027502 DOI: 10.3389/fgene.2021.644803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
Telomeres, repetitive nucleoprotein complexes that protect chromosomal termini and prevent them from activating inappropriate DNA damage responses (DDRs), shorten with cell division and thus with aging. Here, we characterized the human cellular response to targeted telomeric double-strand breaks (DSBs) in telomerase-positive and telomerase-independent alternative lengthening of telomere (ALT) cells, specifically in G1 phase. Telomeric DSBs in human G1 cells elicited early signatures of a DDR; however, localization of 53BP1, an important regulator of resection at broken ends, was not observed at telomeric break sites. Consistent with this finding and previously reported repression of classical non-homologous end-joining (c-NHEJ) at telomeres, evidence for c-NHEJ was also lacking. Likewise, no evidence of homologous recombination (HR)-dependent repair of telomeric DSBs in G1 was observed. Rather, and supportive of rapid truncation events, telomeric DSBs in G1 human cells facilitated formation of extensive tracks of resected 5′ C-rich telomeric single-stranded (ss)DNA, a previously proposed marker of the recombination-dependent ALT pathway. Indeed, induction of telomeric DSBs in human ALT cells resulted in significant increases in 5′ C-rich (ss)telomeric DNA in G1, which rather than RPA, was bound by the complementary telomeric RNA, TERRA, presumably to protect these exposed ends so that they persist into S/G2 for telomerase-mediated or HR-dependent elongation, while also circumventing conventional repair pathways. Results demonstrate the remarkable adaptability of telomeres, and thus they have important implications for persistent telomeric DNA damage in normal human G1/G0 cells (e.g., lymphocytes), as well as for therapeutically relevant targets to improve treatment of ALT-positive tumors.
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Affiliation(s)
- Christopher B Nelson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, United States
| | - Taghreed M Alturki
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, United States
| | - Jared J Luxton
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, United States
| | - Lynn E Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - David G Maranon
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Keiko Muraki
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - John P Murnane
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, United States
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17
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Caracciolo D, Riillo C, Di Martino MT, Tagliaferri P, Tassone P. Alternative Non-Homologous End-Joining: Error-Prone DNA Repair as Cancer's Achilles' Heel. Cancers (Basel) 2021; 13:cancers13061392. [PMID: 33808562 PMCID: PMC8003480 DOI: 10.3390/cancers13061392] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Cancer onset and progression lead to a high rate of DNA damage, due to replicative and metabolic stress. To survive in this dangerous condition, cancer cells switch the DNA repair machinery from faithful systems to error-prone pathways, strongly increasing the mutational rate that, in turn, supports the disease progression and drug resistance. Although DNA repair de-regulation boosts genomic instability, it represents, at the same time, a critical cancer vulnerability that can be exploited for synthetic lethality-based therapeutic intervention. We here discuss the role of the error-prone DNA repair, named Alternative Non-Homologous End Joining (Alt-NHEJ), as inducer of genomic instability and as a potential therapeutic target. We portray different strategies to drug Alt-NHEJ and discuss future challenges for selecting patients who could benefit from Alt-NHEJ inhibition, with the aim of precision oncology. Abstract Error-prone DNA repair pathways promote genomic instability which leads to the onset of cancer hallmarks by progressive genetic aberrations in tumor cells. The molecular mechanisms which foster this process remain mostly undefined, and breakthrough advancements are eagerly awaited. In this context, the alternative non-homologous end joining (Alt-NHEJ) pathway is considered a leading actor. Indeed, there is experimental evidence that up-regulation of major Alt-NHEJ components, such as LIG3, PolQ, and PARP1, occurs in different tumors, where they are often associated with disease progression and drug resistance. Moreover, the Alt-NHEJ addiction of cancer cells provides a promising target to be exploited by synthetic lethality approaches for the use of DNA damage response (DDR) inhibitors and even as a sensitizer to checkpoint-inhibitors immunotherapy by increasing the mutational load. In this review, we discuss recent findings highlighting the role of Alt-NHEJ as a promoter of genomic instability and, therefore, as new cancer’s Achilles’ heel to be therapeutically exploited in precision oncology.
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18
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Lakshmanan LN, Yee Z, Halliwell B, Gruber J, Gunawan R. Thermodynamic analysis of DNA hybridization signatures near mitochondrial DNA deletion breakpoints. iScience 2021; 24:102138. [PMID: 33665557 PMCID: PMC7900216 DOI: 10.1016/j.isci.2021.102138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/14/2021] [Accepted: 01/29/2021] [Indexed: 11/17/2022] Open
Abstract
Broad evidence in the literature supports double-strand breaks (DSBs) as initiators of mitochondrial DNA (mtDNA) deletion mutations. While DNA misalignment during DSB repair is commonly proposed as the mechanism by which DSBs cause deletion mutations, details such as the specific DNA repair errors are still lacking. Here, we used DNA hybridization thermodynamics to infer the sequence lengths of mtDNA misalignments that are associated with mtDNA deletions. We gathered and analyzed 9,921 previously reported mtDNA deletion breakpoints in human, rhesus monkey, mouse, rat, and Caenorhabditis elegans. Our analysis shows that a large fraction of mtDNA breakpoint positions can be explained by the thermodynamics of short ≤ 5-nt misalignments. The significance of short DNA misalignments supports an important role for erroneous non-homologous and micro-homology-dependent DSB repair in mtDNA deletion formation. The consistency of the results of our analysis across species further suggests a shared mode of mtDNA deletion mutagenesis.
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Affiliation(s)
- Lakshmi Narayanan Lakshmanan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Zhuangli Yee
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Barry Halliwell
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jan Gruber
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Ageing Research Laboratory, Science Division, Yale-NUS College, Singapore, Singapore
| | - Rudiyanto Gunawan
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY, USA
- Corresponding author
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19
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Falk M, Hausmann M. A Paradigm Revolution or Just Better Resolution-Will Newly Emerging Superresolution Techniques Identify Chromatin Architecture as a Key Factor in Radiation-Induced DNA Damage and Repair Regulation? Cancers (Basel) 2020; 13:E18. [PMID: 33374540 PMCID: PMC7793109 DOI: 10.3390/cancers13010018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023] Open
Abstract
DNA double-strand breaks (DSBs) have been recognized as the most serious lesions in irradiated cells. While several biochemical pathways capable of repairing these lesions have been identified, the mechanisms by which cells select a specific pathway for activation at a given DSB site remain poorly understood. Our knowledge of DSB induction and repair has increased dramatically since the discovery of ionizing radiation-induced foci (IRIFs), initiating the possibility of spatiotemporally monitoring the assembly and disassembly of repair complexes in single cells. IRIF exploration revealed that all post-irradiation processes-DSB formation, repair and misrepair-are strongly dependent on the characteristics of DSB damage and the microarchitecture of the whole affected chromatin domain in addition to the cell status. The microscale features of IRIFs, such as their morphology, mobility, spatiotemporal distribution, and persistence kinetics, have been linked to repair mechanisms. However, the influence of various biochemical and structural factors and their specific combinations on IRIF architecture remains unknown, as does the hierarchy of these factors in the decision-making process for a particular repair mechanism at each individual DSB site. New insights into the relationship between the physical properties of the incident radiation, chromatin architecture, IRIF architecture, and DSB repair mechanisms and repair efficiency are expected from recent developments in optical superresolution microscopy (nanoscopy) techniques that have shifted our ability to analyze chromatin and IRIF architectures towards the nanoscale. In the present review, we discuss this relationship, attempt to correlate still rather isolated nanoscale studies with already better-understood aspects of DSB repair at the microscale, and consider whether newly emerging "correlated multiscale structuromics" can revolutionarily enhance our knowledge in this field.
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Affiliation(s)
- Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany;
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20
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Marin PA, Obonaga R, Pavani RS, da Silva MS, de Araujo CB, Lima AA, Avila CC, Cestari I, Machado CR, Elias MC. ATR Kinase Is a Crucial Player Mediating the DNA Damage Response in Trypanosoma brucei. Front Cell Dev Biol 2020; 8:602956. [PMID: 33415107 PMCID: PMC7783291 DOI: 10.3389/fcell.2020.602956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/02/2020] [Indexed: 12/26/2022] Open
Abstract
DNA double-strand breaks (DSBs) are among the most deleterious lesions that threaten genome integrity. To address DSBs, eukaryotic cells of model organisms have evolved a complex network of cellular pathways that are able to detect DNA damage, activate a checkpoint response to delay cell cycle progression, recruit the proper repair machinery, and resume the cell cycle once the DNA damage is repaired. Cell cycle checkpoints are primarily regulated by the apical kinases ATR and ATM, which are conserved throughout the eukaryotic kingdom. Trypanosoma brucei is a divergent pathogenic protozoan parasite that causes human African trypanosomiasis (HAT), a neglected disease that can be fatal when left untreated. The proper signaling and accuracy of DNA repair is fundamental to T. brucei not only to ensure parasite survival after genotoxic stress but also because DSBs are involved in the process of generating antigenic variations used by this parasite to evade the host immune system. DSBs trigger a strong DNA damage response and efficient repair process in T. brucei, but it is unclear how these processes are coordinated. Here, by knocking down ATR in T. brucei using two different approaches (conditional RNAi and an ATR inhibitor), we show that ATR is required to mediate intra-S and partial G1/S checkpoint responses. ATR is also involved in replication fork stalling, is critical for H2A histone phosphorylation in a small group of cells and is necessary for the recruitment and upregulation of the HR-mediated DNA repair protein RAD51 after ionizing radiation (IR) induces DSBs. In summary, this work shows that apical ATR kinase plays a central role in signal transduction and is critical for orchestrating the DNA damage response in T. brucei.
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Affiliation(s)
- Paula Andrea Marin
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Ricardo Obonaga
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Raphael Souza Pavani
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Marcelo Santos da Silva
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Christiane Bezerra de Araujo
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - André Arruda Lima
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Carla Cristi Avila
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Igor Cestari
- Institute of Parasitology, McGill University, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Carlos Renato Machado
- Biochemical and Immunology Department, Institute of Biomedical Science, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Maria Carolina Elias
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
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21
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Saha T, Sundaravinayagam D, Di Virgilio M. Charting a DNA Repair Roadmap for Immunoglobulin Class Switch Recombination. Trends Biochem Sci 2020; 46:184-199. [PMID: 33250286 DOI: 10.1016/j.tibs.2020.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/08/2020] [Accepted: 10/23/2020] [Indexed: 01/18/2023]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the process occurring in mature B cells that diversifies the effector component of antibody responses. CSR is initiated by the activity of the B cell-specific enzyme activation-induced cytidine deaminase (AID), which leads to the formation of programmed DNA double-strand breaks (DSBs) at the Ig heavy chain (Igh) locus. Mature B cells use a multilayered and complex regulatory framework to ensure that AID-induced DNA breaks are channeled into productive repair reactions leading to CSR, and to avoid aberrant repair events causing lymphomagenic chromosomal translocations. Here, we review the DNA repair pathways acting on AID-induced DSBs and their functional interplay, with a particular focus on the latest developments in their molecular composition and mechanistic regulation.
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Affiliation(s)
- Tannishtha Saha
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Devakumar Sundaravinayagam
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
| | - Michela Di Virgilio
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany; Charité-Universitätsmedizin Berlin, Berlin 10117, Germany.
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22
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Hanscom T, McVey M. Regulation of Error-Prone DNA Double-Strand Break Repair and Its Impact on Genome Evolution. Cells 2020; 9:E1657. [PMID: 32660124 PMCID: PMC7407515 DOI: 10.3390/cells9071657] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
Abstract
Double-strand breaks are one of the most deleterious DNA lesions. Their repair via error-prone mechanisms can promote mutagenesis, loss of genetic information, and deregulation of the genome. These detrimental outcomes are significant drivers of human diseases, including many cancers. Mutagenic double-strand break repair also facilitates heritable genetic changes that drive organismal adaptation and evolution. In this review, we discuss the mechanisms of various error-prone DNA double-strand break repair processes and the cellular conditions that regulate them, with a focus on alternative end joining. We provide examples that illustrate how mutagenic double-strand break repair drives genome diversity and evolution. Finally, we discuss how error-prone break repair can be crucial to the induction and progression of diseases such as cancer.
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Affiliation(s)
| | - Mitch McVey
- Department. of Biology, Tufts University, Medford, MA 02155, USA;
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23
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A physicochemical model of reaction kinetics supports peroxyl radical recombination as the main determinant of the FLASH effect. Radiother Oncol 2020; 153:303-310. [PMID: 32534957 DOI: 10.1016/j.radonc.2020.06.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 05/08/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND AND PURPOSE FLASH radiotherapy, a technique based on delivering large doses in a single fraction at the micro/millisecond timescale, spares normal tissues from late radiation-induced toxicity, in an oxygen-dependent process, whilst keeping full anti-tumor efficiency. We present a theoretical model taking into account the kinetics of formation and decay of reactive oxygen species, in particular of organic peroxyl radicals ROO. formed by addition of O2 to primary carbon-centred radicals R. and known to play a major role at the origin radio-induced complications. MATERIALS AND METHODS The model focuses on the time-dependent evolution of radiolytic products in living matter exposed to continuous irradiation at dose-rates in the range 10-3-107Gy·s-1. The 9 differential rate equations resulting from the radiolytic and enzymatic reactions network were solved using the published values of these reactions rate constants in a cellular environment. RESULTS The model suggests a correlation between the area-under-the-curve of time-evolving [ROO.] and the probability of normal tissue complications. The model does not lend weight to the hypothesis of transient oxygen depletion as a main determinant of FLASH but rather suggests a major role of radical-radical recombination. CONCLUSION The model gives support to the reduction of ROO. lifetime as the main root of FLASH and compares favorably with published experimental results. We conclude that any process - in this case radical recombination - that shortens the lifetime or limits the radiolytic yield of ROO. is likely to protect normoxic tissues against the deleterious effects of radiation.
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24
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Fouillade C, Curras-Alonso S, Giuranno L, Quelennec E, Heinrich S, Bonnet-Boissinot S, Beddok A, Leboucher S, Karakurt HU, Bohec M, Baulande S, Vooijs M, Verrelle P, Dutreix M, Londoño-Vallejo A, Favaudon V. FLASH Irradiation Spares Lung Progenitor Cells and Limits the Incidence of Radio-induced Senescence. Clin Cancer Res 2020; 26:1497-1506. [PMID: 31796518 DOI: 10.1158/1078-0432.ccr-19-1440] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/29/2019] [Accepted: 11/27/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE One of the main limitations to anticancer radiotherapy lies in irreversible damage to healthy tissues located within the radiation field. "FLASH" irradiation at very high dose-rate is a new treatment modality that has been reported to specifically spare normal tissue from late radiation-induced toxicity in animal models and therefore could be a promising strategy to reduce treatment toxicity. EXPERIMENTAL DESIGN Lung responses to FLASH irradiation were investigated by qPCR, single-cell RNA sequencing (sc-RNA-Seq), and histologic methods during the acute wound healing phase as well as at late stages using C57BL/6J wild-type and Terc-/- mice exposed to bilateral thorax irradiation as well as human lung cells grown in vitro. RESULTS In vitro studies gave evidence of a reduced level of DNA damage and induced lethality at the advantage of FLASH. In mouse lung, sc-RNA-seq and the monitoring of proliferating cells revealed that FLASH minimized the induction of proinflammatory genes and reduced the proliferation of progenitor cells after injury. At late stages, FLASH-irradiated lungs presented less persistent DNA damage and senescent cells than after CONV exposure, suggesting a higher potential for lung regeneration with FLASH. Consistent with this hypothesis, the beneficial effect of FLASH was lost in Terc-/- mice harboring critically short telomeres and lack of telomerase activity. CONCLUSIONS The results suggest that, compared with conventional radiotherapy, FLASH minimizes DNA damage in normal cells, spares lung progenitor cells from excessive damage, and reduces the risk of replicative senescence.
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Affiliation(s)
- Charles Fouillade
- Institut Curie, Inserm U 1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France.
| | - Sandra Curras-Alonso
- Institut Curie, Inserm U 1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France
- Institut Curie, CNRS UMR 3244, PSL Research University, Paris, France
| | - Lorena Giuranno
- Department of Radiotherapy, Grow-School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Eddy Quelennec
- Institut Curie, Inserm U 1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France
| | - Sophie Heinrich
- Institut Curie, Inserm U 1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France
- Institut Curie, Translational Research Department, Experimental Radiotherapy Platform, PSL Research University, Centre Universitaire, Orsay, France
| | - Sarah Bonnet-Boissinot
- Institut Curie, Inserm U 1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France
| | - Arnaud Beddok
- Institut Curie, Inserm U 1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France
| | - Sophie Leboucher
- Institut Curie, CNRS UMR 3348, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France
| | | | - Mylène Bohec
- Institut Curie Genomics of Excellence (ICGex) Platform, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Paris, France
| | - Marc Vooijs
- Department of Radiotherapy, Grow-School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Pierre Verrelle
- Radiation Oncology Department, Institut Curie, Paris, France
- Institut Curie, Inserm U 1196-CNRS UMR 9187, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France
| | - Marie Dutreix
- Institut Curie, Inserm U 1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France
| | | | - Vincent Favaudon
- Institut Curie, Inserm U 1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France.
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25
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DNA Damage and DNA Damage Response in Chronic Myeloid Leukemia. Int J Mol Sci 2020; 21:ijms21041177. [PMID: 32053969 PMCID: PMC7072846 DOI: 10.3390/ijms21041177] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/31/2020] [Accepted: 02/08/2020] [Indexed: 12/31/2022] Open
Abstract
DNA damage and alterations in the DNA damage response (DDR) are critical sources of genetic instability that might be involved in BCR-ABL1 kinase-mediated blastic transformation of chronic myeloid leukemia (CML). Here, increased DNA damage is detected by γH2AX foci analysis in peripheral blood mononuclear cells (PBMCs) of de novo untreated chronic phase (CP)-CML patients (n = 5; 2.5 γH2AX foci per PBMC ± 0.5) and blast phase (BP)-CML patients (n = 3; 4.4 γH2AX foci per PBMC ± 0.7) as well as CP-CML patients with loss of major molecular response (MMR) (n = 5; 1.8 γH2AX foci per PBMC ± 0.4) when compared to DNA damage in PBMC of healthy donors (n = 8; 1.0 γH2AX foci per PBMC ± 0.1) and CP-CML patients in deep molecular response or MMR (n = 26; 1.0 γH2AX foci per PBMC ± 0.1). Progressive activation of erroneous non-homologous end joining (NHEJ) repair mechanisms during blastic transformation in CML is indicated by abundant co-localization of γH2AX/53BP1 foci, while a decline of the DDR is suggested by defective expression of (p-)ATM and (p-)CHK2. In summary, our data provide evidence for the accumulation of DNA damage in the course of CML and suggest ongoing DNA damage, erroneous NHEJ repair mechanisms, and alterations in the DDR as critical mediators of blastic transformation in CML.
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26
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Tahseen D, Rady PL, Tyring SK. Human polyomavirus modulation of the host DNA damage response. Virus Genes 2020; 56:128-135. [PMID: 31997082 DOI: 10.1007/s11262-020-01736-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/18/2020] [Indexed: 12/20/2022]
Abstract
The human DNA damage response (DDR) is a complex signaling network constituting many factors responsible for the preservation of genomic integrity. Human polyomaviruses (HPyVs) are able to harness the DDR machinery during their infectious cycle by expressing an array of tumor (T) antigens. These molecular interactions between human polyomavirus T antigens and the DDR create conditions that promote viral replication at the expense of host genomic stability to cause disease as well as carcinogenesis in the cases of the Merkel cell polyomavirus and BK polyomavirus. This review focuses on the six HPyVs with disease association, emphasizing strain-dependent differences in their selective manipulation of the DDR. Appreciation of the HPyV-DDR interface at a molecular scale is conducive to the development of novel therapeutic approaches.
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Affiliation(s)
- Danyal Tahseen
- Department of Dermatology, University of Texas Medical School At Houston, Houston, TX, 77030, USA
| | - Peter L Rady
- Department of Dermatology, University of Texas Medical School At Houston, Houston, TX, 77030, USA
| | - Stephen K Tyring
- Department of Dermatology, University of Texas Medical School At Houston, Houston, TX, 77030, USA.
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27
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Entrenching role of cell cycle checkpoints and autophagy for maintenance of genomic integrity. DNA Repair (Amst) 2019; 86:102748. [PMID: 31790874 DOI: 10.1016/j.dnarep.2019.102748] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/19/2019] [Accepted: 11/08/2019] [Indexed: 12/22/2022]
Abstract
Genomic integrity of the cell is crucial for the successful transmission of genetic information to the offspring and its survival. Persistent DNA damage induced by endogenous and exogenous agents leads to various metabolic manifestations. To combat this, eukaryotes have developed complex DNA damage response (DDR) pathway which senses the DNA damage and activates an arsenal of enzymes for the repair of damaged DNA. The active pathways for DNA repair are nucleotide excision repair (NER), base excision repair (BER) and mismatch repair (MMR) for single-strand break repair whereas homologous recombination (HR) and non-homologous end-joining (NHEJ) for double-strand break repair. OGG1 is a DNA glycosylase which initiates BER while Mre11-Rad50-Nbs1 (MRN) protein complex is the primary responder to DSBs which gets localized to damage sites. DNA damage response is meticulously executed by three related kinases: ATM, ATR, and DNA-PK. ATM- and ATR-dependent phosphorylation of p53, Chk1, and Chk2 regulate the G1/S, intra-S, or G2/M checkpoints of the cell cycle, respectively. Autophagy is an evolutionarily conserved process that plays a pivotal role in the regulation of DNA repair and maintains the cellular homeostasis. Genotoxic stress-induced altered autophagy occurs in a P53 dependent manner which is also the master regulator of genotoxic stress. A plethora of proteins involved in autophagy is regulated by p53 which involve DRAM, DAPK, and AMPK. As evident, the mtDNA is more prone to damage than nuclear DNA because of its close proximity to the site of ROS generation. Depending on the extent of damage either the repair mechanism or mitophagy gets triggered. SIRT1 is the master regulator which directs the stress response to mitophagy. Nix, a LC3 adapter also participates in Parkin mediated mitophagy. This review highlights the intricate crosstalks between DNA damage and cell cycle checkpoints activation. The DNA damage mediated regulation of autophagy and mitophagy is also reviewed in detail.
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28
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Liu L, Cai S, Han C, Banerjee A, Wu D, Cui T, Xie G, Zhang J, Zhang X, McLaughlin E, Yin M, Backes FJ, Chakravarti A, Zheng Y, Wang QE. ALDH1A1 Contributes to PARP Inhibitor Resistance via Enhancing DNA Repair in BRCA2 -/- Ovarian Cancer Cells. Mol Cancer Ther 2019; 19:199-210. [PMID: 31534014 DOI: 10.1158/1535-7163.mct-19-0242] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/09/2019] [Accepted: 09/11/2019] [Indexed: 01/10/2023]
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) are approved to treat recurrent ovarian cancer with BRCA1 or BRCA2 mutations, and as maintenance therapy for recurrent platinum-sensitive ovarian cancer (BRCA wild-type or mutated) after treatment with platinum. However, the acquired resistance against PARPi remains a clinical hurdle. Here, we demonstrated that PARP inhibitor (olaparib)-resistant epithelial ovarian cancer (EOC) cells exhibited an elevated aldehyde dehydrogenase (ALDH) activity, mainly contributed by increased expression of ALDH1A1 due to olaparib-induced expression of BRD4, a member of bromodomain and extraterminal (BET) family protein. We also revealed that ALDH1A1 enhanced microhomology-mediated end joining (MMEJ) activity in EOC cells with inactivated BRCA2, a key protein that promotes homologous recombination (HR) by using an intrachromosomal MMEJ reporter. Moreover, NCT-501, an ALDH1A1-selective inhibitor, can synergize with olaparib in killing EOC cells carrying BRCA2 mutation in both in vitro cell culture and the in vivo xenograft animal model. Given that MMEJ activity has been reported to be responsible for PARPi resistance in HR-deficient cells, we conclude that ALDH1A1 contributes to the resistance to PARP inhibitors via enhancing MMEJ in BRCA2-/- ovarian cancer cells. Our findings provide a novel mechanism underlying PARPi resistance in BRCA2-mutated EOC cells and suggest that inhibition of ALDH1A1 could be exploited for preventing and overcoming PARPi resistance in EOC patients carrying BRCA2 mutation.
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Affiliation(s)
- Lu Liu
- Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Shurui Cai
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Chunhua Han
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Ananya Banerjee
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.,School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
| | - Dayong Wu
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Tiantian Cui
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Guozhen Xie
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Junran Zhang
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Xiaoli Zhang
- Center for Biostatistics, Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Eric McLaughlin
- Center for Biostatistics, Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Ming Yin
- Division of Medical Oncology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Floor J Backes
- Department of Obstetrics and Gynecology, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Arnab Chakravarti
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Yanfang Zheng
- Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Qi-En Wang
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio. .,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
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29
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PARP Inhibitors in Ovarian Cancer: The Route to "Ithaca". Diagnostics (Basel) 2019; 9:diagnostics9020055. [PMID: 31109041 PMCID: PMC6627688 DOI: 10.3390/diagnostics9020055] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/12/2019] [Accepted: 05/16/2019] [Indexed: 12/14/2022] Open
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors are a novel class of therapeutic agents that target tumors with deficiencies in the homologous recombination DNA repair pathway. Genomic instability characterizes high-grade serous ovarian cancer (HGSOC), with one half of all tumors displaying defects in the important DNA repair pathway of homologous recombination. Early studies have shown significant efficacy for PARP inhibitors in patients with germline breast related cancer antigens 1 and 2 (BRCA1/2) mutations. It has also become evident that BRCA wild-type patients with other defects in the homologous recombination repair pathway benefit from this treatment. Companion homologous recombination deficiency (HRD) scores are being developed to guide the selection of patients that are most likely to benefit from PARP inhibition. The choice of which PARP inhibitor is mainly based upon the number of prior therapies and the presence of a BRCA mutation or HRD. The identification of patients most likely to benefit from PARP inhibitor therapy in view of HRD and other biomarker assessments is still challenging. The aim of this review is to describe the current evidence for PARP inhibitors in ovarian cancer, their mechanism of action, and the outstanding issues, including the rate of long-term toxicities and the evolution of resistance.
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30
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Shanbhag NM, Evans MD, Mao W, Nana AL, Seeley WW, Adame A, Rissman RA, Masliah E, Mucke L. Early neuronal accumulation of DNA double strand breaks in Alzheimer's disease. Acta Neuropathol Commun 2019; 7:77. [PMID: 31101070 PMCID: PMC6524256 DOI: 10.1186/s40478-019-0723-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023] Open
Abstract
The maintenance of genomic integrity is essential for normal cellular functions. However, it is difficult to maintain over a lifetime in postmitotic cells such as neurons, in which DNA damage increases with age and is exacerbated by multiple neurological disorders, including Alzheimer's disease (AD). Here we used immunohistochemical staining to detect DNA double strand breaks (DSBs), the most severe form of DNA damage, in postmortem brain tissues from patients with mild cognitive impairment (MCI) or AD and from cognitively unimpaired controls. Immunostaining for γH2AX-a post-translational histone modification that is widely used as a marker of DSBs-revealed increased proportions of γH2AX-labeled neurons and astrocytes in the hippocampus and frontal cortex of MCI and AD patients, as compared to age-matched controls. In contrast to the focal pattern associated with DSBs, some neurons and glia in humans and mice showed diffuse pan-nuclear patterns of γH2AX immunoreactivity. In mouse brains and primary neuronal cultures, such pan-nuclear γH2AX labeling could be elicited by increasing neuronal activity. To assess whether pan-nuclear γH2AX represents DSBs, we used a recently developed technology, DNA damage in situ ligation followed by proximity ligation assay, to detect close associations between γH2AX sites and free DSB ends. This assay revealed no evidence of DSBs in neurons or astrocytes with prominent pan-nuclear γH2AX labeling. These findings suggest that focal, but not pan-nuclear, increases in γH2AX immunoreactivity are associated with DSBs in brain tissue and that these distinct patterns of γH2AX formation may have different causes and consequences. We conclude that AD is associated with an accumulation of DSBs in vulnerable neuronal and glial cell populations from early stages onward. Because of the severe adverse effects this type of DNA damage can have on gene expression, chromatin stability and cellular functions, DSBs could be an important causal driver of neurodegeneration and cognitive decline in this disease.
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Affiliation(s)
- Niraj M Shanbhag
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Mark D Evans
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - Wenjie Mao
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - Alissa L Nana
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - William W Seeley
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Anthony Adame
- Department of Neurosciences, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Robert A Rissman
- Department of Neurosciences, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California at San Diego, La Jolla, CA, 92093, USA
- Present address: Division of Neuroscience, National Institute on Aging, Bethesda, MD, 20892, USA
| | - Lennart Mucke
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA.
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA.
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31
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Kohutova A, Raška J, Kruta M, Seneklova M, Barta T, Fojtik P, Jurakova T, Walter CA, Hampl A, Dvorak P, Rotrekl V. Ligase 3–mediated end‐joining maintains genome stability of human embryonic stem cells. FASEB J 2019; 33:6778-6788. [DOI: 10.1096/fj.201801877rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Aneta Kohutova
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Jan Raška
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | - Miriama Kruta
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | | | - Tomas Barta
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | - Petr Fojtik
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | | | - Christi A. Walter
- Department of Cell Systems and AnatomyThe University of Texas Health Science Center at San AntonioSan AntonioTexasUSA
| | - Ales Hampl
- Department of Histology and EmbryologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Petr Dvorak
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Vladimir Rotrekl
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
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32
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53BP1: A key player of DNA damage response with critical functions in cancer. DNA Repair (Amst) 2019; 73:110-119. [DOI: 10.1016/j.dnarep.2018.11.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023]
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Popp HD, Flach J, Brendel S, Ruppenthal S, Kleiner H, Seifarth W, Schneider S, Schulze TJ, Weiss C, Wenz F, Hofmann WK, Fabarius A. Accumulation of DNA damage and alteration of the DNA damage response in monoclonal B-cell lymphocytosis and chronic lymphocytic leukemia. Leuk Lymphoma 2018; 60:795-804. [DOI: 10.1080/10428194.2018.1498494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Henning D. Popp
- Department of Hematology and Oncology, Heidelberg University, Mannheim, Germany
| | - Johanna Flach
- Department of Hematology and Oncology, Heidelberg University, Mannheim, Germany
| | - Susanne Brendel
- Department of Hematology and Oncology, Heidelberg University, Mannheim, Germany
| | - Sabrina Ruppenthal
- Department of Hematology and Oncology, Heidelberg University, Mannheim, Germany
| | - Helga Kleiner
- Department of Hematology and Oncology, Heidelberg University, Mannheim, Germany
| | - Wolfgang Seifarth
- Department of Hematology and Oncology, Heidelberg University, Mannheim, Germany
| | - Sven Schneider
- Institute for Clinical Chemistry, Heidelberg University, Mannheim, Germany
| | - Torsten J. Schulze
- Institute of Transfusion Medicine and Immunology, Heidelberg University, German Red-Cross Blood Service Baden-Württemberg – Hessen, Mannheim, Germany
| | - Christel Weiss
- Department of Medical Statistics and Biomathematics, Heidelberg University, Mannheim, Germany
| | - Frederik Wenz
- Department of Radiation Oncology, Heidelberg University, Mannheim, Germany
| | | | - Alice Fabarius
- Department of Hematology and Oncology, Heidelberg University, Mannheim, Germany
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34
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Sallmyr A, Tomkinson AE. Repair of DNA double-strand breaks by mammalian alternative end-joining pathways. J Biol Chem 2018. [PMID: 29530982 DOI: 10.1074/jbc.tm117.000375] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alternative end-joining (a-EJ) pathways, which repair DNA double-strand breaks (DSBs), are initiated by end resection that generates 3' single strands. This reaction is shared, at least in part, with homologous recombination but distinguishes a-EJ from the major nonhomologous end-joining pathway. Although the a-EJ pathways make only a minor and poorly understood contribution to DSB repair in nonmalignant cells, there is growing interest in these pathways, as they generate genomic rearrangements that are hallmarks of cancer cells. Here, we review and discuss the current understanding of the mechanisms and regulation of a-EJ pathways, the role of a-EJ in human disease, and the potential utility of a-EJ as a therapeutic target in cancer.
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Affiliation(s)
- Annahita Sallmyr
- From the Departments of Internal Medicine and Molecular Genetics and Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico 87131
| | - Alan E Tomkinson
- From the Departments of Internal Medicine and Molecular Genetics and Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico 87131
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35
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Canny MD, Moatti N, Wan LCK, Fradet-Turcotte A, Krasner D, Mateos-Gomez PA, Zimmermann M, Orthwein A, Juang YC, Zhang W, Noordermeer SM, Seclen E, Wilson MD, Vorobyov A, Munro M, Ernst A, Ng TF, Cho T, Cannon PM, Sidhu SS, Sicheri F, Durocher D. Inhibition of 53BP1 favors homology-dependent DNA repair and increases CRISPR-Cas9 genome-editing efficiency. Nat Biotechnol 2017; 36:95-102. [PMID: 29176614 PMCID: PMC5762392 DOI: 10.1038/nbt.4021] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 10/20/2017] [Indexed: 02/06/2023]
Abstract
Programmable nucleases, such as Cas9, are used for precise genome editing by homology-dependent repair (HDR)1–3. However, HDR efficiency is constrained by competition from other double-strand break (DSB) repair pathways, including non-homologous end-joining (NHEJ)4. We report the discovery of a genetically encoded inhibitor of 53BP1 that increases the efficiency of HDR-dependent genome editing in human and mouse cells. 53BP1 is a key regulator of DSB repair pathway choice in eukaryotic cells4, 5 and functions to favor NHEJ over HDR by suppressing end resection, which is the rate-limiting step in the initiation of HDR. We screened an existing combinatorial library of engineered ubiquitin variants6 for inhibitors of 53BP1. Expression of one variant, named i53 (inhibitor of 53BP1), in human and mouse cells blocked accumulation of 53BP1 at sites of DNA damage and improved gene targeting and chromosomal gene conversion with either double-stranded DNA or single-stranded oligonucleotide donors by up to 5.6-fold. Inhibition of 53BP1 is a robust method to increase efficiency of HDR-based precise genome editing.
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Affiliation(s)
- Marella D Canny
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Nathalie Moatti
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Leo C K Wan
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Amélie Fradet-Turcotte
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Danielle Krasner
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Pedro A Mateos-Gomez
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, New York, USA
| | - Michal Zimmermann
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Alexandre Orthwein
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Yu-Chi Juang
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Wei Zhang
- The Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
| | - Sylvie M Noordermeer
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Eduardo Seclen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Marcus D Wilson
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Andrew Vorobyov
- The Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
| | - Meagan Munro
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Andreas Ernst
- The Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
| | - Timothy F Ng
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Tiffany Cho
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Paula M Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, Ontario, Canada.,The Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
| | - Frank Sicheri
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, Canada
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36
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Seol JH, Shim EY, Lee SE. Microhomology-mediated end joining: Good, bad and ugly. Mutat Res 2017; 809:81-87. [PMID: 28754468 DOI: 10.1016/j.mrfmmm.2017.07.002] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/21/2017] [Accepted: 07/03/2017] [Indexed: 01/06/2023]
Abstract
DNA double-strand breaks (DSBs) are induced by a variety of genotoxic agents, including ionizing radiation and chemotherapy drugs for treating cancers. The elimination of DSBs proceeds via distinctive error-free and error-prone pathways. Repair by homologous recombination (HR) is largely error-free and mediated by RAD51/BRCA2 gene products. Classical non-homologous end joining (C-NHEJ) requires the Ku heterodimer and can efficiently rejoin breaks, with occasional loss or gain of DNA information. Recently, evidence has unveiled another DNA end-joining mechanism that is independent of recombination factors and Ku proteins, termed alternative non-homologous end joining (A-NHEJ). While A-NHEJ-mediated repair does not require homology, in a subtype of A-NHEJ, DSB breaks are sealed by microhomology (MH)-mediated base-pairing of DNA single strands, followed by nucleolytic trimming of DNA flaps, DNA gap filling, and DNA ligation, yielding products that are always associated with DNA deletion. This highly error-prone DSB repair pathway is termed microhomology-mediated end joining (MMEJ). Dissecting the mechanisms of MMEJ is of great interest because of its potential to destabilize the genome through gene deletions and chromosomal rearrangements in cells deficient in canonical repair pathways, including HR and C-NHEJ. In addition, evidence now suggests that MMEJ plays a physiological role in normal cells.
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Affiliation(s)
- Ja-Hwan Seol
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, United States
| | - Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, United States
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, United States; Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, United States.
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37
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Fujii N. Potential Strategies to Target Protein-Protein Interactions in the DNA Damage Response and Repair Pathways. J Med Chem 2017; 60:9932-9959. [PMID: 28654754 DOI: 10.1021/acs.jmedchem.7b00358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review article discusses some insights about generating novel mechanistic inhibitors of the DNA damage response and repair (DDR) pathways by focusing on protein-protein interactions (PPIs) of the key DDR components. General requirements for PPI strategies, such as selecting the target PPI site on the basis of its functionality, are discussed first. Next, on the basis of functional rationale and biochemical feasibility to identify a PPI inhibitor, 26 PPIs in DDR pathways (BER, MMR, NER, NHEJ, HR, TLS, and ICL repair) are specifically discussed for inhibitor discovery to benefit cancer therapies using a DNA-damaging agent.
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Affiliation(s)
- Naoaki Fujii
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, MS1000, Memphis, Tennessee 38105, United States
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38
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Increase of DNA damage and alteration of the DNA damage response in myelodysplastic syndromes and acute myeloid leukemias. Leuk Res 2017; 57:112-118. [PMID: 28359030 DOI: 10.1016/j.leukres.2017.03.011] [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: 12/14/2016] [Revised: 03/09/2017] [Accepted: 03/20/2017] [Indexed: 11/23/2022]
Abstract
Increased DNA damage and alteration of the DNA damage response (DDR) are critical features of genetic instability presumably implicated in pathogenesis of myelodysplastic syndromes (MDS) and acute myeloid leukemias (AML). We used immunofluorescence staining of γH2AX and 53BP1 for analyzing DNA double-strand breaks (DSB) in MDS and AML cell lines, in CD34+ selected cells of normal and MDS bone marrow (including three cases of chronic myelomonocytic leukemias) and in blasts of AML bone marrow. In addition, we screened for activation of the DDR by immunoblotting of p-ATM, p-ATR, p-CHK1, p-CHK2 and p-TP53. As compared to γH2AX foci levels in normal bone marrow samples (0.2 focus per CD34+ cell±0.0; mean±standard error of mean), increased levels of γH2AX foci were detected in 16/16 MDS bone marrow samples (2.8 foci per CD34+ cell±0.5), 18/18 AML bone marrow samples (5.5 foci per blast±0.5), 1/1 MDS cell line (6.4 foci per cell) and 6/6 AML cell lines (12.0 foci per cell±0.6). γH2AX and 53BP1 co-localized in all tested samples forming diffuse, clustered and marginal patterns. Further, DDR proteins were expressed heterogeneously suggesting impairment of the DDR. In summary, our results provide evidence for a continuous increase of DSB across the spectrum from MDS to AML in conjunction with an impaired DDR. Co-localization of γH2AX and 53BP1 indicates promotion of (in)effective nonhomologous end-joining repair mechanisms at sites of DSB. Moreover, γH2AX/53BP1 foci distribution presumably reveals a non-random spatial organization of the genome in MDS and AML.
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39
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Aida T, Nakade S, Sakuma T, Izu Y, Oishi A, Mochida K, Ishikubo H, Usami T, Aizawa H, Yamamoto T, Tanaka K. Gene cassette knock-in in mammalian cells and zygotes by enhanced MMEJ. BMC Genomics 2016; 17:979. [PMID: 27894274 PMCID: PMC5126809 DOI: 10.1186/s12864-016-3331-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 11/22/2016] [Indexed: 01/10/2023] Open
Abstract
Background Although CRISPR/Cas enables one-step gene cassette knock-in, assembling targeting vectors containing long homology arms is a laborious process for high-throughput knock-in. We recently developed the CRISPR/Cas-based precise integration into the target chromosome (PITCh) system for a gene cassette knock-in without long homology arms mediated by microhomology-mediated end-joining. Results Here, we identified exonuclease 1 (Exo1) as an enhancer for PITCh in human cells. By combining the Exo1 and PITCh-directed donor vectors, we achieved convenient one-step knock-in of gene cassettes and floxed allele both in human cells and mouse zygotes. Conclusions Our results provide a technical platform for high-throughput knock-in. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3331-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tomomi Aida
- Laboratory of Molecular Neuroscience, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510, Japan. .,Laboratory of Recombinant Animals, MRI, TMDU, 2-3-10, Surugadai, Kanda, Chiyoda, Tokyo, 101-0062, Japan. .,Present address: McGovern Institute for Brain Research, Massachusetts Institute of Technology, 43 Vassar St., Cambridge, MA, 02139, USA.
| | - Shota Nakade
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Yayoi Izu
- Department of Animal Risk Management, Chiba Institute of Science, 3 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
| | - Ayu Oishi
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.,Present address: Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Keiji Mochida
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Harumi Ishikubo
- Laboratory of Molecular Neuroscience, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510, Japan.,Laboratory of Recombinant Animals, MRI, TMDU, 2-3-10, Surugadai, Kanda, Chiyoda, Tokyo, 101-0062, Japan
| | - Takako Usami
- Laboratory of Recombinant Animals, MRI, TMDU, 2-3-10, Surugadai, Kanda, Chiyoda, Tokyo, 101-0062, Japan
| | - Hidenori Aizawa
- Laboratory of Molecular Neuroscience, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510, Japan.,Department of Neurobiology, Institute of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Kohichi Tanaka
- Laboratory of Molecular Neuroscience, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510, Japan. .,The Center for Brain Integration Research (CBIR), TMDU, Tokyo, 113-8510, Japan.
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40
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Differences in the recruitment of DNA repair proteins at subtelomeric and interstitial I-SceI endonuclease-induced DNA double-strand breaks. DNA Repair (Amst) 2016; 49:1-8. [PMID: 27842255 DOI: 10.1016/j.dnarep.2016.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/21/2016] [Accepted: 10/26/2016] [Indexed: 12/28/2022]
Abstract
Telomeres are nucleoprotein structures that are required to protect chromosome ends. Dysfunctional telomeres are recognized as DNA double-strand breaks (DSBs), and elicit the activation of a DNA damage response (DDR). We have previously reported that DSBs near telomeres are poorly repaired, resulting in a high frequency of large deletions and gross chromosome rearrangements (GCRs). Our previous genetic studies have demonstrated that this sensitivity of telomeric regions to DSBs is a result of excessive processing. In the current study, we have further investigated the sensitivity of telomeric regions to DSBs through the analysis of repair proteins associated with DSBs at interstitial and telomeric sites. Following the inducible expression of I-SceI endonuclease, chromatin immunoprecipitation (ChIP) and real-time quantitative PCR were used to compare the recruitment of repair proteins at I-SceI-induced DSBs at interstitial and subtelomeric sites. We observed that proteins that are specifically associated with processing of DSBs during homologous recombination repair, RAD51, BRCA1, and CtIP, are present at a much greater abundance at subtelomeric DSBs. In contrast, Ku70, which is specifically involved in classical nonhomologous end joining, showed no difference at interstitial and subtelomeric DSBs. Importantly, ATM was lower in abundance at subtelomeric DSBs, while ATR was in greater abundance at subtelomeric DSBs, consistent with the accumulation of processed DSBs near telomeres, since processing is accompanied by a transition from ATM to ATR binding. Combined, our results suggest that excessive processing is responsible for the increased frequency of large deletions and GCRs at DSBs near telomeres.
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41
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Woods ML, Barnes CP. Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair. PLoS Comput Biol 2016; 12:e1005131. [PMID: 27741226 PMCID: PMC5065155 DOI: 10.1371/journal.pcbi.1005131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 09/05/2016] [Indexed: 12/12/2022] Open
Abstract
DNA double-strand breaks are lesions that form during metabolism, DNA replication and exposure to mutagens. When a double-strand break occurs one of a number of repair mechanisms is recruited, all of which have differing propensities for mutational events. Despite DNA repair being of crucial importance, the relative contribution of these mechanisms and their regulatory interactions remain to be fully elucidated. Understanding these mutational processes will have a profound impact on our knowledge of genomic instability, with implications across health, disease and evolution. Here we present a new method to model the combined activation of non-homologous end joining, single strand annealing and alternative end joining, following exposure to ionising radiation. We use Bayesian statistics to integrate eight biological data sets of double-strand break repair curves under varying genetic knockouts and confirm that our model is predictive by re-simulating and comparing to additional data. Analysis of the model suggests that there are at least three disjoint modes of repair, which we assign as fast, slow and intermediate. Our results show that when multiple data sets are combined, the rate for intermediate repair is variable amongst genetic knockouts. Further analysis suggests that the ratio between slow and intermediate repair depends on the presence or absence of DNA-PKcs and Ku70, which implies that non-homologous end joining and alternative end joining are not independent. Finally, we consider the proportion of double-strand breaks within each mechanism as a time series and predict activity as a function of repair rate. We outline how our insights can be directly tested using imaging and sequencing techniques and conclude that there is evidence of variable dynamics in alternative repair pathways. Our approach is an important step towards providing a unifying theoretical framework for the dynamics of DNA repair processes.
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Affiliation(s)
- Mae L. Woods
- Department of Cell and Developmental Biology, University College London, London, England
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, England
- Department of Genetics, Evolution and Environment, University College London, London, England
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42
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Foertsch F, Szambowska A, Weise A, Zielinski A, Schlott B, Kraft F, Mrasek K, Borgmann K, Pospiech H, Grosse F, Melle C. S100A11 plays a role in homologous recombination and genome maintenance by influencing the persistence of RAD51 in DNA repair foci. Cell Cycle 2016; 15:2766-79. [PMID: 27590262 DOI: 10.1080/15384101.2016.1220457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is an essential process in maintenance of chromosomal stability. A key player of HR is the strand exchange factor RAD51 whose assembly at sites of DNA damage is tightly regulated. We detected an endogenous complex of RAD51 with the calcium-binding protein S100A11, which is localized at sites of DNA repair in HaCaT cells as well as in normal human epidermal keratinocytes (NHEK) synchronized in S phase. In biochemical assays, we revealed that S100A11 enhanced the RAD51 strand exchange activity. When cells expressing a S100A11 mutant lacking the ability to bind Ca(2+), a prolonged persistence of RAD51 in repair sites and nuclear γH2AX foci was observed suggesting an incomplete DNA repair. The same phenotype became apparent when S100A11 was depleted by RNA interference. Furthermore, down-regulation of S100A11 resulted in both reduced sister chromatid exchange confirming the restriction of the recombination capacity of the cells, and in an increase of chromosomal aberrations reflecting the functional requirement of S100A11 for the maintenance of genomic stability. Our data indicate that S100A11 is involved in homologous recombination by regulating the appearance of RAD51 in DSB repair sites. This function requires the calcium-binding activity of S100A11.
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Affiliation(s)
- Franziska Foertsch
- a Biomolecular Photonics Group , Jena University Hospital , Jena , Germany
| | - Anna Szambowska
- b Research Group Biochemistry, Leibniz Institute on Aging - Fritz Lipmann Institute , Jena , Germany
| | - Anja Weise
- c Institute of Human Genetics , Jena University Hospital , Jena , Germany
| | - Alexandra Zielinski
- d Radiobiology & Experimental Radiooncology , University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Bernhard Schlott
- b Research Group Biochemistry, Leibniz Institute on Aging - Fritz Lipmann Institute , Jena , Germany
| | - Florian Kraft
- c Institute of Human Genetics , Jena University Hospital , Jena , Germany
| | - Kristin Mrasek
- c Institute of Human Genetics , Jena University Hospital , Jena , Germany
| | - Kerstin Borgmann
- d Radiobiology & Experimental Radiooncology , University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Helmut Pospiech
- b Research Group Biochemistry, Leibniz Institute on Aging - Fritz Lipmann Institute , Jena , Germany.,e Faculty of Biochemistry and Molecular Medicine , University of Oulu , Finland
| | - Frank Grosse
- b Research Group Biochemistry, Leibniz Institute on Aging - Fritz Lipmann Institute , Jena , Germany
| | - Christian Melle
- a Biomolecular Photonics Group , Jena University Hospital , Jena , Germany
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43
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Sinha S, Villarreal D, Shim EY, Lee SE. Risky business: Microhomology-mediated end joining. Mutat Res 2016; 788:17-24. [PMID: 26790771 DOI: 10.1016/j.mrfmmm.2015.12.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/03/2015] [Accepted: 12/22/2015] [Indexed: 11/16/2022]
Abstract
Prevalence of microhomology (MH) at the breakpoint junctions in somatic and germ-line chromosomal rearrangements and in the programmed immune receptor rearrangements from cells deficient in classical end joining reveals an enigmatic process called MH-mediated end joining (MMEJ). MMEJ repairs DNA double strand breaks (DSBs) by annealing flanking MH and deleting genetic information at the repair junctions from yeast to humans. Being genetically distinct from canonical DNA DSB pathways, MMEJ is involved with the fusions of eroded/uncapped telomeres as well as with the assembly of chromosome fragments in chromothripsis. In this review article, we will discuss an up-to-date model representing the MMEJ process and the mechanism by which cells regulate MMEJ to limit repair-associated mutagenesis. We will also describe the possible therapeutic gains resulting from the inhibition of MMEJ in recombination deficient cancers. Lastly, we will embark on two contentious issues associated with MMEJ such as the significance of MH at the repair junction to be the hallmark of MMEJ and the relationship of MMEJ to other mechanistically related DSB repair pathways.
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Affiliation(s)
- Supriya Sinha
- Department of Molecular Medicine, Institute of Biotechnology, United States
| | - Diana Villarreal
- Children's Hospital of San Antonio, Baylor College of Medicine, San Antonio, TX 78207, United States
| | - Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, TX 78229, United States
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, United States; Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, TX 78229, United States.
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44
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Kan C, Zhang J. BRCA1 Mutation: A Predictive Marker for Radiation Therapy? Int J Radiat Oncol Biol Phys 2015; 93:281-93. [PMID: 26383678 DOI: 10.1016/j.ijrobp.2015.05.037] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/08/2015] [Accepted: 05/21/2015] [Indexed: 02/01/2023]
Abstract
DNA repair, in particular, DNA double-strand break (DSB) repair, is essential for the survival of both normal and cancer cells. An elaborate repair mechanism has been developed in cells to efficiently repair the damaged DNA. The pathways predominately involved in DSB repair are homologous recombination and classic nonhomologous end-joining, although the alternative NHEJ pathway, a third DSB repair pathway, could also be important in certain contexts. The protein of BRCA1 encoded by the tumor suppressor gene BRCA1 regulates all DSB repair pathways. Given that DSBs represent the most biologically significant lesions induced by ionizing radiation and that impaired DSB repair leads to radiation sensitivity, it has been expected that cancer patients with BRCA1 mutations should benefit from radiation therapy. However, the clinical data have been conflicting and inconclusive. We provide an overview about the current status of the data regarding BRCA1 deficiency and radiation therapy sensitivity in both experimental models and clinical investigations. In addition, we discuss a strategy to potentiate the effects of radiation therapy by poly(ADP-ribose) polymerase inhibitors, the pharmacologic drugs being investigated as monotherapy for the treatment of patients with BRCA1/2 mutations.
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Affiliation(s)
- Charlene Kan
- Department of Radiation Oncology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Junran Zhang
- Department of Radiation Oncology, Case Western Reserve University School of Medicine, Cleveland, Ohio.
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45
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Abstract
Programmable nucleases enable engineering of the genome by utilizing endogenous DNA double-strand break (DSB) repair pathways. Although homologous recombination (HR)-mediated gene knock-in is well established, it cannot necessarily be applied in every cell type and organism because of variable HR frequencies. We recently reported an alternative method of gene knock-in, named the PITCh (Precise Integration into Target Chromosome) system, assisted by microhomology-mediated end-joining (MMEJ). MMEJ harnesses independent machinery from HR, and it requires an extremely short homologous sequence (5-25 bp) for DSB repair, resulting in precise gene knock-in with a more easily constructed donor vector. Here we describe a streamlined protocol for PITCh knock-in, including the design and construction of the PITCh vectors, and their delivery to either human cell lines by transfection or to frog embryos by microinjection. The construction of the PITCh vectors requires only a few days, and the entire process takes ∼ 1.5 months to establish knocked-in cells or ∼ 1 week from injection to early genotyping in frog embryos.
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46
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DNA repair factor BRCA1 depletion occurs in Alzheimer brains and impairs cognitive function in mice. Nat Commun 2015; 6:8897. [PMID: 26615780 PMCID: PMC4674776 DOI: 10.1038/ncomms9897] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 10/14/2015] [Indexed: 02/08/2023] Open
Abstract
Maintaining DNA integrity is vital for all cells and organisms. Defective DNA repair may contribute to neurological disorders, including Alzheimer's disease (AD). We found reduced levels of BRCA1, but not of other DNA repair factors, in the brains of AD patients and human amyloid precursor protein (hAPP) transgenic mice. Amyloid-β oligomers reduced BRCA1 levels in primary neuronal cultures. In wild-type mice, knocking down neuronal BRCA1 in the dentate gyrus caused increased DNA double-strand breaks, neuronal shrinkage, synaptic plasticity impairments, and learning and memory deficits, but not apoptosis. Low levels of hAPP/Amyloid-β overexpression exacerbated these effects. Physiological neuronal activation increased BRCA1 levels, whereas stimulating predominantly extrasynaptic N-methyl-D-aspartate receptors promoted the proteasomal degradation of BRCA1. We conclude that BRCA1 is regulated by neuronal activity, protects the neuronal genome, and critically supports neuronal integrity and cognitive functions. Pathological accumulation of Aβ depletes neuronal BRCA1, which may contribute to cognitive deficits in AD.
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47
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Suchánková J, Kozubek S, Legartová S, Sehnalová P, Küntziger T, Bártová E. Distinct kinetics of DNA repair protein accumulation at DNA lesions and cell cycle-dependent formation of γH2AX- and NBS1-positive repair foci. Biol Cell 2015; 107:440-54. [DOI: 10.1111/boc.201500050] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/13/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Jana Suchánková
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno 612 65 the Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno 612 65 the Czech Republic
| | - Soňa Legartová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno 612 65 the Czech Republic
| | - Petra Sehnalová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno 612 65 the Czech Republic
| | | | - Eva Bártová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno 612 65 the Czech Republic
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48
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Willers H, Gheorghiu L, Liu Q, Efstathiou JA, Wirth LJ, Krause M, von Neubeck C. DNA Damage Response Assessments in Human Tumor Samples Provide Functional Biomarkers of Radiosensitivity. Semin Radiat Oncol 2015; 25:237-50. [PMID: 26384272 DOI: 10.1016/j.semradonc.2015.05.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Predictive biomarkers are urgently needed for individualization of radiation therapy and treatment with radiosensitizing anticancer agents. Genomic profiling of human cancers provides us with unprecedented insight into the mutational landscape of genes directly or indirectly involved in the response to radiation-induced DNA damage. However, to what extent this wealth of structural information about the cancer genome produces biomarkers of sensitivity to radiation remains to be seen. Investigators are increasingly studying the subnuclear accumulation (ie, foci) of proteins in the DNA damage response (DDR), such as gamma-H2AX, 53BP1, or RAD51, as a surrogate of treatment sensitivity. Recent findings from preclinical studies have demonstrated the predictive potential of DDR foci by correlating foci with clinically relevant end points such as tumor control probability. Therefore, preclinical investigations of DDR foci responses are increasingly moving into cells and tissues from patients, which is the major focus of this review. The advantage of using DDR foci as functional biomarkers is that they can detect alterations in DNA repair due to various mechanisms. Moreover, they provide a global measurement of DDR network function without needing to know the identities of all the components, many of which remain unknown. Foci assays are thus expected to yield functional insight that may complement or supersede genomic information, thereby giving radiation oncologists unique opportunities to individualize cancer treatments in the near future.
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Affiliation(s)
- Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA.
| | - Liliana Gheorghiu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA
| | - Qi Liu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA
| | - Jason A Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA
| | - Lori J Wirth
- Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Mechthild Krause
- German Cancer Consortium (DKTK) Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology, Germany
| | - Cläre von Neubeck
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
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